This is Part 5 to the gene study analysis and machine learning on a data of elderly 50-94 year old patients, 47 of them with EBV and CHL, EBV and pDLBCL, and EBV and mDLBCL. Read below if you are picking up here to get the information in Part 4, and you will have to go to Part 3 to get Part 2 and Part 1 at the start of the project. We were able to see that using a random forest model with standard or basic settings for classification of the 3 known large B-cell lymphomas of CHL, pDLBCL, and mDLBCL, that the model scored … and a little bit worse with the 4 proposed groups as the CHL and pDLBCL were mostly predicted to be that 4th group in the study (links below). That was using the study genes only that were in the research article. But now we are going to use the genes of top gene differences between average and the median of the group samples in 15 groups, the first 3 known groups by diagnosis, then by gender of 2 genders within each diagnosis, and then by 2 age groups within those 3 diagnosis. To compare the outcomes in accuracy in prediction and also see if some genes we found were more prevalent in the male or younger subgroups of certain diagnosed pathologies are good at predicting gender in a 2 class model or age in a 2 class model.
Part 5 is attached to the end of Part 4 on this document by scrolling down to the ***** Part 5 section after a bunch of equal signs.
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This is Part 4 to analyzing gene expression data from GSE305165. There is a published article that I took the following information from after reading it once and highlighting the important aspects of the study.
This research used Diffuse Large B-Cell Lymphoma or DLBCL to compare it to Classical Hodgkin’s Lymphoma or CHL in Epstein-Barr Virus (EBV) infected patients. The two types of lymphoma affect the elderly populations and have overlap between biomarkers such as IDO1, EBV latent type 2 is specific to CHL, but can be seen in a polymorphic type DLBCL called pDLBCL, and EBV latent type 3 seen mostly in monomorphic DLBCL labeled mDLBCL, but also in pDLBCL. The study saw that the typical region of chromosome 9 specific to high variations of genes in this loci of 9.24 in CHL, had some variations noticed within pDLBCL and mDLBCL. Overall, this study used populations 50 years old or older with no autoimmune or immunodeficient pathologies. However, in the elderly populations there is a natural decline of immune response to pathogens and antigens called immune senescence or IS, and in seriously impacted disease state of the DLBCL there can be a more fatal condition of immune escape, an actual term for both that means pathogens and antigens escape detection by the host immune system and have the ability to make changes that can lead to the host’s death.
This is a very interesting study, not too difficult to read, but overall, these researchers have decides that their clustering of heirarchical did a great job at separating the differences between the classes of large B-cell Lymphomas. They decided that CHL and DLBCLs of pDLBCL and mDLBCL are not separate diseases but the same type of disease where there is a 4th transitional state of disease that overlaps with pDLBCL and CHL that has low interferon gamma.
The four states are the 1st group which IS group which is the mDLBCL that is EBNA2 positive and EBV latent type 3, the 2nd group which is the CHL group that is high in variations at loci of chromosome 9 at 9p24.1 and high in PDL1 gene expression also only EBV latent type 2 gene expression and EBNA2 negative, the 3rd group which is the pDLBCL that is high in interferon gamma or IFN-g and low in variations of 9p24.1 with high gene expression of IDO1 that lead to immune escape and high chance of getting poor prognosis of hemocytic lymphocytosis called HLH that can lead to demise, and the 4th group that is the transition between CHL and pDLBCL where the IFN-g is low and characteristics unlike the other 3 groups as not otherwise specified or NOS.
The study uses 57 samples where 35 are DLBCL with 12 being pDLBCL and 23 being mDLBCL, and the other 22 samples are CHL. All samples have confirmed EBV and no immune deficiency or pathology other than Lymphoma and normal affects of aging in IS.
However, there are only 47 samples in the GSE305605 gene expression omnibus or GEO link above. We will be working with 47 samples.
Please see Part 1, Part 2, and Part 3 for how I got to the following data tables from extracting and reading in CEL files of Affymetrix data, and isolating the top genes without a baseline or control as all samples were EBV infected but with 1 of 3 large B-cell lymphomas, which was take each group and subgroup of the samples avg/median for that group and subgroup. There were the 3 larger groups of each lymphoma, then the subgroups of gender within each group, and age within each group of those less than or equal to 72 years of age and those older than 72 years of age. The groups I am talking about are not the groups the study found of the 4 groups. We will be using our machine learning in this Part 4 to see how well the study genes reflect the study outcomes when the model is using the study genes only to predict 1 of 3 classes of lymphoma with EBV or 1 of the new 4 groups the study found for 4 separate transitional types of lymphomas of type large B-cell by immune condition. We will also see if there is in each of the group and subgroups we made by demographics within the lymphoma known types if they can predict the age or the gender based on those genes. We didn’t have a total set of 15X20 genes of top genes over expressed when avg/median is greater than 1 or under expressed when avg/median is less than 1, due to the top 20 being 10 of each but of probe IDs that only 21k had a gene for out of a list of 27k. Many genes were duplicated in other sets as well as many as 5 groups. We also didn’t find a gene for each of the ones the study identified like EBNA2, EBER, and many CD clotting factors among others.
library(rmarkdown)## Warning: package 'rmarkdown' was built under R version 4.5.3library(randomForest)## randomForest 4.7-1.2## Type rfNews() to see new features/changes/bug fixes.Lets bring in the table on the header demographic information for each group. We changed the new data and topStudied_3Ls tables to have the ID field as first column but the table of demographic information will need to have the information presented differently when we combine this with the other group top genes.
You can get the labels file after edits made here.
labels <- read.csv("compare_df_6labels_47samples.csv", header=T, row.names=1)paged_table(labels)There was another file we need to upload on the feature gene names for each ID that is an Affymetrix ID. The features table has the gene names but enclosed in parenthesis, there may be 20 genes per group of top genes but when combining these Affy IDs with their gene names, the Affy ID might not be matched and dropped leaving maybe only 1-2 genes or more or less. The features data is 5,670 genes less than our data of genes. So some may be excluded for that reason. This file is extremely large for what it is because of the listed groups in each gene of 21k+ genes. This was in the CEL file that was made using bioconductor in part 1 extracting feature information.
This is 116 MB due to that last column. Too big for google sheets but kaggle allows it. Get the features data here.
features <- read.csv("feature.data.csv", header=T, row.names=1)colnames(features)## [1] "ID" "probeset_id" "seqname" "strand" "start"
## [6] "stop" "total_probes" "category" "SPOT_ID" "SPOT_ID.1"Now lets open our data from the end of Part 3 on top genes, where there were 84 genes that were top genes of variation or skew in you can get it here.
topGenes <- read.csv("topGenes_probeMathed2Gene_84genes_54unique_31duplicated.csv", header=T)paged_table(topGenes)Lets get the ‘Research Article’ genes by grepping this from the importance feature of topGenes.
researchGenes <- topGenes[grep('Research Article',topGenes$importance),]
paged_table(researchGenes)We can see by looking at the last few columns which groups that are marked with ‘change’ are over or under estimated values when mean is larger or less than median respectively. Because the median if even set is still averaged and will be 1 if exact.
colnames(researchGenes)## [1] "ID" "pDLBCL" "CHL"
## [4] "pDLBCL.1" "mDLBCL" "CHL.1"
## [7] "mDLBCL.1" "pDLBCL.2" "CHL.2"
## [10] "CHL.3" "CHL.4" "CHL.5"
## [13] "mDLBCL.2" "mDLBCL.3" "CHL.6"
## [16] "CHL.7" "pDLBCL.3" "CHL.8"
## [19] "mDLBCL.4" "mDLBCL.5" "mDLBCL.6"
## [22] "mDLBCL.7" "CHL.9" "mDLBCL.8"
## [25] "CHL.10" "CHL.11" "CHL.12"
## [28] "CHL.13" "mDLBCL.9" "mDLBCL.10"
## [31] "mDLBCL.11" "mDLBCL.12" "mDLBCL.13"
## [34] "mDLBCL.14" "pDLBCL.4" "pDLBCL.5"
## [37] "mDLBCL.15" "mDLBCL.16" "CHL.14"
## [40] "pDLBCL.6" "pDLBCL.7" "CHL.15"
## [43] "CHL.16" "CHL.17" "mDLBCL.17"
## [46] "mDLBCL.18" "mDLBCL.19" "CHL.18"
## [49] "CHL_mean" "pDLBCL_mean" "mDLBCL_mean"
## [52] "CHL_x_mean" "mDLBCL_x_mean" "pDLBCL_x_mean"
## [55] "CHL_y_mean" "mDLBCL_y_mean" "pDLBCL_y_mean"
## [58] "CHL_young72_mean" "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [61] "CHL_old" "mDLBCL_old" "pDLBCL_old"
## [64] "CHL_median" "mDLBCL_median" "pDLBCL_median"
## [67] "CHL_x_median" "mDLBCL_x_median" "pDLBCL_x_median"
## [70] "CHL_y_median" "mDLBCL_y_median" "pDLBCL_y_median"
## [73] "CHL_young72_median" "mDLBCL_young72_median" "pDLBCL_young72_median"
## [76] "CHL_old72_median" "mDLBCL_old72_median" "pDLBCL_old72_median"
## [79] "CHL_change" "pDLBCL_change" "mDLBCL_change"
## [82] "CHL_x_change" "CHL_y_change" "pDLBCL_x_change"
## [85] "pDLBCL_y_change" "mDLBCL_x_change" "mDLBCL_y_change"
## [88] "CHL_old72_change" "CHL_young72_change" "pDLBCL_old_change"
## [91] "pDLBCL_young72_change" "mDLBCL_young72_change" "mDLBCL_old72_change"
## [94] "SPOT_ID.1" "Gene_ID" "importance"Lets look at only the change per gene in the 3 lymphomas.
rs3 <- researchGenes[,c(79:81,95)]
paged_table(rs3)In the study, interferon gamma or IFNG was high and IDO1 was also high in the pDLBCL group but low IFNG in the mDLBCL group. IDO1 was close to the same over estimation in all 3 lymphomas.
Also, CD274 is what was being used to mark PDL1 which is an indicator for chromosome 9p24.1 copy variants for ‘high variation’ at chromosome 9 that is a biomarker indication of CHL. And PDL2 was found using PDCD1LG2 along chromosome 9 that was also high in CHL as well as pDLBCL.
The CD5, MUM1, BCL6, BCL2, and PAX5 as well as others that didn’t have a gene probe representation in this sample like LMP1, EBER, CD3, CD10, CD15, CD20, CD30, and CD79a all used in gene study variation analysis for inflammatory processes with macrophages in body. These are also elevated and over estimated in the pDLBCL group, except for BCL6 which is the only gene under estimated in the pDLBCL group and it is under estimated in the CHL group as well while being slightly normal or close to 1 in the mDLBCL group of 1.0001 indicating avg/median was very close to the same.
MUM1 is elevated only in DLBCL but not CHL.
Looking at copy number variations at 9p24.1 loci for PDL1 represented by CD274 and PDL2 represented by PDCD1LG2, we can see under estimation of PDL2 in mDLBCL change, and underestimation of PDL1 in CHL change, but otherwise there is over estimation of PDL2 in CHL and pDLBCL and over estimation of PDL1 in pDLBCL and mDLBCL.
BCL2, PAX5, and IDO1 are the only genes over estimated in all 3 lymphomas. No gene is consistently underestimated in all lymphomas.
Now lets look at the genders within each lymphoma.
r3_gender <- researchGenes[,c(82:87,95)]
paged_table(r3_gender)Looks like IFNG is over estimated only in the males with CHL and the females with pDLBCL, and otherwise under estimated. And IDO1 is under estimated in both genders of pDLBCL, while over estimated in both genders of CHL and mDLBCL. The trackers for high variation at chromosome 9 at loci 9p24.1 for CD274 or PDL1 and PDCD1LG2 for PDL2 have inconsistencies when spread across separate groups of gender in each class of lymphoma. The PDL1 gene is only over expressed in males with pDLBCL and mDLBCL, while PDL2 is only over expressed in males with CHL or mDLBCL. High variations at 9p24.1 are supposed to be exclusive to only CHL. But PDL1 region of 9p24.1 could be excluded, while PDL2 region of 9p24.1 is only relevant to males with CHL. PAX5, BCL2, and IDO1 were the only genes over estimated in strictly all of the 3 lymphomas, but when spread across separate groups of gender we see distinctions. While PAX5 is over estimated in all genders and groups except the males with pDLBCL. BCL2 is only over estimated in all males of each lymphoma type but none of the females. IDO1 is only under expressed in both genders of pDLBCL> MUM1 is only elevated in all males but both genders with CHL. When including males MUM1 was not over estimated in CHL in either gender. There is some median value with both genders lined up in increasing order that is higher than the average of both genders combined in CHL making MUM1 underexpressed in CHL excluding gender, but over expressed when including gender for both genders.
Looks like gender could be playing a role in BCL2 as it is the only gene that has over estimation in all males but not females. There are close gender discrepencies in the other groups like females included in over expression of MUM1 with all males, and males excluded from over expression of PaX5 only if they have pDLBCL.
And PDL1 is only in males with both types of DLBCL, and PDL2 only in males with CHL or mDLBCL. It seems the 9p24.1 high variations only includes males with either type of lymphoma of large B-cell type. However, we found a gene on the same loci of 9p24.1 not in the study and that was PTPRD, it seems to be high or over estimated only in the CHL and pDLBCL for males and also females, but not in the mDLBCL for either gender. So high variation of 9p24.1 is true for CHL but only for PTPRD.
Now lets see if any age discrepencies in the subgroups by age within each lymphoma.
rs3_6age <- researchGenes[,c(88:93,95)]
paged_table(rs3_6age)The 3 genes over estimated in all lymphomas of IDO1, PAX5, and BCL2 have distinct changes in age parameters. IDO1 is only overestimated in CHL in either age group and in only the older than age 72 group with mDLBCL. PAX5 is only overestimated in both young groups of pDLBCL and mDLBCL. BCL2 is only elevated in both age groups of CHL and only the older than 72 years of age group of both types DLBCL.
PAX5 was seen in both genders with CHL over estimated, but under estimated when grouped by age in CHL for PAX 5, this is likely due to the sampling order as not all samples by gender are in same group by age.
For the genes along loci 9p24.1, PTPRD, PDCD1LG2 for PDL2, and CD274 for PDL1. When we looked at age groups above, PDL2 is over estimated in mDLBCL and CHL both age groups, PDL1 is over estimated in the young with CHL or mDLBCL but the old with pDLBCL.The PTPRD gene is not in the study but is at loci of chromosome 9 or 9p24.1 when we searched for genes at the region in part 2. It is also over expressed only in younger than 72 years of age group with CHL or pDLBCL. So the high variation at 9p24.1 is exclusive to younger than 72 years of age AND also having CHL or pDLBCL.
We can use PTPRD to predict age and the CD247 and PDCD1LG2 genes to predict gender.
We have the sample demographics and can look at it now to see the genders and age
There seems to be some genes not necessarily associated with a class of lymphoma but by age or by gender within those classes of lymphoma. This was what the study was searching for, was a way to more easily classify a large B-cell lymphoma other than current standards, as there is overlap within the 3 classes but those differences could be more distinct if more criteria available to classify the type of lymphoma. In the study they saw a transition state between the CHL and pDLBCL class.
We are testing sample bias by using this change factor based on outliers pulling the real values away from the population true value when taking the group avg/group median. In the study, the groups were said to be high variations at 9p24.1 and PDL1 for CHL with EBV, and high IDO1 and INFG for pDLBCL, while mDLBCL was said to be discovered histologically with immune sensescence, and low IFNG with no distinct affects of changes at loci 9p24.1 is the transition state or 4th group that marks the transition to CHL from pDLBCL as IFNG recruits IDO1 so both are high in pDLBCL but as immune cells exhaust they transition into an inbetween state of exhaustion and low IFNG but due to pressure in immune selection the PDL1 gene expression increases and so does the varition of high 9p24.1 gene expression seen in CHL. Since mDLBCL is found in a method other than gene expression but from histology to find EBNA2 and immune senescence indicated by classification of latency type 3 EBV infection confirmed by a score in a questionaire ECOG-PS greater than 2, also high lactate dehydrogenase (an indicator for specific cell death depending on which one of lactate dehydrogenase found) and CD20 elevated more than 50%. We didn’t have the genes for EBNA2 or CD20 in this data to compare. We didn’t check for LDH either. But we can check to see if the LDH gene is in the features data.
LDH <- features[grep('LDH', features$SPOT_ID.1),]
LDH## ID probeset_id seqname strand start
## TC0100016260.hg.1 TC0100016260.hg.1 TC0100016260.hg.1 chr1 - 165662212
## TC0100018417.hg.1 TC0100018417.hg.1 TC0100018417.hg.1 chr1 - 18871430
## TC0300008660.hg.1 TC0300008660.hg.1 TC0300008660.hg.1 chr3 + 126103640
## TC0300012269.hg.1 TC0300012269.hg.1 TC0300012269.hg.1 chr3 - 126103561
## TC0500011924.hg.1 TC0500011924.hg.1 TC0500011924.hg.1 chr5 - 126541841
## TC0600007198.hg.1 TC0600007198.hg.1 TC0600007198.hg.1 chr6 + 24494852
## TC0600013249.hg.1 TC0600013249.hg.1 TC0600013249.hg.1 chr6 - 134917390
## TC0600013251.hg.1 TC0600013251.hg.1 TC0600013251.hg.1 chr6 - 134960378
## TC0900007187.hg.1 TC0900007187.hg.1 TC0900007187.hg.1 chr9 + 38392664
## TC0900012245.hg.1 TC0900012245.hg.1 TC0900012245.hg.1 chr9 - 72900662
## TC1000011499.hg.1 TC1000011499.hg.1 TC1000011499.hg.1 chr10 - 95605929
## TC1100007003.hg.1 TC1100007003.hg.1 TC1100007003.hg.1 chr11 + 18394388
## TC1100007005.hg.1 TC1100007005.hg.1 TC1100007005.hg.1 chr11 + 18412306
## TC1100007006.hg.1 TC1100007006.hg.1 TC1100007006.hg.1 chr11 + 18455824
## TC1100008174.hg.1 TC1100008174.hg.1 TC1100008174.hg.1 chr11 + 68008547
## TC1100011350.hg.1 TC1100011350.hg.1 TC1100011350.hg.1 chr11 - 67662162
## TC1200010109.hg.1 TC1200010109.hg.1 TC1200010109.hg.1 chr12 - 21635341
## TC1200011770.hg.1 TC1200011770.hg.1 TC1200011770.hg.1 chr12 - 105019784
## TC1200012707.hg.1 TC1200012707.hg.1 TC1200012707.hg.1 chr12 + 111766887
## TC1400009684.hg.1 TC1400009684.hg.1 TC1400009684.hg.1 chr14 - 74056850
## TC1500007396.hg.1 TC1500007396.hg.1 TC1500007396.hg.1 chr15 + 59206816
## TC1500009561.hg.1 TC1500009561.hg.1 TC1500009561.hg.1 chr15 - 57953424
## TC1500010800.hg.1 TC1500010800.hg.1 TC1500010800.hg.1 chr15 + 100877714
## TC1600010866.hg.1 TC1600010866.hg.1 TC1600010866.hg.1 chr16 - 75111860
## TC1700007189.hg.1 TC1700007189.hg.1 TC1700007189.hg.1 chr17 + 19648136
## TC1700010036.hg.1 TC1700010036.hg.1 TC1700010036.hg.1 chr17 - 19737984
## TC1900011778.hg.1 TC1900011778.hg.1 TC1900011778.hg.1 chr19 + 49453169
## stop total_probes category SPOT_ID
## TC0100016260.hg.1 165698863 10 main Multiple_Complex
## TC0100018417.hg.1 18902799 10 main Multiple_Complex
## TC0300008660.hg.1 126108069 10 main Multiple_Complex
## TC0300012269.hg.1 126197994 10 main Multiple_Complex
## TC0500011924.hg.1 126595418 10 main Multiple_Complex
## TC0600007198.hg.1 24537207 10 main Multiple_Complex
## TC0600013249.hg.1 134950122 10 main Multiple_Complex
## TC0600013251.hg.1 135103056 10 main Multiple_Complex
## TC0900007187.hg.1 38398665 10 main Multiple_Complex
## TC0900012245.hg.1 73038722 10 main Multiple_Complex
## TC1000011499.hg.1 95656810 10 main Multiple_Complex
## TC1100007003.hg.1 18408425 10 main Multiple_Complex
## TC1100007005.hg.1 18452058 10 main Coding
## TC1100007006.hg.1 18479600 10 main Coding
## TC1100008174.hg.1 68029282 10 main Multiple_Complex
## TC1100011350.hg.1 67681214 10 main Multiple_Complex
## TC1200010109.hg.1 21757857 10 main Multiple_Complex
## TC1200011770.hg.1 105084577 10 main Multiple_Complex
## TC1200012707.hg.1 111817529 10 main Multiple_Complex
## TC1400009684.hg.1 74084493 10 main Multiple_Complex
## TC1500007396.hg.1 59208586 10 main Coding
## TC1500009561.hg.1 58497866 10 main Multiple_Complex
## TC1500010800.hg.1 100916626 10 main Multiple_Complex
## TC1600010866.hg.1 75116772 10 main Multiple_Complex
## TC1700007189.hg.1 19677598 10 main Multiple_Complex
## TC1700010036.hg.1 19748943 10 main Multiple_Complex
## TC1900011778.hg.1 49471048 10 main Multiple_Complex
## SPOT_ID.1
## TC0100016260.hg.1 NM_000696 // RefSeq // Homo sapiens aldehyde dehydrogenase 9 family, member A1 (ALDH9A1), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000354775 // ENSEMBL // aldehyde dehydrogenase 9 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000461664 // ENSEMBL // aldehyde dehydrogenase 9 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000463610 // ENSEMBL // aldehyde dehydrogenase 9 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000471457 // ENSEMBL // aldehyde dehydrogenase 9 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000491436 // ENSEMBL // aldehyde dehydrogenase 9 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// BC151140 // GenBank // Homo sapiens aldehyde dehydrogenase 9 family, member A1, mRNA (cDNA clone MGC:184052 IMAGE:9057040), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// BC151141 // GenBank // Homo sapiens aldehyde dehydrogenase 9 family, member A1, mRNA (cDNA clone MGC:184053 IMAGE:9057041), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000083899 // Havana transcript // aldehyde dehydrogenase 9 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000083900 // Havana transcript // aldehyde dehydrogenase 9 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000083901 // Havana transcript // aldehyde dehydrogenase 9 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000083902 // Havana transcript // aldehyde dehydrogenase 9 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000313745 // Havana transcript // aldehyde dehydrogenase 9 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000384263 // ENSEMBL // Y RNA [Source:RFAM;Acc:RF00019] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS1250.2 // ccdsGene // aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:HGNC:412] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0003014 // circbase // Jeck2013, Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0005666 // circbase // Jeck2013, Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0015070 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0015071 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0015072 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0015073 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0015074 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0015075 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000696 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001gdh.2 // UCSC Genes // aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:HGNC:412] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057myv.1 // UCSC Genes // Y RNA [Source:RFAM;Acc:RF00019] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057myw.1 // UCSC Genes // aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:HGNC:412] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057myx.1 // UCSC Genes // aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:HGNC:412] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057myy.1 // UCSC Genes // aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:HGNC:412] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057myz.1 // UCSC Genes // aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:HGNC:412] // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT007328 // NONCODE // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT007329 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT007329 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0
## TC0100018417.hg.1 NM_001161504 // RefSeq // Homo sapiens aldehyde dehydrogenase 4 family, member A1 (ALDH4A1), transcript variant 3, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// NM_003748 // RefSeq // Homo sapiens aldehyde dehydrogenase 4 family, member A1 (ALDH4A1), transcript variant P5CDhL, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// NM_170726 // RefSeq // Homo sapiens aldehyde dehydrogenase 4 family, member A1 (ALDH4A1), transcript variant P5CDhS, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000290597 // ENSEMBL // aldehyde dehydrogenase 4 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000375341 // ENSEMBL // aldehyde dehydrogenase 4 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000432718 // ENSEMBL // aldehyde dehydrogenase 4 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000454547 // ENSEMBL // aldehyde dehydrogenase 4 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000538309 // ENSEMBL // aldehyde dehydrogenase 4 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000538839 // ENSEMBL // aldehyde dehydrogenase 4 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC007581 // GenBank // Homo sapiens aldehyde dehydrogenase 4 family, member A1, mRNA (cDNA clone MGC:15564 IMAGE:3139944), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// BC023600 // GenBank // Homo sapiens aldehyde dehydrogenase 4 family, member A1, mRNA (cDNA clone MGC:23086 IMAGE:4548787), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000006954 // Havana transcript // aldehyde dehydrogenase 4 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000006955 // Havana transcript // aldehyde dehydrogenase 4 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000006956 // Havana transcript // aldehyde dehydrogenase 4 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000006957 // Havana transcript // aldehyde dehydrogenase 4 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000476515 // Havana transcript // aldehyde dehydrogenase 4 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS188.1 // ccdsGene // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS53272.1 // ccdsGene // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010231 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010232 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010233 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010234 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010235 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010236 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_001161504 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010237 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010238 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010239 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010240 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0010241 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_003748 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001bbb.4 // UCSC Genes // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001bbc.4 // UCSC Genes // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// uc010ocu.3 // UCSC Genes // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// uc021ohl.2 // UCSC Genes // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057cvb.1 // UCSC Genes // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057cvc.1 // UCSC Genes // aldehyde dehydrogenase 4 family, member A1 [Source:HGNC Symbol;Acc:HGNC:406] // chr1 // 100 // 100 // 0 // --- // 0
## TC0300008660.hg.1 NR_046602 // RefSeq // Homo sapiens ALDH1L1 antisense RNA 1 (ALDH1L1-AS1), long non-coding RNA. // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000512384 // ENSEMBL // ALDH1L1 antisense RNA 1 [gene_biotype:antisense transcript_biotype:antisense] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000512384.1 // lncRNAWiki // ALDH1L1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:40244] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000369856 // Havana transcript // novel transcript // chr3 // 100 // 100 // 0 // --- // 0 /// uc031sbq.2 // UCSC Genes // ALDH1L1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:40244] // chr3 // 100 // 100 // 0 // --- // 0 /// worsweyby.aAug10 // Ace View // Transcript Identified by AceView // chr3 // 100 // 100 // 0 // --- // 0 /// HG496022.1:1..437:ncRNA // RNACentral // long non-coding RNA OTTHUMT00000369856.1 (RP11-124N2.2 gene) // chr3 // 100 // 100 // 0 // --- // 0 /// NONHSAT091647 // NONCODE // Non-coding transcript identified by NONCODE: Antisense // chr3 // 100 // 100 // 0 // --- // 0 /// NR_046602.1:1..437:ncRNA // RNACentral // long non-coding RNA OTTHUMT00000369856.1 (RP11-124N2.2 gene) // chr3 // 100 // 100 // 0 // --- // 0
## TC0300012269.hg.1 NM_001270364 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L1 (ALDH1L1), transcript variant 1, mRNA. // chr3 // 100 // 100 // 0 // --- // 0 /// NM_001270365 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L1 (ALDH1L1), transcript variant 3, mRNA. // chr3 // 100 // 100 // 0 // --- // 0 /// NM_012190 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L1 (ALDH1L1), transcript variant 2, mRNA. // chr3 // 100 // 100 // 0 // --- // 0 /// NR_072979 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L1 (ALDH1L1), transcript variant 4, non-coding RNA. // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000273450 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000393431 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000393434 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000413612 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000452905 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000455064 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000460368 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000462808 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000467370 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000472186 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000473607 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000476245 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000484724 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000488356 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000490367 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000493803 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000509952 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ENST00000511283 // ENSEMBL // aldehyde dehydrogenase 1 family, member L1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr3 // 100 // 100 // 0 // --- // 0 /// BC027241 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member L1, mRNA (cDNA clone MGC:21310 IMAGE:4484301), complete cds. // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000102803 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000246897 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354391 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354392 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354393 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354394 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354395 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354396 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354397 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354398 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354399 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354400 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000354401 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000370525 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000370526 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000370527 // Havana transcript // aldehyde dehydrogenase 1 family, member L1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr3 // 100 // 100 // 0 // --- // 0 /// ALDH1L1.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 10840 // chr3 // 100 // 100 // 0 // --- // 0 /// ALDH1L1.dAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 10840 // chr3 // 100 // 100 // 0 // --- // 0 /// ALDH1L1.mAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 10840 // chr3 // 100 // 100 // 0 // --- // 0 /// ALDH1L1.nAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 10840 // chr3 // 100 // 100 // 0 // --- // 0 /// ALDH1L1.oAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 10840 // chr3 // 100 // 100 // 0 // --- // 0 /// CCDS3034.1 // ccdsGene // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// CCDS58850.1 // ccdsGene // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// CCDS58851.1 // ccdsGene // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0067127 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_012190 // chr3 // 100 // 100 // 0 // --- // 0 /// uc003eim.3 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc003ein.2 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc003eio.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc011bki.3 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc031sbp.2 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062njt.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nju.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062njv.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062njw.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062njx.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062njy.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062njz.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nka.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nkb.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nkc.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nkd.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nke.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// uc062nkf.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L1 [Source:HGNC Symbol;Acc:HGNC:3978] // chr3 // 100 // 100 // 0 // --- // 0 /// NONHSAT091648 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr3 // 100 // 100 // 0 // --- // 0 /// NONHSAT091648 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr3 // 100 // 100 // 0 // --- // 0
## TC0500011924.hg.1 NM_001182 // RefSeq // Homo sapiens aldehyde dehydrogenase 7 family, member A1 (ALDH7A1), transcript variant 1, mRNA. // chr5 // 100 // 100 // 0 // --- // 0 /// NM_001201377 // RefSeq // Homo sapiens aldehyde dehydrogenase 7 family, member A1 (ALDH7A1), transcript variant 1, mRNA. // chr5 // 100 // 100 // 0 // --- // 0 /// NM_001202404 // RefSeq // Homo sapiens aldehyde dehydrogenase 7 family, member A1 (ALDH7A1), transcript variant 2, mRNA. // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000409134 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000412186 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000413020 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000433026 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000447989 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000458249 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000476328 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000479989 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000485852 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000497231 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000503281 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000509270 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000509459 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000510111 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000511266 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr5 // 100 // 100 // 0 // --- // 0 /// ENST00000553117 // ENSEMBL // aldehyde dehydrogenase 7 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// BC002515 // GenBank // Homo sapiens aldehyde dehydrogenase 7 family, member A1, mRNA (cDNA clone MGC:1569 IMAGE:3139235), complete cds. // chr5 // 100 // 100 // 0 // --- // 0 /// BC071712 // GenBank // Homo sapiens aldehyde dehydrogenase 7 family, member A1, mRNA (cDNA clone MGC:88005 IMAGE:5518212), complete cds. // chr5 // 100 // 100 // 0 // --- // 0 /// BC073174 // GenBank // Homo sapiens aldehyde dehydrogenase 7 family, member A1, mRNA (cDNA clone MGC:90324 IMAGE:6501646), complete cds. // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000250921 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330456 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330457 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330458 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330459 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330460 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330462 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330463 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000330464 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000371752 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000371753 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000371754 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000372272 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000372273 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000405796 // Havana transcript // aldehyde dehydrogenase 7 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr5 // 100 // 100 // 0 // --- // 0 /// ALDH7A1.dAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 501 // chr5 // 100 // 100 // 0 // --- // 0 /// ALDH7A1.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 501 // chr5 // 100 // 100 // 0 // --- // 0 /// ALDH7A1.lAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 501 // chr5 // 100 // 100 // 0 // --- // 0 /// CCDS4137.2 // ccdsGene // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// CCDS56380.1 // ccdsGene // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009072 // circbase // Jeck2013, Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001201377 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073722 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073723 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073724 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073725 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073726 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073727 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073728 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073729 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073730 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073731 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073732 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073733 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073734 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073735 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073736 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073737 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0073738 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001182 // chr5 // 100 // 100 // 0 // --- // 0 /// uc003ktx.5 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc011cxa.3 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gnt.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gnu.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gnv.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gnw.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gnx.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gny.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gnz.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063goa.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gob.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063goc.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063god.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063goe.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gof.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// uc063gog.1 // UCSC Genes // aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:HGNC:877] // chr5 // 100 // 100 // 0 // --- // 0 /// NONHSAT103587 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr5 // 100 // 100 // 0 // --- // 0 /// NONHSAT103587 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr5 // 100 // 100 // 0 // --- // 0 /// NONHSAT103588 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr5 // 100 // 100 // 0 // --- // 0 /// NONHSAT103588 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr5 // 100 // 100 // 0 // --- // 0 /// NONHSAT103590 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr5 // 100 // 100 // 0 // --- // 0 /// NONHSAT103590 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr5 // 100 // 100 // 0 // --- // 0
## TC0600007198.hg.1 NM_001080 // RefSeq // Homo sapiens aldehyde dehydrogenase 5 family, member A1 (ALDH5A1), transcript variant 2, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// NM_170740 // RefSeq // Homo sapiens aldehyde dehydrogenase 5 family, member A1 (ALDH5A1), transcript variant 1, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000348925 // ENSEMBL // aldehyde dehydrogenase 5 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000357578 // ENSEMBL // aldehyde dehydrogenase 5 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000479394 // ENSEMBL // aldehyde dehydrogenase 5 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000491546 // ENSEMBL // aldehyde dehydrogenase 5 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000492697 // ENSEMBL // aldehyde dehydrogenase 5 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr6 // 100 // 100 // 0 // --- // 0 /// BC034321 // GenBank // Homo sapiens aldehyde dehydrogenase 5 family, member A1, mRNA (cDNA clone MGC:41874 IMAGE:4829533), complete cds. // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000040007 // Havana transcript // aldehyde dehydrogenase 5 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000353913 // Havana transcript // aldehyde dehydrogenase 5 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000353914 // Havana transcript // aldehyde dehydrogenase 5 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000353916 // Havana transcript // aldehyde dehydrogenase 5 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000353917 // Havana transcript // aldehyde dehydrogenase 5 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr6 // 100 // 100 // 0 // --- // 0 /// ALDH5A1.bAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 7915, RefSeq ID(s) NM_170740 // chr6 // 100 // 100 // 0 // --- // 0 /// ALDH5A1.dAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 7915 // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS4555.1 // ccdsGene // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS4556.1 // ccdsGene // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0075844 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_170740 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0075845 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_170740 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0075846 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_170740 // chr6 // 100 // 100 // 0 // --- // 0 /// uc003nef.4 // UCSC Genes // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// uc003neg.4 // UCSC Genes // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063mdx.1 // UCSC Genes // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063mdy.1 // UCSC Genes // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063mdz.1 // UCSC Genes // aldehyde dehydrogenase 5 family, member A1 [Source:HGNC Symbol;Acc:HGNC:408] // chr6 // 100 // 100 // 0 // --- // 0 /// NONHSAT108113 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr6 // 100 // 100 // 0 // --- // 0 /// NONHSAT108113 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr6 // 100 // 100 // 0 // --- // 0
## TC0600013249.hg.1 NM_001193480 // RefSeq // Homo sapiens aldehyde dehydrogenase 8 family, member A1 (ALDH8A1), transcript variant 3, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// NM_022568 // RefSeq // Homo sapiens aldehyde dehydrogenase 8 family, member A1 (ALDH8A1), transcript variant 1, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// NM_170771 // RefSeq // Homo sapiens aldehyde dehydrogenase 8 family, member A1 (ALDH8A1), transcript variant 2, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000265605 // ENSEMBL // aldehyde dehydrogenase 8 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000349305 // ENSEMBL // aldehyde dehydrogenase 8 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000367845 // ENSEMBL // aldehyde dehydrogenase 8 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000367847 // ENSEMBL // aldehyde dehydrogenase 8 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000460753 // ENSEMBL // aldehyde dehydrogenase 8 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000534012 // ENSEMBL // aldehyde dehydrogenase 8 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// BC113862 // GenBank // Homo sapiens aldehyde dehydrogenase 8 family, member A1, mRNA (cDNA clone MGC:138650 IMAGE:40033493), complete cds. // chr6 // 100 // 100 // 0 // --- // 0 /// BC114473 // GenBank // Homo sapiens aldehyde dehydrogenase 8 family, member A1, mRNA (cDNA clone MGC:138649 IMAGE:40033488), complete cds. // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042334 // Havana transcript // aldehyde dehydrogenase 8 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042335 // Havana transcript // aldehyde dehydrogenase 8 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042336 // Havana transcript // aldehyde dehydrogenase 8 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391395 // Havana transcript // aldehyde dehydrogenase 8 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391396 // Havana transcript // aldehyde dehydrogenase 8 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391397 // Havana transcript // aldehyde dehydrogenase 8 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// uc003qew.3 // UCSC Genes // Homo sapiens aldehyde dehydrogenase 8 family, member A1 (ALDH8A1), transcript variant 1, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS5171.1 // ccdsGene // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS5172.1 // ccdsGene // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS55057.1 // ccdsGene // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// HBS1LandALDH8A1.uAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 64577; 10767 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0077898 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_022568 // chr6 // 100 // 100 // 0 // --- // 0 /// uc003qex.4 // UCSC Genes // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// uc011ecx.3 // UCSC Genes // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rot.1 // UCSC Genes // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rou.1 // UCSC Genes // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063row.1 // UCSC Genes // aldehyde dehydrogenase 8 family, member A1 [Source:HGNC Symbol;Acc:HGNC:15471] // chr6 // 100 // 100 // 0 // --- // 0 /// chr6_135263546_135265104 // Guo // circRNA transcript identified by Guo, et al. on chr6 from 135263546-135265104 on Hg19 // chr6 // 100 // 100 // 0 // --- // 0
## TC0600013251.hg.1 NM_001145158 // RefSeq // Homo sapiens HBS1-like translational GTPase (HBS1L), transcript variant 2, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// NM_001145207 // RefSeq // Homo sapiens HBS1-like translational GTPase (HBS1L), transcript variant 3, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// NM_006620 // RefSeq // Homo sapiens HBS1-like translational GTPase (HBS1L), transcript variant 1, mRNA. // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000314674 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000367820 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000367822 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000367826 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000367837 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000415177 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000524715 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000525067 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000526100 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000527005 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000527507 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000527578 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000529169 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000529641 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000529882 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// ENST00000533274 // ENSEMBL // HBS1-like translational GTPase [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// BC001465 // GenBank // Homo sapiens HBS1-like (S. cerevisiae), mRNA (cDNA clone MGC:1869 IMAGE:3138910), complete cds. // chr6 // 100 // 100 // 0 // --- // 0 /// BC040849 // GenBank // Homo sapiens HBS1-like (S. cerevisiae), mRNA (cDNA clone MGC:49906 IMAGE:5104748), complete cds. // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042339 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042341 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042342 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000042344 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391463 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391464 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391465 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391466 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391467 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391468 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391469 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391470 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391471 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391472 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391545 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000391546 // Havana transcript // HBS1-like (S. cerevisiae)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS47479.1 // ccdsGene // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS47480.1 // ccdsGene // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// CCDS5173.1 // ccdsGene // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// HBS1LandALDH8A1.iAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 64577; 10767 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0001641 // circbase // Jeck2013, Memczak2013, Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001145207 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0003504 // circbase // Jeck2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_006620 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0077899 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_006620 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0077900 // circbase // Salzman2013 ALT_ACCEPTOR, CDS, coding, INTERNAL, intronic, OVCODE, OVEXON best transcript NM_006620 // chr6 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0077901 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_006620 // chr6 // 100 // 100 // 0 // --- // 0 /// uc003qey.4 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc003qez.4 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc003qfa.3 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc011eda.3 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rox.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063roy.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063roz.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpa.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpb.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpc.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpd.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpe.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpf.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpg.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rph.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0 /// uc063rpi.1 // UCSC Genes // HBS1-like translational GTPase [Source:HGNC Symbol;Acc:HGNC:4834] // chr6 // 100 // 100 // 0 // --- // 0
## TC0900007187.hg.1 NM_000692 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member B1 (ALDH1B1), mRNA. // chr9 // 100 // 100 // 0 // --- // 0 /// ENST00000377698 // ENSEMBL // aldehyde dehydrogenase 1 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// BC001619 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member B1, mRNA (cDNA clone MGC:2230 IMAGE:3356389), complete cds. // chr9 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000052492 // Havana transcript // aldehyde dehydrogenase 1 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// CCDS6615.1 // ccdsGene // aldehyde dehydrogenase 1 family, member B1 [Source:HGNC Symbol;Acc:HGNC:407] // chr9 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0087092 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3, UTR5 best transcript NM_000692 // chr9 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0087093 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3, UTR5 best transcript NM_000692 // chr9 // 100 // 100 // 0 // --- // 0 /// uc004aay.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member B1 [Source:HGNC Symbol;Acc:HGNC:407] // chr9 // 100 // 100 // 0 // --- // 0
## TC0900012245.hg.1 NM_000689 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A1 (ALDH1A1), mRNA. // chr9 // 100 // 100 // 0 // --- // 0 /// ENST00000297785 // ENSEMBL // aldehyde dehydrogenase 1 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// ENST00000376939 // ENSEMBL // aldehyde dehydrogenase 1 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// ENST00000446946 // ENSEMBL // aldehyde dehydrogenase 1 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// ENST00000482210 // ENSEMBL // aldehyde dehydrogenase 1 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr9 // 100 // 100 // 0 // --- // 0 /// ENST00000493113 // ENSEMBL // aldehyde dehydrogenase 1 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr9 // 100 // 100 // 0 // --- // 0 /// BC001505 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member A1, mRNA (cDNA clone MGC:2318 IMAGE:2988388), complete cds. // chr9 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000052679 // Havana transcript // aldehyde dehydrogenase 1 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000052680 // Havana transcript // aldehyde dehydrogenase 1 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000052681 // Havana transcript // aldehyde dehydrogenase 1 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr9 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000052682 // Havana transcript // aldehyde dehydrogenase 1 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr9 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000052683 // Havana transcript // aldehyde dehydrogenase 1 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr9 // 100 // 100 // 0 // --- // 0 /// CCDS6644.1 // ccdsGene // aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:HGNC:402] // chr9 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0087206 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000689 // chr9 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0087207 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000689 // chr9 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0087208 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000689 // chr9 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0087209 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_000689 // chr9 // 100 // 100 // 0 // --- // 0 /// uc004ajd.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:HGNC:402] // chr9 // 100 // 100 // 0 // --- // 0 /// uc064tsz.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:HGNC:402] // chr9 // 100 // 100 // 0 // --- // 0 /// uc064tta.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:HGNC:402] // chr9 // 100 // 100 // 0 // --- // 0 /// uc064ttc.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:HGNC:402] // chr9 // 100 // 100 // 0 // --- // 0 /// uc064ttd.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:HGNC:402] // chr9 // 100 // 100 // 0 // --- // 0
## TC1000011499.hg.1 NM_001017423 // RefSeq // Homo sapiens aldehyde dehydrogenase 18 family, member A1 (ALDH18A1), transcript variant 2, mRNA. // chr10 // 100 // 100 // 0 // --- // 0 /// NM_002860 // RefSeq // Homo sapiens aldehyde dehydrogenase 18 family, member A1 (ALDH18A1), transcript variant 1, mRNA. // chr10 // 100 // 100 // 0 // --- // 0 /// ENST00000371221 // ENSEMBL // aldehyde dehydrogenase 18 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr10 // 100 // 100 // 0 // --- // 0 /// ENST00000371224 // ENSEMBL // aldehyde dehydrogenase 18 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr10 // 100 // 100 // 0 // --- // 0 /// ENST00000483788 // ENSEMBL // aldehyde dehydrogenase 18 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr10 // 100 // 100 // 0 // --- // 0 /// ENST00000485428 // ENSEMBL // aldehyde dehydrogenase 18 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr10 // 100 // 100 // 0 // --- // 0 /// ENST00000489386 // ENSEMBL // aldehyde dehydrogenase 18 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr10 // 100 // 100 // 0 // --- // 0 /// BC106054 // GenBank // Homo sapiens aldehyde dehydrogenase 18 family, member A1, mRNA (cDNA clone MGC:117316 IMAGE:6156087), complete cds. // chr10 // 100 // 100 // 0 // --- // 0 /// BC117240 // GenBank // Homo sapiens aldehyde dehydrogenase 18 family, member A1, mRNA (cDNA clone MGC:150849 IMAGE:40125791), complete cds. // chr10 // 100 // 100 // 0 // --- // 0 /// BC117242 // GenBank // Homo sapiens aldehyde dehydrogenase 18 family, member A1, mRNA (cDNA clone MGC:150851 IMAGE:40125793), complete cds. // chr10 // 100 // 100 // 0 // --- // 0 /// BC143930 // GenBank // Homo sapiens aldehyde dehydrogenase 18 family, member A1, mRNA (cDNA clone MGC:177465 IMAGE:9052448), complete cds. // chr10 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000049552 // Havana transcript // aldehyde dehydrogenase 18 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr10 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000049553 // Havana transcript // aldehyde dehydrogenase 18 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr10 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000049554 // Havana transcript // aldehyde dehydrogenase 18 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr10 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000049555 // Havana transcript // aldehyde dehydrogenase 18 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr10 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000049556 // Havana transcript // aldehyde dehydrogenase 18 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr10 // 100 // 100 // 0 // --- // 0 /// ALDH18A1.mAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 5832 // chr10 // 100 // 100 // 0 // --- // 0 /// CCDS31257.1 // ccdsGene // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0 /// CCDS7443.1 // ccdsGene // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0004882 // circbase // Jeck2013, Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_002860 // chr10 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0019257 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_002860 // chr10 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0019258 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_002860 // chr10 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0019259 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_002860 // chr10 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0019260 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_002860 // chr10 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0019261 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_002860 // chr10 // 100 // 100 // 0 // --- // 0 /// uc001kky.4 // UCSC Genes // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0 /// uc001kkz.4 // UCSC Genes // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0 /// uc057vau.1 // UCSC Genes // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0 /// uc057vav.1 // UCSC Genes // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0 /// uc057vaw.1 // UCSC Genes // aldehyde dehydrogenase 18 family, member A1 [Source:HGNC Symbol;Acc:HGNC:9722] // chr10 // 100 // 100 // 0 // --- // 0
## TC1100007003.hg.1 NM_001135239 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165414 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165415 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 4, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165416 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 5, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_005566 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NR_028500 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 6, non-coding RNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000227157 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000375710 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000379412 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396222 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000422447 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000430553 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000460405 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000469976 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000478970 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000486690 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000494573 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000495052 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000535451 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000536528 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000537296 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000538451 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000539814 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000540430 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000541097 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000542179 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000543445 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000543695 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545215 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545467 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000625635 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC067223 // GenBank // Homo sapiens lactate dehydrogenase A, mRNA (cDNA clone MGC:72033 IMAGE:4096518), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258172 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258173 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258174 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258175 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258176 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258177 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258178 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258179 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258180 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395876 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395877 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395878 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395879 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395880 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395881 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395882 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395883 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395885 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395886 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395887 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395888 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395889 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395890 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// uc010rdd.2 // UCSC Genes // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS44549.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53609.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53610.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53611.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7839.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0006469 // circbase // Jeck2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021446 // circbase // Salzman2013 ANNOTATED, coding, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021447 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021448 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021449 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021450 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021451 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021452 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021453 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001135239 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001165415 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.gAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NR_028500 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.pAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.uAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.vgAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mok.4 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mol.4 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc010rdc.2 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc021qep.2 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqs.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqt.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqu.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqv.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqw.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqx.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqy.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqz.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zra.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrb.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrc.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrd.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zre.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrf.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrg.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrh.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zri.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrj.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrk.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrl.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT018284 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT018284 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr11 // 100 // 100 // 0 // --- // 0
## TC1100007005.hg.1 NM_002301 // RefSeq // Homo sapiens lactate dehydrogenase C (LDHC), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_017448 // RefSeq // Homo sapiens lactate dehydrogenase C (LDHC), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000280704 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396215 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000535809 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000536880 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000537486 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000539369 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000541669 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000544105 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545848 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000546146 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC019249 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:26530 IMAGE:4839028), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC064388 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:74967 IMAGE:5744600), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC090043 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:111073 IMAGE:30387780), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395892 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395893 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395894 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395895 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395896 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395897 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395898 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395899 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395900 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395901 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7840.1 // ccdsGene // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// LDHC.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3948 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHC.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3948 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mom.5 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mon.5 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrn.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zro.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrp.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrq.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrr.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrs.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrt.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zru.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0
## TC1100007006.hg.1 NM_001144071 // RefSeq // Homo sapiens lactate dehydrogenase A-like 6A (LDHAL6A), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_144972 // RefSeq // Homo sapiens lactate dehydrogenase A-like 6A (LDHAL6A), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000280706 // ENSEMBL // lactate dehydrogenase A-like 6A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396213 // ENSEMBL // lactate dehydrogenase A-like 6A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000615355 // ENSEMBL // lactate dehydrogenase A-like 6A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC014340 // GenBank // Homo sapiens lactate dehydrogenase A-like 6A, mRNA (cDNA clone MGC:23940 IMAGE:3935569), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395903 // Havana transcript // lactate dehydrogenase A-like 6A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395904 // Havana transcript // lactate dehydrogenase A-like 6A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7841.1 // ccdsGene // lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:HGNC:28335] // chr11 // 100 // 100 // 0 // --- // 0 /// LDHAL6A.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 160287, RefSeq ID(s) NM_144972 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mop.2 // UCSC Genes // lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:HGNC:28335] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001moq.3 // UCSC Genes // lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:HGNC:28335] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrv.1 // UCSC Genes // lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:HGNC:28335] // chr11 // 100 // 100 // 0 // --- // 0
## TC1100008174.hg.1 NM_000694 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B1 (ALDH3B1), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001030010 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B1 (ALDH3B1), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001161473 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B1 (ALDH3B1), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001290058 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B1 (ALDH3B1), transcript variant 4, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001290059 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B1 (ALDH3B1), transcript variant 5, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000342456 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000527514 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000612297 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000614849 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000615368 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000615463 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000616697 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000617288 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000617449 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000619675 // ENSEMBL // aldehyde dehydrogenase 3 family, member B1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// BC013584 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, member B1, mRNA (cDNA clone MGC:9573 IMAGE:3878124), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC033099 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, member B1, mRNA (cDNA clone MGC:45675 IMAGE:5446816), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000337614 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000337615 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395036 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395037 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395038 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395039 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395040 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395042 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395043 // Havana transcript // aldehyde dehydrogenase 3 family, member B1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ALDH3B1.gAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 221 // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS73335.1 // ccdsGene // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS73336.1 // ccdsGene // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0023133 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3, UTR5 best transcript NM_001161473 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0023134 // circbase // Salzman2013 ALT_ACCEPTOR, ALT_DONOR, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001161473 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0023135 // circbase // Salzman2013 ALT_ACCEPTOR, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3 best transcript NM_001161473 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0023136 // circbase // Salzman2013 ALT_DONOR, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001161473 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0023137 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3 best transcript NM_001161473 // chr11 // 100 // 100 // 0 // --- // 0 /// uc031xti.2 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc031xtj.2 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc031xtk.2 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc031xtl.2 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ekp.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ekq.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ekr.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058eks.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ekt.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058eku.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B1 [Source:HGNC Symbol;Acc:HGNC:410] // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:1 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:10 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:11 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:12 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:13 // lncRNAWiki // Transcript Originally Identified by LNCipedia, alternate transcript name: NONHSAT022488 // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:2 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:3 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:4 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:5 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:6 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:7 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:8 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// lnc-NDUFS8-1:9 // lncRNAWiki // Transcript Originally Identified by LNCipedia // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT022488 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr11 // 100 // 100 // 0 // --- // 0
## TC1100011350.hg.1 NM_000695 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B2 (ALDH3B2), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001031615 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member B2 (ALDH3B2), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000349015 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000525827 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000528756 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000530069 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000531248 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000531881 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000533962 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000534425 // ENSEMBL // aldehyde dehydrogenase 3 family, member B2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// BC007685 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, member B2, mRNA (cDNA clone MGC:3627 IMAGE:3636326), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394004 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394006 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394007 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394008 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394009 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394010 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000394011 // Havana transcript // aldehyde dehydrogenase 3 family, member B2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr11 // 100 // 100 // 0 // --- // 0 /// ALDH3B2.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 222 // chr11 // 100 // 100 // 0 // --- // 0 /// ALDH3B2.mAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 222 // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS31622.1 // ccdsGene // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001omr.4 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001oms.4 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ejw.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ejx.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ejy.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ejz.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058eka.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// uc058ekb.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member B2 [Source:HGNC Symbol;Acc:HGNC:411] // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT022461 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT022461 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr11 // 100 // 100 // 0 // --- // 0
## TC1200010109.hg.1 NM_001174097 // RefSeq // Homo sapiens lactate dehydrogenase B (LDHB), transcript variant 2, mRNA. // chr12 // 100 // 100 // 0 // --- // 0 /// NM_002300 // RefSeq // Homo sapiens lactate dehydrogenase B (LDHB), transcript variant 1, mRNA. // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000350669 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000396075 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000396076 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000450584 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000470280 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000470985 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000535112 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000539782 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000542765 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000544151 // ENSEMBL // lactate dehydrogenase B [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// BC002362 // GenBank // Homo sapiens lactate dehydrogenase B, mRNA (cDNA clone MGC:8627 IMAGE:2961445), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// BC015122 // GenBank // Homo sapiens lactate dehydrogenase B, mRNA (cDNA clone MGC:24208 IMAGE:3685985), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// BC071860 // GenBank // Homo sapiens lactate dehydrogenase B, mRNA (cDNA clone MGC:88529 IMAGE:4902461), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258219 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258220 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258221 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258222 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258224 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000402397 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000402398 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000402399 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000402415 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000402416 // Havana transcript // lactate dehydrogenase B[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr12 // 100 // 100 // 0 // --- // 0 /// CCDS8691.1 // ccdsGene // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025590 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025591 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025592 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025593 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025594 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025595 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025596 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3, UTR5 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025597 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3, UTR5 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025598 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3, UTR5 best transcript NM_002300 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025599 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025600 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON, UTR5 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025601 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025602 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001174097 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0025603 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_002300 // chr12 // 100 // 100 // 0 // --- // 0 /// LDHB.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3945, RefSeq ID(s) NM_002300 // chr12 // 100 // 100 // 0 // --- // 0 /// LDHB.lAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3945 // chr12 // 100 // 100 // 0 // --- // 0 /// uc001rfd.4 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc001rfe.4 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvm.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvn.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvo.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvp.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvq.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvr.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvs.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058lvt.1 // UCSC Genes // lactate dehydrogenase B [Source:HGNC Symbol;Acc:HGNC:6541] // chr12 // 100 // 100 // 0 // --- // 0 /// NONHSAT027256 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr12 // 100 // 100 // 0 // --- // 0 /// NONHSAT027256 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr12 // 100 // 100 // 0 // --- // 0 /// NONHSAT027257 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr12 // 100 // 100 // 0 // --- // 0 /// NONHSAT027257 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr12 // 100 // 100 // 0 // --- // 0
## TC1200011770.hg.1 NM_001034173 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L2 (ALDH1L2), transcript variant 1, mRNA. // chr12 // 100 // 100 // 0 // --- // 0 /// NR_027752 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L2 (ALDH1L2), transcript variant 2, non-coding RNA. // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000258494 // ENSEMBL // aldehyde dehydrogenase 1 family, member L2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000548418 // ENSEMBL // aldehyde dehydrogenase 1 family, member L2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000549335 // ENSEMBL // aldehyde dehydrogenase 1 family, member L2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000552270 // ENSEMBL // aldehyde dehydrogenase 1 family, member L2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000552427 // ENSEMBL // aldehyde dehydrogenase 1 family, member L2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// BC103934 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member L2, mRNA (cDNA clone MGC:119536 IMAGE:40008174), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// BC103935 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member L2, mRNA (cDNA clone MGC:119537 IMAGE:40008176), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000406097 // Havana transcript // aldehyde dehydrogenase 1 family, member L2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000406098 // Havana transcript // aldehyde dehydrogenase 1 family, member L2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000406099 // Havana transcript // aldehyde dehydrogenase 1 family, member L2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000406100 // Havana transcript // aldehyde dehydrogenase 1 family, member L2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000406101 // Havana transcript // aldehyde dehydrogenase 1 family, member L2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr12 // 100 // 100 // 0 // --- // 0 /// CCDS31891.1 // ccdsGene // aldehyde dehydrogenase 1 family, member L2 [Source:HGNC Symbol;Acc:HGNC:26777] // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0027972 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001034173 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0027973 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001034173 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0027974 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001034173 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0027975 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001034173 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0027976 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001034173 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0027977 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001034173 // chr12 // 100 // 100 // 0 // --- // 0 /// uc001tlc.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member L2 [Source:HGNC Symbol;Acc:HGNC:26777] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058spf.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L2 [Source:HGNC Symbol;Acc:HGNC:26777] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058spg.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L2 [Source:HGNC Symbol;Acc:HGNC:26777] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058sph.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L2 [Source:HGNC Symbol;Acc:HGNC:26777] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058spi.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member L2 [Source:HGNC Symbol;Acc:HGNC:26777] // chr12 // 100 // 100 // 0 // --- // 0
## TC1200012707.hg.1 NM_000690 // RefSeq // Homo sapiens aldehyde dehydrogenase 2 family (mitochondrial) (ALDH2), transcript variant 1, mRNA. // chr12 // 100 // 100 // 0 // --- // 0 /// NM_001204889 // RefSeq // Homo sapiens aldehyde dehydrogenase 2 family (mitochondrial) (ALDH2), transcript variant 2, mRNA. // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000261733 // ENSEMBL // aldehyde dehydrogenase 2 family (mitochondrial) [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000416293 // ENSEMBL // aldehyde dehydrogenase 2 family (mitochondrial) [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000548536 // ENSEMBL // aldehyde dehydrogenase 2 family (mitochondrial) [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000549106 // ENSEMBL // aldehyde dehydrogenase 2 family (mitochondrial) [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000551450 // ENSEMBL // aldehyde dehydrogenase 2 family (mitochondrial) [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr12 // 100 // 100 // 0 // --- // 0 /// BC002967 // GenBank // Homo sapiens aldehyde dehydrogenase 2 family (mitochondrial), mRNA (cDNA clone MGC:1806 IMAGE:3543343), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// BC071839 // GenBank // Homo sapiens aldehyde dehydrogenase 2 family (mitochondrial), mRNA (cDNA clone MGC:88499 IMAGE:5477768), complete cds. // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000405007 // Havana transcript // aldehyde dehydrogenase 2 family (mitochondrial)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000405008 // Havana transcript // aldehyde dehydrogenase 2 family (mitochondrial)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000405011 // Havana transcript // aldehyde dehydrogenase 2 family (mitochondrial)[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000405013 // Havana transcript // aldehyde dehydrogenase 2 family (mitochondrial)[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr12 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000405014 // Havana transcript // aldehyde dehydrogenase 2 family (mitochondrial)[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr12 // 100 // 100 // 0 // --- // 0 /// ALDH2.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 217 // chr12 // 100 // 100 // 0 // --- // 0 /// CCDS55885.1 // ccdsGene // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// CCDS9155.1 // ccdsGene // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// ENST00000551450.1 // lncRNAWiki // N/A // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028302 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR5 best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028303 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028304 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028305 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028306 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028307 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0028308 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_000690 // chr12 // 100 // 100 // 0 // --- // 0 /// uc001tst.4 // UCSC Genes // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// uc010syi.3 // UCSC Genes // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058tix.1 // UCSC Genes // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058tiy.1 // UCSC Genes // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// uc058tiz.1 // UCSC Genes // aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:HGNC:404] // chr12 // 100 // 100 // 0 // --- // 0 /// HG505176.1:1..569:ncRNA // RNACentral // long non-coding RNA OTTHUMT00000405014.1 (RP3-462E2.3 gene // chr12 // 100 // 100 // 0 // --- // 0 /// NONHSAT030755 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr12 // 100 // 100 // 0 // --- // 0
## TC1400009684.hg.1 NM_001278593 // RefSeq // Homo sapiens aldehyde dehydrogenase 6 family, member A1 (ALDH6A1), transcript variant 2, mRNA. // chr14 // 100 // 100 // 0 // --- // 0 /// NM_001278594 // RefSeq // Homo sapiens aldehyde dehydrogenase 6 family, member A1 (ALDH6A1), transcript variant 3, mRNA. // chr14 // 100 // 100 // 0 // --- // 0 /// NM_005589 // RefSeq // Homo sapiens aldehyde dehydrogenase 6 family, member A1 (ALDH6A1), transcript variant 1, mRNA. // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000350259 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000553458 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000553814 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000554231 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000554501 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000555126 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr14 // 100 // 100 // 0 // --- // 0 /// ENST00000556852 // ENSEMBL // aldehyde dehydrogenase 6 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr14 // 100 // 100 // 0 // --- // 0 /// BC004909 // GenBank // Homo sapiens aldehyde dehydrogenase 6 family, member A1, mRNA (cDNA clone MGC:4657 IMAGE:3530715), complete cds. // chr14 // 100 // 100 // 0 // --- // 0 /// BC032371 // GenBank // Homo sapiens aldehyde dehydrogenase 6 family, member A1, mRNA (cDNA clone MGC:40271 IMAGE:5163797), complete cds. // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412309 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412310 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412311 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412312 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412313 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412314 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr14 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000412315 // Havana transcript // aldehyde dehydrogenase 6 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr14 // 100 // 100 // 0 // --- // 0 /// CCDS61501.1 // ccdsGene // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// CCDS9826.1 // ccdsGene // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc001xpo.5 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc010tuq.4 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc059dgv.1 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc059dgw.1 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc059dgx.1 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc059dgy.1 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0 /// uc059dgz.1 // UCSC Genes // aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:HGNC:7179] // chr14 // 100 // 100 // 0 // --- // 0
## TC1500007396.hg.1 NM_033195 // RefSeq // Homo sapiens lactate dehydrogenase A-like 6B (LDHAL6B), mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000307144 // ENSEMBL // lactate dehydrogenase A-like 6B [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// BC022034 // GenBank // Homo sapiens lactate dehydrogenase A-like 6B, mRNA (cDNA clone MGC:26983 IMAGE:4825988), complete cds. // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000256015 // Havana transcript // lactate dehydrogenase A-like 6B[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// CCDS10171.1 // ccdsGene // lactate dehydrogenase A-like 6B [Source:HGNC Symbol;Acc:HGNC:21481] // chr15 // 100 // 100 // 0 // --- // 0 /// uc002agb.5 // UCSC Genes // lactate dehydrogenase A-like 6B [Source:HGNC Symbol;Acc:HGNC:21481] // chr15 // 100 // 100 // 0 // --- // 0
## TC1500009561.hg.1 NM_001206897 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), transcript variant 4, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// NM_003888 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), transcript variant 1, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// NM_170696 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), transcript variant 2, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// NM_170697 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), transcript variant 3, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000249750 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000347587 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000430119 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000537372 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000557967 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558073 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558231 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558239 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558384 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558504 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558524 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558595 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558603 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558946 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000559266 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000559297 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000559517 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000559579 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000559625 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000560122 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000560312 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000560863 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000560923 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000561070 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000561098 // ENSEMBL // aldehyde dehydrogenase 1 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// BC030589 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member A2, mRNA (cDNA clone MGC:26444 IMAGE:4826743), complete cds. // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000255869 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000255870 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416215 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416264 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416306 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416307 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416308 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416309 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416310 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416311 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416312 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416313 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416314 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416315 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416316 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416317 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416318 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416319 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416320 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416321 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416322 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416323 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416324 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416360 // Havana transcript // aldehyde dehydrogenase 1 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// uc010ugv.2 // UCSC Genes // Homo sapiens aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), transcript variant 4, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// ALDH1A2.bAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 8854 // chr15 // 100 // 100 // 0 // --- // 0 /// ALDH1A2.hAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 8854 // chr15 // 100 // 100 // 0 // --- // 0 /// ALDH1A2.kAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 8854 // chr15 // 100 // 100 // 0 // --- // 0 /// ALDH1A2.vdAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 8854 // chr15 // 100 // 100 // 0 // --- // 0 /// CCDS10163.1 // ccdsGene // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// CCDS10164.1 // ccdsGene // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// CCDS45266.1 // ccdsGene // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// CCDS55968.1 // ccdsGene // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035438 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035439 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3, UTR5 best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035440 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035441 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035442 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035443 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035444 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035445 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0035446 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001206897 // chr15 // 100 // 100 // 0 // --- // 0 /// uc002aew.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc002aex.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc002aey.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc010ugw.3 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jql.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqm.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqn.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqp.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqq.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqr.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqs.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqt.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqu.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqv.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqw.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqx.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jqz.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jrc.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jrd.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jre.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jrf.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jrg.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jrh.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059jri.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:HGNC:15472] // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044082 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044082 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044085 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044085 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044086 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044086 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044087 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044087 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044088 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044088 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044089 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044089 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044093 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044093 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044095 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044095 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044103 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044103 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044104 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044104 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044105 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044105 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044106 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044106 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044107 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT044107 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT140242 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr15 // 100 // 100 // 0 // --- // 0 /// NONHSAT140242 // NONCODE // Non-coding transcript identified by NONCODE: Antisense,Exonic // chr15 // 100 // 100 // 0 // --- // 0
## TC1500010800.hg.1 NM_000693 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A3 (ALDH1A3), transcript variant 1, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// NM_001293815 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member A3 (ALDH1A3), transcript variant 2, mRNA. // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000329841 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000346623 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000557963 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558033 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000558869 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000560555 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// ENST00000561338 // ENSEMBL // aldehyde dehydrogenase 1 family, member A3 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// BC069274 // GenBank // Homo sapiens aldehyde dehydrogenase 1 family, member A3, mRNA (cDNA clone MGC:78582 IMAGE:6208628), complete cds. // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000313620 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416653 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416655 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416656 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416658 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416659 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr15 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000416660 // Havana transcript // aldehyde dehydrogenase 1 family, member A3[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr15 // 100 // 100 // 0 // --- // 0 /// CCDS10389.1 // ccdsGene // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0037070 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3 best transcript NM_000693 // chr15 // 100 // 100 // 0 // --- // 0 /// uc002bwn.5 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// uc010bpb.4 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059nxd.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059nxe.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059nxf.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059nxg.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0 /// uc059nxi.1 // UCSC Genes // aldehyde dehydrogenase 1 family, member A3 [Source:HGNC Symbol;Acc:HGNC:409] // chr15 // 100 // 100 // 0 // --- // 0
## TC1600010866.hg.1 NM_153486 // RefSeq // Homo sapiens lactate dehydrogenase D (LDHD), transcript variant 1, mRNA. // chr16 // 100 // 100 // 0 // --- // 0 /// NM_194436 // RefSeq // Homo sapiens lactate dehydrogenase D (LDHD), transcript variant 2, mRNA. // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000300051 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000450168 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000568164 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000569876 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr16 // 100 // 100 // 0 // --- // 0 /// BC040279 // GenBank // Homo sapiens lactate dehydrogenase D, mRNA (cDNA clone MGC:34649 IMAGE:5162826), complete cds. // chr16 // 100 // 100 // 0 // --- // 0 /// BC047902 // GenBank // Homo sapiens lactate dehydrogenase D, mRNA (cDNA clone MGC:57726 IMAGE:5762691), complete cds. // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000269018 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434651 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434652 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434653 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr16 // 100 // 100 // 0 // --- // 0 /// CCDS10913.1 // ccdsGene // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// CCDS45529.1 // ccdsGene // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc002fdm.4 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc002fdn.4 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc059xeh.1 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc059xei.1 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0
## TC1700007189.hg.1 NM_000382 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member A2 (ALDH3A2), transcript variant 2, mRNA. // chr17 // 100 // 100 // 0 // --- // 0 /// NM_001031806 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member A2 (ALDH3A2), transcript variant 1, mRNA. // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000176643 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000339618 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000395575 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000446398 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000467473 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000472059 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000476965 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000571163 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000571537 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000573505 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000573565 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000573947 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000574078 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000574597 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000575384 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000578614 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000578696 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000579403 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000579855 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000580550 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000581518 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000582991 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000584332 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000626500 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000630662 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000631291 // ENSEMBL // aldehyde dehydrogenase 3 family, member A2 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// BC002430 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, member A2, mRNA (cDNA clone MGC:2136 IMAGE:3346862), complete cds. // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132268 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132269 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132270 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132271 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132272 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132273 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132274 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441024 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441025 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441026 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441027 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441029 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441030 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441031 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442290 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442291 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442292 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442293 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442294 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442295 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442296 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442297 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442298 // Havana transcript // aldehyde dehydrogenase 3 family, member A2[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ALDH3A2.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 224, RefSeq ID(s) NM_001031806 // chr17 // 100 // 100 // 0 // --- // 0 /// CCDS11210.1 // ccdsGene // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// CCDS32589.1 // ccdsGene // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0008603 // circbase // Jeck2013, Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001031806 // chr17 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0042381 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR5 best transcript NM_001031806 // chr17 // 100 // 100 // 0 // --- // 0 /// uc002gwa.2 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc002gwb.2 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmh.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmi.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmj.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmk.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cml.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmm.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmn.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmo.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmp.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmq.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmr.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cms.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmt.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmu.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmw.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmx.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmy.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cmz.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnb.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnc.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnd.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cne.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnf.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cng.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:HGNC:403] // chr17 // 100 // 100 // 0 // --- // 0 /// NONHSAT146516 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr17 // 100 // 100 // 0 // --- // 0 /// NONHSAT146516 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr17 // 100 // 100 // 0 // --- // 0 /// NONHSAT146517 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr17 // 100 // 100 // 0 // --- // 0 /// NONHSAT146517 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr17 // 100 // 100 // 0 // --- // 0
## TC1700010036.hg.1 NM_000691 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member A1 (ALDH3A1), transcript variant 2, mRNA. // chr17 // 100 // 100 // 0 // --- // 0 /// NM_001135167 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member A1 (ALDH3A1), transcript variant 3, mRNA. // chr17 // 100 // 100 // 0 // --- // 0 /// NM_001135168 // RefSeq // Homo sapiens aldehyde dehydrogenase 3 family, member A1 (ALDH3A1), transcript variant 1, mRNA. // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000225740 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000395555 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000426645 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000439102 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000444455 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000457500 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000468746 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000479677 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000485231 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000485472 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000487650 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000494157 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000570414 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000573368 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000574162 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000575103 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ENST00000575860 // ENSEMBL // aldehyde dehydrogenase 3 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// BC004370 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, memberA1, mRNA (cDNA clone MGC:10406 IMAGE:3622758), complete cds. // chr17 // 100 // 100 // 0 // --- // 0 /// BC008892 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, memberA1, mRNA (cDNA clone MGC:10584 IMAGE:3688887), complete cds. // chr17 // 100 // 100 // 0 // --- // 0 /// BC021194 // GenBank // Homo sapiens aldehyde dehydrogenase 3 family, memberA1, mRNA (cDNA clone MGC:3727 IMAGE:3610317), complete cds. // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132256 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132257 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132260 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132261 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132262 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132263 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132264 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132265 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000132266 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441126 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441128 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441129 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441130 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441131 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000441132 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000442302 // Havana transcript // aldehyde dehydrogenase 3 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr17 // 100 // 100 // 0 // --- // 0 /// ALDH3A1.sAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 218 // chr17 // 100 // 100 // 0 // --- // 0 /// CCDS11212.1 // ccdsGene // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0042382 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3 best transcript NM_001135168 // chr17 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0042383 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_001135168 // chr17 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0042384 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON, UTR5 best transcript NM_000691 // chr17 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0042385 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON, UTR5 best transcript NM_000691 // chr17 // 100 // 100 // 0 // --- // 0 /// uc002gwj.4 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc010cqu.4 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc010vzd.3 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnp.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnq.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnr.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cns.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnt.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnu.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnv.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnw.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnx.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cny.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cnz.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060coa.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060cob.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// uc060coc.1 // UCSC Genes // aldehyde dehydrogenase 3 family, member A1 [Source:HGNC Symbol;Acc:HGNC:405] // chr17 // 100 // 100 // 0 // --- // 0 /// NONHSAT146524 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr17 // 100 // 100 // 0 // --- // 0 /// NONHSAT146524 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr17 // 100 // 100 // 0 // --- // 0
## TC1900011778.hg.1 NM_001145396 // RefSeq // Homo sapiens aldehyde dehydrogenase 16 family, member A1 (ALDH16A1), transcript variant 2, mRNA. // chr19 // 100 // 100 // 0 // --- // 0 /// NM_153329 // RefSeq // Homo sapiens aldehyde dehydrogenase 16 family, member A1 (ALDH16A1), transcript variant 1, mRNA. // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000293350 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000455361 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000540132 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000593417 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000594549 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000598015 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000599652 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr19 // 100 // 100 // 0 // --- // 0 /// ENST00000600265 // ENSEMBL // aldehyde dehydrogenase 16 family, member A1 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr19 // 100 // 100 // 0 // --- // 0 /// BC014895 // GenBank // Homo sapiens aldehyde dehydrogenase 16 family, member A1, mRNA (cDNA clone MGC:10204 IMAGE:3910527), complete cds. // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465358 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465359 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465360 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465361 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465362 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465363 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465364 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr19 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000465368 // Havana transcript // aldehyde dehydrogenase 16 family, member A1[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr19 // 100 // 100 // 0 // --- // 0 /// ALDH16A1.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 126133 // chr19 // 100 // 100 // 0 // --- // 0 /// ALDH16A1.dAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 126133 // chr19 // 100 // 100 // 0 // --- // 0 /// ALDH16A1.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 126133 // chr19 // 100 // 100 // 0 // --- // 0 /// ALDH16A1.iAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 126133 // chr19 // 100 // 100 // 0 // --- // 0 /// ALDH16A1.kAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 126133 // chr19 // 100 // 100 // 0 // --- // 0 /// CCDS12766.1 // ccdsGene // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// CCDS46141.1 // ccdsGene // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0051879 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_153329 // chr19 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0051880 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_153329 // chr19 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0051881 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_153329 // chr19 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0051882 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_153329 // chr19 // 100 // 100 // 0 // --- // 0 /// uc002pnt.4 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc010yar.3 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc010yat.5 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc061bdi.1 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc061bdj.1 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc061bdk.1 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc061bdm.1 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// uc061bdn.1 // UCSC Genes // aldehyde dehydrogenase 16 family, member A1 [Source:HGNC Symbol;Acc:HGNC:28114] // chr19 // 100 // 100 // 0 // --- // 0 /// NONHSAT067189 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr19 // 100 // 100 // 0 // --- // 0 /// NONHSAT067189 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr19 // 100 // 100 // 0 // --- // 0There are many entries with LDH, but it is a common set of letters seen in other gene names. There are a few lactate dehydrogenase family members of LDHA [12] and LDHC [13] and also LDHD [24]. The others are like it or an aldehyde dehydrogenase.
Lets make this data set. We need to read in our larger data set from part 3, dataset
data <- read.csv("Data_27189X123_GSE305165_summaryStatsChangeAvg_med.csv", header=T)
colnames(data)## [1] "ID" "pDLBCL"
## [3] "CHL" "pDLBCL.1"
## [5] "mDLBCL" "CHL.1"
## [7] "mDLBCL.1" "pDLBCL.2"
## [9] "CHL.2" "CHL.3"
## [11] "CHL.4" "CHL.5"
## [13] "mDLBCL.2" "mDLBCL.3"
## [15] "CHL.6" "CHL.7"
## [17] "pDLBCL.3" "CHL.8"
## [19] "mDLBCL.4" "mDLBCL.5"
## [21] "mDLBCL.6" "mDLBCL.7"
## [23] "CHL.9" "mDLBCL.8"
## [25] "CHL.10" "CHL.11"
## [27] "CHL.12" "CHL.13"
## [29] "mDLBCL.9" "mDLBCL.10"
## [31] "mDLBCL.11" "mDLBCL.12"
## [33] "mDLBCL.13" "mDLBCL.14"
## [35] "pDLBCL.4" "pDLBCL.5"
## [37] "mDLBCL.15" "mDLBCL.16"
## [39] "CHL.14" "pDLBCL.6"
## [41] "pDLBCL.7" "CHL.15"
## [43] "CHL.16" "CHL.17"
## [45] "mDLBCL.17" "mDLBCL.18"
## [47] "mDLBCL.19" "CHL.18"
## [49] "CHL_mean" "pDLBCL_mean"
## [51] "mDLBCL_mean" "CHL_x_mean"
## [53] "mDLBCL_x_mean" "pDLBCL_x_mean"
## [55] "CHL_y_mean" "mDLBCL_y_mean"
## [57] "pDLBCL_y_mean" "CHL_young72_mean"
## [59] "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [61] "CHL_old" "mDLBCL_old"
## [63] "pDLBCL_old" "CHL_median"
## [65] "mDLBCL_median" "pDLBCL_median"
## [67] "CHL_x_median" "mDLBCL_x_median"
## [69] "pDLBCL_x_median" "CHL_y_median"
## [71] "mDLBCL_y_median" "pDLBCL_y_median"
## [73] "CHL_young72_median" "mDLBCL_young72_median"
## [75] "pDLBCL_young72_median" "CHL_old72_median"
## [77] "mDLBCL_old72_median" "pDLBCL_old72_median"
## [79] "ID.1" "CHL_mean.1"
## [81] "pDLBCL_mean.1" "mDLBCL_mean.1"
## [83] "CHL_x_mean.1" "mDLBCL_x_mean.1"
## [85] "pDLBCL_x_mean.1" "CHL_y_mean.1"
## [87] "mDLBCL_y_mean.1" "pDLBCL_y_mean.1"
## [89] "CHL_young72_mean.1" "mDLBCL_young72_mean.1"
## [91] "pDLBCL_young72_mean.1" "CHL_old.1"
## [93] "mDLBCL_old.1" "pDLBCL_old.1"
## [95] "CHL_median.1" "mDLBCL_median.1"
## [97] "pDLBCL_median.1" "CHL_x_median.1"
## [99] "mDLBCL_x_median.1" "pDLBCL_x_median.1"
## [101] "CHL_y_median.1" "mDLBCL_y_median.1"
## [103] "pDLBCL_y_median.1" "CHL_young72_median.1"
## [105] "mDLBCL_young72_median.1" "pDLBCL_young72_median.1"
## [107] "CHL_old72_median.1" "mDLBCL_old72_median.1"
## [109] "pDLBCL_old72_median.1" "CHL_change"
## [111] "pDLBCL_change" "mDLBCL_change"
## [113] "CHL_x_change" "CHL_y_change"
## [115] "pDLBCL_x_change" "pDLBCL_y_change"
## [117] "mDLBCL_x_change" "mDLBCL_y_change"
## [119] "CHL_old72_change" "CHL_young72_change"
## [121] "pDLBCL_old_change" "pDLBCL_young72_change"
## [123] "mDLBCL_young72_change"data$mDLBCL_old72_change <- data$mDLBCL_old/data$mDLBCL_old72_medianData <- data[,c(1:78,110:124)]
rm(data)
colnames(Data)## [1] "ID" "pDLBCL" "CHL"
## [4] "pDLBCL.1" "mDLBCL" "CHL.1"
## [7] "mDLBCL.1" "pDLBCL.2" "CHL.2"
## [10] "CHL.3" "CHL.4" "CHL.5"
## [13] "mDLBCL.2" "mDLBCL.3" "CHL.6"
## [16] "CHL.7" "pDLBCL.3" "CHL.8"
## [19] "mDLBCL.4" "mDLBCL.5" "mDLBCL.6"
## [22] "mDLBCL.7" "CHL.9" "mDLBCL.8"
## [25] "CHL.10" "CHL.11" "CHL.12"
## [28] "CHL.13" "mDLBCL.9" "mDLBCL.10"
## [31] "mDLBCL.11" "mDLBCL.12" "mDLBCL.13"
## [34] "mDLBCL.14" "pDLBCL.4" "pDLBCL.5"
## [37] "mDLBCL.15" "mDLBCL.16" "CHL.14"
## [40] "pDLBCL.6" "pDLBCL.7" "CHL.15"
## [43] "CHL.16" "CHL.17" "mDLBCL.17"
## [46] "mDLBCL.18" "mDLBCL.19" "CHL.18"
## [49] "CHL_mean" "pDLBCL_mean" "mDLBCL_mean"
## [52] "CHL_x_mean" "mDLBCL_x_mean" "pDLBCL_x_mean"
## [55] "CHL_y_mean" "mDLBCL_y_mean" "pDLBCL_y_mean"
## [58] "CHL_young72_mean" "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [61] "CHL_old" "mDLBCL_old" "pDLBCL_old"
## [64] "CHL_median" "mDLBCL_median" "pDLBCL_median"
## [67] "CHL_x_median" "mDLBCL_x_median" "pDLBCL_x_median"
## [70] "CHL_y_median" "mDLBCL_y_median" "pDLBCL_y_median"
## [73] "CHL_young72_median" "mDLBCL_young72_median" "pDLBCL_young72_median"
## [76] "CHL_old72_median" "mDLBCL_old72_median" "pDLBCL_old72_median"
## [79] "CHL_change" "pDLBCL_change" "mDLBCL_change"
## [82] "CHL_x_change" "CHL_y_change" "pDLBCL_x_change"
## [85] "pDLBCL_y_change" "mDLBCL_x_change" "mDLBCL_y_change"
## [88] "CHL_old72_change" "CHL_young72_change" "pDLBCL_old_change"
## [91] "pDLBCL_young72_change" "mDLBCL_young72_change" "mDLBCL_old72_change"We had to do some edits because it wasn’t written out to csv after making edits to it in part 3.
Now lets merge this with the features data that only include the LDHA, LDHC, and LDHD.
LDH <- LDH[c(12,13,24),]
LDH$SPOT_ID.1## [1] "NM_001135239 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165414 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165415 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 4, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165416 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 5, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_005566 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NR_028500 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 6, non-coding RNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000227157 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000375710 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000379412 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396222 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000422447 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000430553 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000460405 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000469976 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000478970 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000486690 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000494573 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000495052 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000535451 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000536528 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000537296 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000538451 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000539814 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000540430 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000541097 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000542179 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000543445 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000543695 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545215 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545467 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000625635 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC067223 // GenBank // Homo sapiens lactate dehydrogenase A, mRNA (cDNA clone MGC:72033 IMAGE:4096518), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258172 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258173 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258174 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258175 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258176 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258177 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258178 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258179 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258180 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395876 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395877 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395878 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395879 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395880 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395881 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395882 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395883 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395885 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395886 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395887 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395888 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395889 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395890 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// uc010rdd.2 // UCSC Genes // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS44549.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53609.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53610.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53611.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7839.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0006469 // circbase // Jeck2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021446 // circbase // Salzman2013 ANNOTATED, coding, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021447 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021448 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021449 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021450 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021451 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021452 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021453 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001135239 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001165415 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.gAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NR_028500 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.pAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.uAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.vgAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mok.4 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mol.4 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc010rdc.2 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc021qep.2 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqs.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqt.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqu.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqv.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqw.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqx.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqy.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqz.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zra.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrb.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrc.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrd.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zre.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrf.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrg.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrh.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zri.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrj.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrk.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrl.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT018284 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT018284 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr11 // 100 // 100 // 0 // --- // 0"
## [2] "NM_002301 // RefSeq // Homo sapiens lactate dehydrogenase C (LDHC), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_017448 // RefSeq // Homo sapiens lactate dehydrogenase C (LDHC), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000280704 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396215 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000535809 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000536880 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000537486 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000539369 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000541669 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000544105 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545848 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000546146 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC019249 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:26530 IMAGE:4839028), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC064388 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:74967 IMAGE:5744600), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC090043 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:111073 IMAGE:30387780), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395892 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395893 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395894 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395895 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395896 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395897 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395898 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395899 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395900 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395901 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7840.1 // ccdsGene // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// LDHC.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3948 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHC.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3948 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mom.5 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mon.5 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrn.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zro.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrp.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrq.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrr.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrs.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrt.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zru.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0"
## [3] "NM_153486 // RefSeq // Homo sapiens lactate dehydrogenase D (LDHD), transcript variant 1, mRNA. // chr16 // 100 // 100 // 0 // --- // 0 /// NM_194436 // RefSeq // Homo sapiens lactate dehydrogenase D (LDHD), transcript variant 2, mRNA. // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000300051 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000450168 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000568164 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000569876 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr16 // 100 // 100 // 0 // --- // 0 /// BC040279 // GenBank // Homo sapiens lactate dehydrogenase D, mRNA (cDNA clone MGC:34649 IMAGE:5162826), complete cds. // chr16 // 100 // 100 // 0 // --- // 0 /// BC047902 // GenBank // Homo sapiens lactate dehydrogenase D, mRNA (cDNA clone MGC:57726 IMAGE:5762691), complete cds. // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000269018 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434651 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434652 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434653 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr16 // 100 // 100 // 0 // --- // 0 /// CCDS10913.1 // ccdsGene // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// CCDS45529.1 // ccdsGene // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc002fdm.4 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc002fdn.4 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc059xeh.1 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc059xei.1 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0"LDH$Gene_ID <- c("LDHA","LDHC","LDHD")
LDH$importance <- "Research Article GSE305165 genes in the data that had an ID match a gene from the study importance genes"
colnames(LDH)## [1] "ID" "probeset_id" "seqname" "strand" "start"
## [6] "stop" "total_probes" "category" "SPOT_ID" "SPOT_ID.1"
## [11] "Gene_ID" "importance"LDH <- LDH[,c(1,10:12)]
LDH## ID
## TC1100007003.hg.1 TC1100007003.hg.1
## TC1100007005.hg.1 TC1100007005.hg.1
## TC1600010866.hg.1 TC1600010866.hg.1
## SPOT_ID.1
## TC1100007003.hg.1 NM_001135239 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165414 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165415 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 4, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_001165416 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 5, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_005566 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NR_028500 // RefSeq // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 6, non-coding RNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000227157 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000375710 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000379412 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396222 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000422447 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000430553 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000460405 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000469976 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000478970 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000486690 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000494573 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000495052 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000535451 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000536528 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000537296 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000538451 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000539814 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000540430 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000541097 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000542179 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000543445 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000543695 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545215 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545467 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000625635 // ENSEMBL // lactate dehydrogenase A [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC067223 // GenBank // Homo sapiens lactate dehydrogenase A, mRNA (cDNA clone MGC:72033 IMAGE:4096518), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258172 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258173 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258174 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258175 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258176 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258177 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258178 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258179 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000258180 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395876 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395877 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395878 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395879 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395880 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395881 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395882 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395883 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395885 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395886 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395887 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395888 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395889 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395890 // Havana transcript // lactate dehydrogenase A[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr11 // 100 // 100 // 0 // --- // 0 /// uc010rdd.2 // UCSC Genes // Homo sapiens lactate dehydrogenase A (LDHA), transcript variant 3, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS44549.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53609.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53610.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS53611.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7839.1 // ccdsGene // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0006469 // circbase // Jeck2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021446 // circbase // Salzman2013 ANNOTATED, coding, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021447 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021448 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR5 best transcript NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021449 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021450 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021451 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021452 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0021453 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001165414 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_005566 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001135239 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NM_001165415 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.gAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939, RefSeq ID(s) NR_028500 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.pAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.uAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHA.vgAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3939 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mok.4 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mol.4 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc010rdc.2 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc021qep.2 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqs.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqt.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqu.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqv.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqw.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqx.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqy.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zqz.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zra.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrb.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrc.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrd.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zre.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrf.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrg.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrh.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zri.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrj.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrk.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrl.1 // UCSC Genes // lactate dehydrogenase A [Source:HGNC Symbol;Acc:HGNC:6535] // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT018284 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr11 // 100 // 100 // 0 // --- // 0 /// NONHSAT018284 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr11 // 100 // 100 // 0 // --- // 0
## TC1100007005.hg.1 NM_002301 // RefSeq // Homo sapiens lactate dehydrogenase C (LDHC), transcript variant 1, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// NM_017448 // RefSeq // Homo sapiens lactate dehydrogenase C (LDHC), transcript variant 2, mRNA. // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000280704 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000396215 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000535809 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000536880 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000537486 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000539369 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000541669 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000544105 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000545848 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// ENST00000546146 // ENSEMBL // lactate dehydrogenase C [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// BC019249 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:26530 IMAGE:4839028), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC064388 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:74967 IMAGE:5744600), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// BC090043 // GenBank // Homo sapiens lactate dehydrogenase C, mRNA (cDNA clone MGC:111073 IMAGE:30387780), complete cds. // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395892 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395893 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395894 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395895 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395896 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395897 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395898 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395899 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395900 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000395901 // Havana transcript // actate dehydrogenase C[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr11 // 100 // 100 // 0 // --- // 0 /// CCDS7840.1 // ccdsGene // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// LDHC.eAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3948 // chr11 // 100 // 100 // 0 // --- // 0 /// LDHC.fAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 3948 // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mom.5 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc001mon.5 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrn.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zro.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrp.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrq.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrr.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrs.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zrt.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0 /// uc057zru.1 // UCSC Genes // lactate dehydrogenase C [Source:HGNC Symbol;Acc:HGNC:6544] // chr11 // 100 // 100 // 0 // --- // 0
## TC1600010866.hg.1 NM_153486 // RefSeq // Homo sapiens lactate dehydrogenase D (LDHD), transcript variant 1, mRNA. // chr16 // 100 // 100 // 0 // --- // 0 /// NM_194436 // RefSeq // Homo sapiens lactate dehydrogenase D (LDHD), transcript variant 2, mRNA. // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000300051 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000450168 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000568164 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr16 // 100 // 100 // 0 // --- // 0 /// ENST00000569876 // ENSEMBL // lactate dehydrogenase D [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr16 // 100 // 100 // 0 // --- // 0 /// BC040279 // GenBank // Homo sapiens lactate dehydrogenase D, mRNA (cDNA clone MGC:34649 IMAGE:5162826), complete cds. // chr16 // 100 // 100 // 0 // --- // 0 /// BC047902 // GenBank // Homo sapiens lactate dehydrogenase D, mRNA (cDNA clone MGC:57726 IMAGE:5762691), complete cds. // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000269018 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434651 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434652 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr16 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000434653 // Havana transcript // lactate dehydrogenase D[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr16 // 100 // 100 // 0 // --- // 0 /// CCDS10913.1 // ccdsGene // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// CCDS45529.1 // ccdsGene // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc002fdm.4 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc002fdn.4 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc059xeh.1 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0 /// uc059xei.1 // UCSC Genes // lactate dehydrogenase D [Source:HGNC Symbol;Acc:HGNC:19708] // chr16 // 100 // 100 // 0 // --- // 0
## Gene_ID
## TC1100007003.hg.1 LDHA
## TC1100007005.hg.1 LDHC
## TC1600010866.hg.1 LDHD
## importance
## TC1100007003.hg.1 Research Article GSE305165 genes in the data that had an ID match a gene from the study importance genes
## TC1100007005.hg.1 Research Article GSE305165 genes in the data that had an ID match a gene from the study importance genes
## TC1600010866.hg.1 Research Article GSE305165 genes in the data that had an ID match a gene from the study importance genesLDH_data <- merge(LDH, Data, by.x="ID", by.y="ID")
colnames(LDH_data)## [1] "ID" "SPOT_ID.1" "Gene_ID"
## [4] "importance" "pDLBCL" "CHL"
## [7] "pDLBCL.1" "mDLBCL" "CHL.1"
## [10] "mDLBCL.1" "pDLBCL.2" "CHL.2"
## [13] "CHL.3" "CHL.4" "CHL.5"
## [16] "mDLBCL.2" "mDLBCL.3" "CHL.6"
## [19] "CHL.7" "pDLBCL.3" "CHL.8"
## [22] "mDLBCL.4" "mDLBCL.5" "mDLBCL.6"
## [25] "mDLBCL.7" "CHL.9" "mDLBCL.8"
## [28] "CHL.10" "CHL.11" "CHL.12"
## [31] "CHL.13" "mDLBCL.9" "mDLBCL.10"
## [34] "mDLBCL.11" "mDLBCL.12" "mDLBCL.13"
## [37] "mDLBCL.14" "pDLBCL.4" "pDLBCL.5"
## [40] "mDLBCL.15" "mDLBCL.16" "CHL.14"
## [43] "pDLBCL.6" "pDLBCL.7" "CHL.15"
## [46] "CHL.16" "CHL.17" "mDLBCL.17"
## [49] "mDLBCL.18" "mDLBCL.19" "CHL.18"
## [52] "CHL_mean" "pDLBCL_mean" "mDLBCL_mean"
## [55] "CHL_x_mean" "mDLBCL_x_mean" "pDLBCL_x_mean"
## [58] "CHL_y_mean" "mDLBCL_y_mean" "pDLBCL_y_mean"
## [61] "CHL_young72_mean" "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [64] "CHL_old" "mDLBCL_old" "pDLBCL_old"
## [67] "CHL_median" "mDLBCL_median" "pDLBCL_median"
## [70] "CHL_x_median" "mDLBCL_x_median" "pDLBCL_x_median"
## [73] "CHL_y_median" "mDLBCL_y_median" "pDLBCL_y_median"
## [76] "CHL_young72_median" "mDLBCL_young72_median" "pDLBCL_young72_median"
## [79] "CHL_old72_median" "mDLBCL_old72_median" "pDLBCL_old72_median"
## [82] "CHL_change" "pDLBCL_change" "mDLBCL_change"
## [85] "CHL_x_change" "CHL_y_change" "pDLBCL_x_change"
## [88] "pDLBCL_y_change" "mDLBCL_x_change" "mDLBCL_y_change"
## [91] "CHL_old72_change" "CHL_young72_change" "pDLBCL_old_change"
## [94] "pDLBCL_young72_change" "mDLBCL_young72_change" "mDLBCL_old72_change"LDH_df <- LDH_data[,c(1,5:96,2:4)]
colnames(LDH_df)## [1] "ID" "pDLBCL" "CHL"
## [4] "pDLBCL.1" "mDLBCL" "CHL.1"
## [7] "mDLBCL.1" "pDLBCL.2" "CHL.2"
## [10] "CHL.3" "CHL.4" "CHL.5"
## [13] "mDLBCL.2" "mDLBCL.3" "CHL.6"
## [16] "CHL.7" "pDLBCL.3" "CHL.8"
## [19] "mDLBCL.4" "mDLBCL.5" "mDLBCL.6"
## [22] "mDLBCL.7" "CHL.9" "mDLBCL.8"
## [25] "CHL.10" "CHL.11" "CHL.12"
## [28] "CHL.13" "mDLBCL.9" "mDLBCL.10"
## [31] "mDLBCL.11" "mDLBCL.12" "mDLBCL.13"
## [34] "mDLBCL.14" "pDLBCL.4" "pDLBCL.5"
## [37] "mDLBCL.15" "mDLBCL.16" "CHL.14"
## [40] "pDLBCL.6" "pDLBCL.7" "CHL.15"
## [43] "CHL.16" "CHL.17" "mDLBCL.17"
## [46] "mDLBCL.18" "mDLBCL.19" "CHL.18"
## [49] "CHL_mean" "pDLBCL_mean" "mDLBCL_mean"
## [52] "CHL_x_mean" "mDLBCL_x_mean" "pDLBCL_x_mean"
## [55] "CHL_y_mean" "mDLBCL_y_mean" "pDLBCL_y_mean"
## [58] "CHL_young72_mean" "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [61] "CHL_old" "mDLBCL_old" "pDLBCL_old"
## [64] "CHL_median" "mDLBCL_median" "pDLBCL_median"
## [67] "CHL_x_median" "mDLBCL_x_median" "pDLBCL_x_median"
## [70] "CHL_y_median" "mDLBCL_y_median" "pDLBCL_y_median"
## [73] "CHL_young72_median" "mDLBCL_young72_median" "pDLBCL_young72_median"
## [76] "CHL_old72_median" "mDLBCL_old72_median" "pDLBCL_old72_median"
## [79] "CHL_change" "pDLBCL_change" "mDLBCL_change"
## [82] "CHL_x_change" "CHL_y_change" "pDLBCL_x_change"
## [85] "pDLBCL_y_change" "mDLBCL_x_change" "mDLBCL_y_change"
## [88] "CHL_old72_change" "CHL_young72_change" "pDLBCL_old_change"
## [91] "pDLBCL_young72_change" "mDLBCL_young72_change" "mDLBCL_old72_change"
## [94] "SPOT_ID.1" "Gene_ID" "importance"colnames(topGenes)## [1] "ID" "pDLBCL" "CHL"
## [4] "pDLBCL.1" "mDLBCL" "CHL.1"
## [7] "mDLBCL.1" "pDLBCL.2" "CHL.2"
## [10] "CHL.3" "CHL.4" "CHL.5"
## [13] "mDLBCL.2" "mDLBCL.3" "CHL.6"
## [16] "CHL.7" "pDLBCL.3" "CHL.8"
## [19] "mDLBCL.4" "mDLBCL.5" "mDLBCL.6"
## [22] "mDLBCL.7" "CHL.9" "mDLBCL.8"
## [25] "CHL.10" "CHL.11" "CHL.12"
## [28] "CHL.13" "mDLBCL.9" "mDLBCL.10"
## [31] "mDLBCL.11" "mDLBCL.12" "mDLBCL.13"
## [34] "mDLBCL.14" "pDLBCL.4" "pDLBCL.5"
## [37] "mDLBCL.15" "mDLBCL.16" "CHL.14"
## [40] "pDLBCL.6" "pDLBCL.7" "CHL.15"
## [43] "CHL.16" "CHL.17" "mDLBCL.17"
## [46] "mDLBCL.18" "mDLBCL.19" "CHL.18"
## [49] "CHL_mean" "pDLBCL_mean" "mDLBCL_mean"
## [52] "CHL_x_mean" "mDLBCL_x_mean" "pDLBCL_x_mean"
## [55] "CHL_y_mean" "mDLBCL_y_mean" "pDLBCL_y_mean"
## [58] "CHL_young72_mean" "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [61] "CHL_old" "mDLBCL_old" "pDLBCL_old"
## [64] "CHL_median" "mDLBCL_median" "pDLBCL_median"
## [67] "CHL_x_median" "mDLBCL_x_median" "pDLBCL_x_median"
## [70] "CHL_y_median" "mDLBCL_y_median" "pDLBCL_y_median"
## [73] "CHL_young72_median" "mDLBCL_young72_median" "pDLBCL_young72_median"
## [76] "CHL_old72_median" "mDLBCL_old72_median" "pDLBCL_old72_median"
## [79] "CHL_change" "pDLBCL_change" "mDLBCL_change"
## [82] "CHL_x_change" "CHL_y_change" "pDLBCL_x_change"
## [85] "pDLBCL_y_change" "mDLBCL_x_change" "mDLBCL_y_change"
## [88] "CHL_old72_change" "CHL_young72_change" "pDLBCL_old_change"
## [91] "pDLBCL_young72_change" "mDLBCL_young72_change" "mDLBCL_old72_change"
## [94] "SPOT_ID.1" "Gene_ID" "importance"Lets add the LDH genes to the topGenes data
topGenes2 <- rbind(topGenes,LDH_df)Lets just look at the research genes again.
researchGenes <- topGenes2[grep('Research Article', topGenes2$importance),]
researchGenes[,c(95,79:81)]## Gene_ID CHL_change pDLBCL_change mDLBCL_change
## 22 PTPRD 1.0132904 1.024186 0.9814230
## 23 PDCD1LG2 1.0247912 1.065183 0.9982401
## 24 PAX5 1.0084634 1.005947 1.0025111
## 30 MUM1 0.9564051 1.024056 1.0267764
## 49 IFNG 1.0144939 1.010136 0.9622795
## 50 IDO1 1.0309266 1.039835 1.0314197
## 56 ERP44 0.9963785 1.017518 1.0088861
## 78 CD5 0.9952703 1.011232 1.0010026
## 79 CD274 0.9984760 1.009721 1.0108712
## 81 BCL6 0.9886459 0.989588 1.0001106
## 82 BCL2 1.0132740 1.004808 1.0029256
## 85 LDHA 0.9757991 1.003289 0.9971806
## 86 LDHC 0.9915320 1.017192 0.9879837
## 87 LDHD 1.0109017 1.001947 1.0008851LDHD is overestimated in all 3 lymphomas but closer to normal in the DLBCL groups, while LDHA and LDHC are only over estimated in the pDLBCL group.
The article said that the LDH was high but not using gene expression, just clinically in blood lab work for mDLBCL. The gene expression data using this change type says otherwise. But it could be higher across samples. Lets see.
researchGenes[c(12:14),c(95,2:48)]## Gene_ID pDLBCL CHL pDLBCL.1 mDLBCL CHL.1 mDLBCL.1 pDLBCL.2
## 85 LDHA 8.658361 7.858679 9.184861 9.338661 5.792496 8.716444 8.707534
## 86 LDHC 3.985598 4.007080 4.101672 3.650014 4.342355 3.828057 4.128118
## 87 LDHD 5.712537 6.230099 5.258146 5.503446 5.596182 5.653517 5.386853
## CHL.2 CHL.3 CHL.4 CHL.5 mDLBCL.2 mDLBCL.3 CHL.6 CHL.7
## 85 8.685312 8.980201 8.782031 8.994080 10.007422 8.880994 8.760310 8.390140
## 86 3.997067 4.064068 3.970572 4.475421 3.969665 4.494151 4.522051 3.688503
## 87 5.428130 5.699283 5.174769 5.795505 5.112403 5.504082 5.147836 5.363676
## pDLBCL.3 CHL.8 mDLBCL.4 mDLBCL.5 mDLBCL.6 mDLBCL.7 CHL.9 mDLBCL.8
## 85 9.195272 8.636065 9.858830 9.411728 10.192753 9.538618 8.203157 9.712842
## 86 3.708710 3.929166 3.244598 3.710451 3.895005 3.659041 4.450271 4.151815
## 87 5.116153 5.299886 5.224443 5.223130 5.609946 5.521872 5.581232 5.587457
## CHL.10 CHL.11 CHL.12 CHL.13 mDLBCL.9 mDLBCL.10 mDLBCL.11 mDLBCL.12
## 85 8.428529 8.651220 9.391049 7.980798 9.063086 9.446182 9.497101 9.781190
## 86 3.789925 3.863195 3.386810 3.950610 4.057919 4.283066 4.380149 3.909456
## 87 5.632588 5.475959 5.158768 5.547694 5.761411 5.455434 5.684329 5.955431
## mDLBCL.13 mDLBCL.14 pDLBCL.4 pDLBCL.5 mDLBCL.15 mDLBCL.16 CHL.14 pDLBCL.6
## 85 8.907587 8.819691 8.458703 9.000184 9.675630 9.904595 7.335124 9.761196
## 86 3.207274 3.748995 3.555433 3.570633 3.294096 3.421933 3.944531 3.562440
## 87 5.252791 5.658986 5.531630 5.398580 5.464599 5.499535 5.980378 5.465887
## pDLBCL.7 CHL.15 CHL.16 CHL.17 mDLBCL.17 mDLBCL.18 mDLBCL.19 CHL.18
## 85 8.909913 9.031017 8.432458 9.025153 9.456874 9.917845 8.877298 9.037384
## 86 3.005343 3.439547 3.338988 3.597280 3.879847 3.894580 4.129958 3.554003
## 87 5.397123 5.435433 5.266639 5.339224 5.475541 5.467432 5.556917 5.245798In all the samples of mDLBCL the LDHA was higher than LDHC and LDHD, with LDHD higher than LDHC. In all these lymphoma samples this is true. But comparing LDH elevations in mDLBCL to pDLBCL and CHL can be done with our median columns.
researchGenes[c(12:14),c(95,64:66)]## Gene_ID CHL_median mDLBCL_median pDLBCL_median
## 85 LDHA 8.651220 9.476988 8.955049
## 86 LDHC 3.944531 3.887213 3.639672
## 87 LDHD 5.435433 5.503764 5.397851There is higher LDHA in mDLBCL using the median of all samples in that group compared to CHL and pDLBCL. The LDHC is higher in CHL, then mDLBCL, and lastly pDLBCL. The LDHD is highest in mDLBCL as well compared to CHL and pDLBCL.
Lets get ready to start a test on groups of genes using these research genes to predict class of the sample by these genes. We have to save the gene labels and make a class vector for the arrangement of the samples.
samples_rs <- researchGenes[,c(2:48)]
genes_rs <- researchGenes$Gene_ID
IDs <- colnames(researchGenes)[2:48]
IDs## [1] "pDLBCL" "CHL" "pDLBCL.1" "mDLBCL" "CHL.1" "mDLBCL.1"
## [7] "pDLBCL.2" "CHL.2" "CHL.3" "CHL.4" "CHL.5" "mDLBCL.2"
## [13] "mDLBCL.3" "CHL.6" "CHL.7" "pDLBCL.3" "CHL.8" "mDLBCL.4"
## [19] "mDLBCL.5" "mDLBCL.6" "mDLBCL.7" "CHL.9" "mDLBCL.8" "CHL.10"
## [25] "CHL.11" "CHL.12" "CHL.13" "mDLBCL.9" "mDLBCL.10" "mDLBCL.11"
## [31] "mDLBCL.12" "mDLBCL.13" "mDLBCL.14" "pDLBCL.4" "pDLBCL.5" "mDLBCL.15"
## [37] "mDLBCL.16" "CHL.14" "pDLBCL.6" "pDLBCL.7" "CHL.15" "CHL.16"
## [43] "CHL.17" "mDLBCL.17" "mDLBCL.18" "mDLBCL.19" "CHL.18"class <- c("pDLBCL" , "CHL" , "pDLBCL" , "mDLBCL" , "CHL" , "mDLBCL" , "pDLBCL" , "CHL" , "CHL" , "CHL" ,
"CHL" , "mDLBCL" , "mDLBCL" , "CHL" , "CHL" , "pDLBCL" , "CHL" , "mDLBCL" , "mDLBCL" , "mDLBCL" ,
"mDLBCL" , "CHL" , "mDLBCL" ,"CHL" , "CHL" , "CHL" , "CHL" , "mDLBCL" , "mDLBCL", "mDLBCL",
"mDLBCL", "mDLBCL" ,"mDLBCL" ,"pDLBCL" , "pDLBCL" , "mDLBCL" ,"mDLBCL" ,"CHL" , "pDLBCL" , "pDLBCL" ,
"CHL" , "CHL" , "CHL" , "mDLBCL" ,"mDLBCL" ,"mDLBCL" ,"CHL" )
rm(IDs)
unique(class)## [1] "pDLBCL" "CHL" "mDLBCL"Lets make our matrix.
sample_rs_df <- data.frame(t(samples_rs))
colnames(sample_rs_df) <- genes_rs
sample_rs_df$class <- as.factor(class)
sample_rs_df## PTPRD PDCD1LG2 PAX5 MUM1 IFNG IDO1 ERP44
## pDLBCL 3.685317 4.634469 5.837732 1.878937 3.069225 5.266947 5.575510
## CHL 3.676430 2.942214 7.448931 2.237178 2.962287 3.515371 4.191834
## pDLBCL.1 3.148372 4.499253 6.307865 1.766060 3.226458 5.319546 5.138372
## mDLBCL 3.455512 4.373373 6.419925 2.484003 3.193519 3.651946 5.291534
## CHL.1 4.022412 3.864916 6.990574 2.135487 4.000244 3.497938 3.627553
## mDLBCL.1 3.541898 5.254167 7.070463 2.082015 2.865105 3.424882 5.344731
## pDLBCL.2 3.398471 4.465464 6.104317 2.482157 2.636234 3.835786 5.076654
## CHL.2 3.771869 4.698898 6.380601 2.270221 3.312958 3.445356 5.082100
## CHL.3 3.356006 4.789598 6.751569 2.262848 2.993484 4.282418 5.143249
## CHL.4 3.531764 4.302539 6.779292 2.694966 2.872059 3.533667 5.088958
## CHL.5 4.031001 4.900090 6.554107 2.766866 2.846098 3.440680 5.213799
## mDLBCL.2 3.221535 5.578819 6.658492 2.434437 1.954850 3.004267 5.620760
## mDLBCL.3 3.692095 3.659990 6.705532 2.699674 2.565927 3.535909 5.279476
## CHL.6 3.412819 4.314726 6.135404 2.744835 3.621671 3.842913 5.313366
## CHL.7 3.451064 3.479858 6.052747 2.223445 2.899106 3.281838 5.088203
## pDLBCL.3 2.983141 4.062027 7.398400 2.139963 3.404577 4.762571 5.496741
## CHL.8 4.329820 3.876076 6.762964 2.403510 2.003622 3.442793 5.562172
## mDLBCL.4 3.077683 4.935213 7.208099 4.337290 2.505606 3.189192 5.563635
## mDLBCL.5 3.609745 4.231856 7.431777 2.415194 2.953850 3.590060 5.504069
## mDLBCL.6 3.551329 4.578427 6.782725 2.250006 2.900375 3.672584 6.149064
## mDLBCL.7 3.633576 4.960384 7.397093 2.399275 2.973138 3.495786 5.632225
## CHL.9 3.063946 3.718218 6.606534 2.597851 2.899324 3.231478 5.176768
## mDLBCL.8 3.638433 4.949566 6.216256 2.173263 3.714553 4.702419 5.199758
## CHL.10 3.289788 4.854521 6.575761 2.680258 2.972220 3.412869 4.840189
## CHL.11 3.486482 4.865561 6.376813 2.245216 2.833512 3.270835 5.851499
## CHL.12 3.592392 6.170380 6.207869 2.768394 2.915523 3.817595 5.756560
## CHL.13 3.673980 4.249046 6.533770 2.852737 2.697077 3.442922 5.280367
## mDLBCL.9 3.394398 5.363083 7.032194 2.972367 2.293754 3.494170 6.078944
## mDLBCL.10 4.003065 3.558593 7.322739 1.893677 3.120178 4.035177 4.829168
## mDLBCL.11 3.024652 4.500945 6.940962 2.005839 2.215032 3.550920 5.336893
## mDLBCL.12 2.729431 5.675743 6.698119 2.835851 2.810134 4.298867 5.395473
## mDLBCL.13 3.280114 5.450906 6.779600 2.551476 2.879991 4.253456 6.052639
## mDLBCL.14 3.446065 5.200995 6.928266 2.777856 3.027688 3.812757 5.145139
## pDLBCL.4 3.111890 4.543541 6.501964 2.428017 2.902845 3.992336 5.364440
## pDLBCL.5 3.248538 3.932478 6.263106 2.205217 2.779238 4.760222 5.632315
## mDLBCL.15 2.647033 4.358680 7.318072 2.749662 2.458244 3.066835 5.464782
## mDLBCL.16 3.586893 4.855219 7.485727 2.434373 2.394065 3.501029 5.695070
## CHL.14 3.981202 4.211558 6.903905 2.015950 2.197446 3.652181 4.102102
## pDLBCL.6 3.500345 6.198815 6.627168 2.051298 3.340810 6.899326 6.122227
## pDLBCL.7 3.130425 6.192865 6.503495 2.847189 2.771015 6.879421 6.658610
## CHL.15 3.229043 4.723221 6.578960 2.935235 2.299081 3.116050 5.566924
## CHL.16 3.551180 4.134288 7.528055 2.763743 3.430004 3.261750 5.846060
## CHL.17 3.628847 4.129567 6.737099 2.836168 2.587612 3.407501 5.734322
## mDLBCL.17 3.120526 4.505849 6.622961 2.390182 2.950387 4.166414 6.061316
## mDLBCL.18 3.477699 4.412282 7.378854 2.305522 3.130588 3.411087 5.473001
## mDLBCL.19 3.912454 7.327919 6.642691 1.602243 2.376897 3.237192 5.232096
## CHL.18 3.289102 5.549601 6.153209 3.269919 3.542248 4.542451 6.237398
## CD5 CD274 BCL6 BCL2 LDHA LDHC LDHD
## pDLBCL 6.412200 6.521790 4.810390 6.988205 8.658361 3.985598 5.712537
## CHL 6.252281 4.592286 4.601292 7.230086 7.858679 4.007080 6.230099
## pDLBCL.1 6.460336 7.084118 4.573067 7.455283 9.184861 4.101672 5.258146
## mDLBCL 6.647232 6.452860 5.211272 7.019910 9.338661 3.650014 5.503446
## CHL.1 6.405831 4.696020 5.291846 7.822121 5.792496 4.342355 5.596182
## mDLBCL.1 6.283571 7.835426 5.040143 6.847939 8.716444 3.828057 5.653517
## pDLBCL.2 6.417821 6.744887 5.131215 7.239416 8.707534 4.128118 5.386853
## CHL.2 7.262511 6.579888 5.081345 7.108641 8.685312 3.997067 5.428130
## CHL.3 7.126876 6.194723 5.115395 7.002661 8.980201 4.064068 5.699283
## CHL.4 7.336942 6.055063 5.670942 7.059933 8.782031 3.970572 5.174769
## CHL.5 6.569752 6.050932 5.445840 7.129604 8.994080 4.475421 5.795505
## mDLBCL.2 6.542083 6.054614 5.290428 6.492504 10.007422 3.969665 5.112403
## mDLBCL.3 6.968191 5.597942 5.105497 7.272078 8.880994 4.494151 5.504082
## CHL.6 6.705105 7.242420 5.332240 6.981597 8.760310 4.522051 5.147836
## CHL.7 7.547240 6.261641 5.701903 7.263808 8.390140 3.688503 5.363676
## pDLBCL.3 7.051024 6.556098 5.345204 7.176817 9.195272 3.708710 5.116153
## CHL.8 7.066170 5.898913 4.730280 7.074783 8.636065 3.929166 5.299886
## mDLBCL.4 6.232854 7.673782 5.180383 7.098472 9.858830 3.244598 5.224443
## mDLBCL.5 6.860914 5.898791 5.566423 7.270708 9.411728 3.710451 5.223130
## mDLBCL.6 6.692568 5.837361 5.418009 6.945680 10.192753 3.895005 5.609946
## mDLBCL.7 6.852710 7.344261 5.424370 7.081180 9.538618 3.659041 5.521872
## CHL.9 6.962995 5.383059 5.429172 7.226607 8.203157 4.450271 5.581232
## mDLBCL.8 6.253627 7.616847 5.824775 7.124863 9.712842 4.151815 5.587457
## CHL.10 6.821408 7.047635 5.136576 7.394500 8.428529 3.789925 5.632588
## CHL.11 6.528702 5.557824 5.084341 7.110367 8.651220 3.863195 5.475959
## CHL.12 6.601854 7.383035 5.915606 7.105207 9.391049 3.386810 5.158768
## CHL.13 6.999369 6.014271 5.360682 7.400672 7.980798 3.950610 5.547694
## mDLBCL.9 6.485916 7.417413 4.993347 7.438141 9.063086 4.057919 5.761411
## mDLBCL.10 6.485993 5.027237 5.372846 7.411634 9.446182 4.283066 5.455434
## mDLBCL.11 6.806347 5.379237 5.262921 7.394885 9.497101 4.380149 5.684329
## mDLBCL.12 6.905681 6.765949 4.870469 6.901166 9.781190 3.909456 5.955431
## mDLBCL.13 6.881819 6.377471 5.052154 7.052345 8.907587 3.207274 5.252791
## mDLBCL.14 6.655850 6.982544 5.326902 7.315581 8.819691 3.748995 5.658986
## pDLBCL.4 6.892991 5.378472 5.232217 7.316012 8.458703 3.555433 5.531630
## pDLBCL.5 6.814038 6.466849 4.857462 6.972438 9.000184 3.570633 5.398580
## mDLBCL.15 6.671599 5.119697 5.320457 7.099695 9.675630 3.294096 5.464599
## mDLBCL.16 6.493284 6.647098 5.240318 7.610189 9.904595 3.421933 5.499535
## CHL.14 6.810164 5.499239 4.854063 6.991149 7.335124 3.944531 5.980378
## pDLBCL.6 6.559307 7.867803 5.539399 6.898820 9.761196 3.562440 5.465887
## pDLBCL.7 6.593189 7.101126 5.533159 6.885508 8.909913 3.005343 5.397123
## CHL.15 6.794859 5.486161 5.409903 7.072722 9.031017 3.439547 5.435433
## CHL.16 7.171274 5.100444 5.608524 7.482945 8.432458 3.338988 5.266639
## CHL.17 6.918259 6.914670 5.419001 7.374372 9.025153 3.597280 5.339224
## mDLBCL.17 6.452621 7.538983 5.043645 6.847151 9.456874 3.879847 5.475541
## mDLBCL.18 6.558975 6.055738 5.669209 7.066109 9.917845 3.894580 5.467432
## mDLBCL.19 6.462646 6.074863 4.830440 7.098906 8.877298 4.129958 5.556917
## CHL.18 6.943623 6.834273 4.973301 7.058475 9.037384 3.554003 5.245798
## class
## pDLBCL pDLBCL
## CHL CHL
## pDLBCL.1 pDLBCL
## mDLBCL mDLBCL
## CHL.1 CHL
## mDLBCL.1 mDLBCL
## pDLBCL.2 pDLBCL
## CHL.2 CHL
## CHL.3 CHL
## CHL.4 CHL
## CHL.5 CHL
## mDLBCL.2 mDLBCL
## mDLBCL.3 mDLBCL
## CHL.6 CHL
## CHL.7 CHL
## pDLBCL.3 pDLBCL
## CHL.8 CHL
## mDLBCL.4 mDLBCL
## mDLBCL.5 mDLBCL
## mDLBCL.6 mDLBCL
## mDLBCL.7 mDLBCL
## CHL.9 CHL
## mDLBCL.8 mDLBCL
## CHL.10 CHL
## CHL.11 CHL
## CHL.12 CHL
## CHL.13 CHL
## mDLBCL.9 mDLBCL
## mDLBCL.10 mDLBCL
## mDLBCL.11 mDLBCL
## mDLBCL.12 mDLBCL
## mDLBCL.13 mDLBCL
## mDLBCL.14 mDLBCL
## pDLBCL.4 pDLBCL
## pDLBCL.5 pDLBCL
## mDLBCL.15 mDLBCL
## mDLBCL.16 mDLBCL
## CHL.14 CHL
## pDLBCL.6 pDLBCL
## pDLBCL.7 pDLBCL
## CHL.15 CHL
## CHL.16 CHL
## CHL.17 CHL
## mDLBCL.17 mDLBCL
## mDLBCL.18 mDLBCL
## mDLBCL.19 mDLBCL
## CHL.18 CHLLets use random forest classifier to see how well these genes we found in the study predict the class of CHL, pDLBCL, or mDLBCL. We use the standard 80% training and 20% hold our validation testing set of data.
set.seed(123)
inTrain <- sample(1:47,.8*47)
training <- sample_rs_df[inTrain,]
testing <- sample_rs_df[-inTrain,]
table(training$class)##
## CHL mDLBCL pDLBCL
## 15 16 6There are 15 CHL, 16 mDLBCL, and 6 pDLBCL samples in the training set to build a random forest classifier with.
table(testing$class)##
## CHL mDLBCL pDLBCL
## 4 4 2There are 4 CHL, 4 mDLBCL, and 2 pDLBCL samples to predict in our testing set.
rf <- randomForest(training[1:14],training$class, mtry=5, ntree=5000, confusion=T)
rf$confusion## CHL mDLBCL pDLBCL class.error
## CHL 11 3 1 0.2666667
## mDLBCL 4 12 0 0.2500000
## pDLBCL 4 1 1 0.8333333The training model scored poor on the pDLBCL class by only predicting 1/6 classes correctly with most classes being predicted as CHL. The CHL class was 73% accurate by predicting 11/15 correctly with most wrong classifications as mDLBCL. The mDLBCL scored the best with 75% accuracty by predicting 12/16 correctly, with all incorrect predictions made as mDLBCL.
Lets see how well it learns and predicts on the testing model.
predicted <- predict(rf,testing)
results <- data.frame(predicted=predicted, actual=testing$class)
results## predicted actual
## pDLBCL pDLBCL pDLBCL
## CHL CHL CHL
## mDLBCL.1 mDLBCL mDLBCL
## mDLBCL.6 mDLBCL mDLBCL
## mDLBCL.8 pDLBCL mDLBCL
## CHL.10 CHL CHL
## mDLBCL.13 mDLBCL mDLBCL
## pDLBCL.7 pDLBCL pDLBCL
## CHL.17 mDLBCL CHL
## CHL.18 pDLBCL CHLIt predicted 7/10 correctly. There were 2 pDLBCL, and all of those were predicted correctly with 100% accuracy. There were 4 mDLBCL samples, but 3/4 predicted correctly with 75% accuracy, while the 1/4 predicted as pDLBCL. There were 4 CHL and only 2/4 predicted correctly at 50% accuracy, and the other two CHL each predicted as either of mDLBCL or pDLBCL. This could be indicative of the overlap, but lets try using only the genes of IFNG, CD247, IDO1, PDCD1LG2, and PTPRD.
select_df <- sample_rs_df[,c(1,2,5,6,9,15)]
paged_table(select_df)Lets keep the same inTrain sampling set but change data frames to our selected features.
training <- select_df[inTrain,]
testing <- select_df[-inTrain,]
table(training$class)##
## CHL mDLBCL pDLBCL
## 15 16 6table(testing$class)##
## CHL mDLBCL pDLBCL
## 4 4 2rf_study5 <- randomForest(training[1:5], training$class, mtry=2, ntree=5000, confusion=T)
rf$confusion## CHL mDLBCL pDLBCL class.error
## CHL 11 3 1 0.2666667
## mDLBCL 4 12 0 0.2500000
## pDLBCL 4 1 1 0.8333333Looks like a similar outcome in prediction with CHL and mDLBCL scoring better than pDLBCL classification. Lets see how well it predicts on the hold out set. There are also twice as many CHL and mDLBCL as the pDLBCL samples.
prediction <- predict(rf_study5, testing)
results <- data.frame(predicted=prediction, actual=testing$class)
results## predicted actual
## pDLBCL pDLBCL pDLBCL
## CHL CHL CHL
## mDLBCL.1 mDLBCL mDLBCL
## mDLBCL.6 CHL mDLBCL
## mDLBCL.8 pDLBCL mDLBCL
## CHL.10 mDLBCL CHL
## mDLBCL.13 mDLBCL mDLBCL
## pDLBCL.7 pDLBCL pDLBCL
## CHL.17 CHL CHL
## CHL.18 pDLBCL CHLThe testing set scored an accuracy of 6/10 for 60% accuracy, worse than with all features using selected features of study. There were 2 pDLBCL samples all predicted correctly at 100%, but the CHL predicted 2/4 accuracy the same as other model with 1 mDLBCL and other pDLBCL. There were 4 mDLBCL samples and 2/4 predicted correctly with 1/4 predicted as pDLBCL and 1/4 predicted as CHL.
Lets see how well these genes predict the new 4 groups that the study mentioned. We have to get the study groups from the labels df earlier input.
labels## pDLBCL CHL
## titleID GSM9163281_02_Clariom_S_Human_.CEL GSM9163282_03_Clariom_S_Human_.CEL
## GSM_ID GSM9163281 GSM9163282
## diagnosis diagnosis: EBV+ pDLBCL diagnosis: EBV+ CHL
## age 62 60
## gender male male
## group IFNG-H IFNG-L
## pDLBCL.1 mDLBCL
## titleID GSM9163283_06_Clariom_S_Human_.CEL GSM9163284_08_Clariom_S_Human_.CEL
## GSM_ID GSM9163283 GSM9163284
## diagnosis diagnosis: EBV+ pDLBCL diagnosis: EBV+ mDLBCL
## age 71 69
## gender male male
## group IFNG-H IFNG-L
## CHL.1 mDLBCL.1
## titleID GSM9163285_09_Clariom_S_Human_.CEL GSM9163286_10_Clariom_S_Human_.CEL
## GSM_ID GSM9163285 GSM9163286
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ mDLBCL
## age 67 75
## gender male female
## group IFNG-L 9p24.1-H
## pDLBCL.2 CHL.2
## titleID GSM9163287_11_Clariom_S_Human_.CEL GSM9163288_12_Clariom_S_Human_.CEL
## GSM_ID GSM9163287 GSM9163288
## diagnosis diagnosis: EBV+ pDLBCL diagnosis: EBV+ CHL
## age 84 72
## gender female male
## group IFNG-L IFNG-L
## CHL.3
## titleID GSM9163289_13_Clariom_S_Human_2.CEL
## GSM_ID GSM9163289
## diagnosis diagnosis: EBV+ CHL
## age 71
## gender male
## group 9p24.1-H
## CHL.4 CHL.5
## titleID GSM9163290_14_Clariom_S_Human_.CEL GSM9163291_15_Clariom_S_Human_.CEL
## GSM_ID GSM9163290 GSM9163291
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ CHL
## age 62 78
## gender male male
## group 9p24.1-H 9p24.1-H
## mDLBCL.2 mDLBCL.3
## titleID GSM9163292_16_Clariom_S_Human_.CEL GSM9163293_17_Clariom_S_Human_.CEL
## GSM_ID GSM9163292 GSM9163293
## diagnosis diagnosis: EBV+ mDLBCL diagnosis: EBV+ mDLBCL
## age 62 62
## gender male female
## group IFNG-L IS
## CHL.6 CHL.7
## titleID GSM9163294_19_Clariom_S_Human_.CEL GSM9163295_20_Clariom_S_Human_.CEL
## GSM_ID GSM9163294 GSM9163295
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ CHL
## age 74 51
## gender female male
## group IFNG-L IFNG-L
## pDLBCL.3 CHL.8
## titleID GSM9163296_21_Clariom_S_Human_.CEL GSM9163297_22_Clariom_S_Human_.CEL
## GSM_ID GSM9163296 GSM9163297
## diagnosis diagnosis: EBV+ pDLBCL diagnosis: EBV+ CHL
## age 71 60
## gender female male
## group IFNG-L IFNG-L
## mDLBCL.4 mDLBCL.5
## titleID GSM9163298_23_Clariom_S_Human_.CEL GSM9163299_24_Clariom_S_Human_.CEL
## GSM_ID GSM9163298 GSM9163299
## diagnosis diagnosis: EBV+ mDLBCL diagnosis: EBV+ mDLBCL
## age 84 50
## gender male male
## group IS IS
## mDLBCL.6 mDLBCL.7
## titleID GSM9163300_25_Clariom_S_Human_.CEL GSM9163301_26_Clariom_S_Human_.CEL
## GSM_ID GSM9163300 GSM9163301
## diagnosis diagnosis: EBV+ mDLBCL diagnosis: EBV+ mDLBCL
## age 81 76
## gender male female
## group IS IS
## CHL.9
## titleID GSM9163302_27_Clariom_S_Human_2.CEL
## GSM_ID GSM9163302
## diagnosis diagnosis: EBV+ CHL
## age 84
## gender male
## group IFNG-L
## mDLBCL.8 CHL.10
## titleID GSM9163303_29_Clariom_S_Human_.CEL GSM9163304_30_Clariom_S_Human_.CEL
## GSM_ID GSM9163303 GSM9163304
## diagnosis diagnosis: EBV+ mDLBCL diagnosis: EBV+ CHL
## age 89 83
## gender male female
## group IFNG-H 9p24.1-H
## CHL.11 CHL.12
## titleID GSM9163305_31_Clariom_S_Human_.CEL GSM9163306_32_Clariom_S_Human_.CEL
## GSM_ID GSM9163305 GSM9163306
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ CHL
## age 63 74
## gender male male
## group IFNG-L 9p24.1-H
## CHL.13 mDLBCL.9
## titleID GSM9163307_34_Clariom_S_Human_.CEL GSM9163308_35_Clariom_S_Human_.CEL
## GSM_ID GSM9163307 GSM9163308
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ mDLBCL
## age 77 74
## gender male male
## group 9p24.1-H IS
## mDLBCL.10
## titleID GSM9163309_36_Clariom_S_Human_.CEL
## GSM_ID GSM9163309
## diagnosis diagnosis: EBV+ mDLBCL
## age 86
## gender male
## group <NA>
## mDLBCL.11
## titleID GSM9163310_37_Clariom_S_Human_2.CEL
## GSM_ID GSM9163310
## diagnosis diagnosis: EBV+ mDLBCL
## age 60
## gender male
## group IS
## mDLBCL.12
## titleID GSM9163311_38_Clariom_S_Human_2.CEL
## GSM_ID GSM9163311
## diagnosis diagnosis: EBV+ mDLBCL
## age 81
## gender male
## group IFNG-L
## mDLBCL.13
## titleID GSM9163312_39_Clariom_S_Human_.CEL
## GSM_ID GSM9163312
## diagnosis diagnosis: EBV+ mDLBCL
## age 94
## gender female
## group IFNG-H
## mDLBCL.14
## titleID GSM9163313_40_Clariom_S_Human_2.CEL
## GSM_ID GSM9163313
## diagnosis diagnosis: EBV+ mDLBCL
## age 78
## gender male
## group 9p24.1-H
## pDLBCL.4 pDLBCL.5
## titleID GSM9163314_41_Clariom_S_Human_.CEL GSM9163315_42_Clariom_S_Human_.CEL
## GSM_ID GSM9163314 GSM9163315
## diagnosis diagnosis: EBV+ pDLBCL diagnosis: EBV+ pDLBCL
## age 67 85
## gender female female
## group IFNG-L IFNG-H
## mDLBCL.15 mDLBCL.16
## titleID GSM9163316_43_Clariom_S_Human_.CEL GSM9163317_44_Clariom_S_Human_.CEL
## GSM_ID GSM9163316 GSM9163317
## diagnosis diagnosis: EBV+ mDLBCL diagnosis: EBV+ mDLBCL
## age 71 82
## gender male male
## group IFNG-L IFNG-H
## CHL.14 pDLBCL.6
## titleID GSM9163318_45_Clariom_S_Human_.CEL GSM9163319_46_Clariom_S_Human_.CEL
## GSM_ID GSM9163318 GSM9163319
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ pDLBCL
## age 51 80
## gender male male
## group IFNG-L IFNG-H
## pDLBCL.7
## titleID GSM9163320_49_Clariom_S_Human_2.CEL
## GSM_ID GSM9163320
## diagnosis diagnosis: EBV+ pDLBCL
## age 74
## gender male
## group IFNG-H
## CHL.15 CHL.16
## titleID GSM9163321_50_Clariom_S_Human_.CEL GSM9163322_51_Clariom_S_Human_.CEL
## GSM_ID GSM9163321 GSM9163322
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ CHL
## age 66 59
## gender female female
## group IFNG-L IFNG-L
## CHL.17 mDLBCL.17
## titleID GSM9163323_52_Clariom_S_Human_.CEL GSM9163324_53_Clariom_S_Human_.CEL
## GSM_ID GSM9163323 GSM9163324
## diagnosis diagnosis: EBV+ CHL diagnosis: EBV+ mDLBCL
## age 79 76
## gender male male
## group 9p24.1-H IS
## mDLBCL.18 mDLBCL.19
## titleID GSM9163325_55_Clariom_S_Human_.CEL GSM9163326_56_Clariom_S_Human_.CEL
## GSM_ID GSM9163325 GSM9163326
## diagnosis diagnosis: EBV+ mDLBCL diagnosis: EBV+ mDLBCL
## age 73 79
## gender male male
## group IS IS
## CHL.18
## titleID GSM9163327_57_Clariom_S_Human_.CEL
## GSM_ID GSM9163327
## diagnosis diagnosis: EBV+ CHL
## age 62
## gender male
## group IFNG-Hlabels_t <- data.frame(t(labels))
group <- labels_t$group
table(group)## group
## 9p24.1-H IFNG-H IFNG-L IS
## 9 9 18 10These are the 4 groups the study came up with, the IS is the mDLBCL class, the IFNG-H is pDLBCL, 9p24.1-H is CHL, and the IFNG-L is the transition state between pDLBCL and CHL moving from pDLBCL to CHL.
df_group <- sample_rs_df
df_group$class <- as.factor(group)
df_group## PTPRD PDCD1LG2 PAX5 MUM1 IFNG IDO1 ERP44
## pDLBCL 3.685317 4.634469 5.837732 1.878937 3.069225 5.266947 5.575510
## CHL 3.676430 2.942214 7.448931 2.237178 2.962287 3.515371 4.191834
## pDLBCL.1 3.148372 4.499253 6.307865 1.766060 3.226458 5.319546 5.138372
## mDLBCL 3.455512 4.373373 6.419925 2.484003 3.193519 3.651946 5.291534
## CHL.1 4.022412 3.864916 6.990574 2.135487 4.000244 3.497938 3.627553
## mDLBCL.1 3.541898 5.254167 7.070463 2.082015 2.865105 3.424882 5.344731
## pDLBCL.2 3.398471 4.465464 6.104317 2.482157 2.636234 3.835786 5.076654
## CHL.2 3.771869 4.698898 6.380601 2.270221 3.312958 3.445356 5.082100
## CHL.3 3.356006 4.789598 6.751569 2.262848 2.993484 4.282418 5.143249
## CHL.4 3.531764 4.302539 6.779292 2.694966 2.872059 3.533667 5.088958
## CHL.5 4.031001 4.900090 6.554107 2.766866 2.846098 3.440680 5.213799
## mDLBCL.2 3.221535 5.578819 6.658492 2.434437 1.954850 3.004267 5.620760
## mDLBCL.3 3.692095 3.659990 6.705532 2.699674 2.565927 3.535909 5.279476
## CHL.6 3.412819 4.314726 6.135404 2.744835 3.621671 3.842913 5.313366
## CHL.7 3.451064 3.479858 6.052747 2.223445 2.899106 3.281838 5.088203
## pDLBCL.3 2.983141 4.062027 7.398400 2.139963 3.404577 4.762571 5.496741
## CHL.8 4.329820 3.876076 6.762964 2.403510 2.003622 3.442793 5.562172
## mDLBCL.4 3.077683 4.935213 7.208099 4.337290 2.505606 3.189192 5.563635
## mDLBCL.5 3.609745 4.231856 7.431777 2.415194 2.953850 3.590060 5.504069
## mDLBCL.6 3.551329 4.578427 6.782725 2.250006 2.900375 3.672584 6.149064
## mDLBCL.7 3.633576 4.960384 7.397093 2.399275 2.973138 3.495786 5.632225
## CHL.9 3.063946 3.718218 6.606534 2.597851 2.899324 3.231478 5.176768
## mDLBCL.8 3.638433 4.949566 6.216256 2.173263 3.714553 4.702419 5.199758
## CHL.10 3.289788 4.854521 6.575761 2.680258 2.972220 3.412869 4.840189
## CHL.11 3.486482 4.865561 6.376813 2.245216 2.833512 3.270835 5.851499
## CHL.12 3.592392 6.170380 6.207869 2.768394 2.915523 3.817595 5.756560
## CHL.13 3.673980 4.249046 6.533770 2.852737 2.697077 3.442922 5.280367
## mDLBCL.9 3.394398 5.363083 7.032194 2.972367 2.293754 3.494170 6.078944
## mDLBCL.10 4.003065 3.558593 7.322739 1.893677 3.120178 4.035177 4.829168
## mDLBCL.11 3.024652 4.500945 6.940962 2.005839 2.215032 3.550920 5.336893
## mDLBCL.12 2.729431 5.675743 6.698119 2.835851 2.810134 4.298867 5.395473
## mDLBCL.13 3.280114 5.450906 6.779600 2.551476 2.879991 4.253456 6.052639
## mDLBCL.14 3.446065 5.200995 6.928266 2.777856 3.027688 3.812757 5.145139
## pDLBCL.4 3.111890 4.543541 6.501964 2.428017 2.902845 3.992336 5.364440
## pDLBCL.5 3.248538 3.932478 6.263106 2.205217 2.779238 4.760222 5.632315
## mDLBCL.15 2.647033 4.358680 7.318072 2.749662 2.458244 3.066835 5.464782
## mDLBCL.16 3.586893 4.855219 7.485727 2.434373 2.394065 3.501029 5.695070
## CHL.14 3.981202 4.211558 6.903905 2.015950 2.197446 3.652181 4.102102
## pDLBCL.6 3.500345 6.198815 6.627168 2.051298 3.340810 6.899326 6.122227
## pDLBCL.7 3.130425 6.192865 6.503495 2.847189 2.771015 6.879421 6.658610
## CHL.15 3.229043 4.723221 6.578960 2.935235 2.299081 3.116050 5.566924
## CHL.16 3.551180 4.134288 7.528055 2.763743 3.430004 3.261750 5.846060
## CHL.17 3.628847 4.129567 6.737099 2.836168 2.587612 3.407501 5.734322
## mDLBCL.17 3.120526 4.505849 6.622961 2.390182 2.950387 4.166414 6.061316
## mDLBCL.18 3.477699 4.412282 7.378854 2.305522 3.130588 3.411087 5.473001
## mDLBCL.19 3.912454 7.327919 6.642691 1.602243 2.376897 3.237192 5.232096
## CHL.18 3.289102 5.549601 6.153209 3.269919 3.542248 4.542451 6.237398
## CD5 CD274 BCL6 BCL2 LDHA LDHC LDHD
## pDLBCL 6.412200 6.521790 4.810390 6.988205 8.658361 3.985598 5.712537
## CHL 6.252281 4.592286 4.601292 7.230086 7.858679 4.007080 6.230099
## pDLBCL.1 6.460336 7.084118 4.573067 7.455283 9.184861 4.101672 5.258146
## mDLBCL 6.647232 6.452860 5.211272 7.019910 9.338661 3.650014 5.503446
## CHL.1 6.405831 4.696020 5.291846 7.822121 5.792496 4.342355 5.596182
## mDLBCL.1 6.283571 7.835426 5.040143 6.847939 8.716444 3.828057 5.653517
## pDLBCL.2 6.417821 6.744887 5.131215 7.239416 8.707534 4.128118 5.386853
## CHL.2 7.262511 6.579888 5.081345 7.108641 8.685312 3.997067 5.428130
## CHL.3 7.126876 6.194723 5.115395 7.002661 8.980201 4.064068 5.699283
## CHL.4 7.336942 6.055063 5.670942 7.059933 8.782031 3.970572 5.174769
## CHL.5 6.569752 6.050932 5.445840 7.129604 8.994080 4.475421 5.795505
## mDLBCL.2 6.542083 6.054614 5.290428 6.492504 10.007422 3.969665 5.112403
## mDLBCL.3 6.968191 5.597942 5.105497 7.272078 8.880994 4.494151 5.504082
## CHL.6 6.705105 7.242420 5.332240 6.981597 8.760310 4.522051 5.147836
## CHL.7 7.547240 6.261641 5.701903 7.263808 8.390140 3.688503 5.363676
## pDLBCL.3 7.051024 6.556098 5.345204 7.176817 9.195272 3.708710 5.116153
## CHL.8 7.066170 5.898913 4.730280 7.074783 8.636065 3.929166 5.299886
## mDLBCL.4 6.232854 7.673782 5.180383 7.098472 9.858830 3.244598 5.224443
## mDLBCL.5 6.860914 5.898791 5.566423 7.270708 9.411728 3.710451 5.223130
## mDLBCL.6 6.692568 5.837361 5.418009 6.945680 10.192753 3.895005 5.609946
## mDLBCL.7 6.852710 7.344261 5.424370 7.081180 9.538618 3.659041 5.521872
## CHL.9 6.962995 5.383059 5.429172 7.226607 8.203157 4.450271 5.581232
## mDLBCL.8 6.253627 7.616847 5.824775 7.124863 9.712842 4.151815 5.587457
## CHL.10 6.821408 7.047635 5.136576 7.394500 8.428529 3.789925 5.632588
## CHL.11 6.528702 5.557824 5.084341 7.110367 8.651220 3.863195 5.475959
## CHL.12 6.601854 7.383035 5.915606 7.105207 9.391049 3.386810 5.158768
## CHL.13 6.999369 6.014271 5.360682 7.400672 7.980798 3.950610 5.547694
## mDLBCL.9 6.485916 7.417413 4.993347 7.438141 9.063086 4.057919 5.761411
## mDLBCL.10 6.485993 5.027237 5.372846 7.411634 9.446182 4.283066 5.455434
## mDLBCL.11 6.806347 5.379237 5.262921 7.394885 9.497101 4.380149 5.684329
## mDLBCL.12 6.905681 6.765949 4.870469 6.901166 9.781190 3.909456 5.955431
## mDLBCL.13 6.881819 6.377471 5.052154 7.052345 8.907587 3.207274 5.252791
## mDLBCL.14 6.655850 6.982544 5.326902 7.315581 8.819691 3.748995 5.658986
## pDLBCL.4 6.892991 5.378472 5.232217 7.316012 8.458703 3.555433 5.531630
## pDLBCL.5 6.814038 6.466849 4.857462 6.972438 9.000184 3.570633 5.398580
## mDLBCL.15 6.671599 5.119697 5.320457 7.099695 9.675630 3.294096 5.464599
## mDLBCL.16 6.493284 6.647098 5.240318 7.610189 9.904595 3.421933 5.499535
## CHL.14 6.810164 5.499239 4.854063 6.991149 7.335124 3.944531 5.980378
## pDLBCL.6 6.559307 7.867803 5.539399 6.898820 9.761196 3.562440 5.465887
## pDLBCL.7 6.593189 7.101126 5.533159 6.885508 8.909913 3.005343 5.397123
## CHL.15 6.794859 5.486161 5.409903 7.072722 9.031017 3.439547 5.435433
## CHL.16 7.171274 5.100444 5.608524 7.482945 8.432458 3.338988 5.266639
## CHL.17 6.918259 6.914670 5.419001 7.374372 9.025153 3.597280 5.339224
## mDLBCL.17 6.452621 7.538983 5.043645 6.847151 9.456874 3.879847 5.475541
## mDLBCL.18 6.558975 6.055738 5.669209 7.066109 9.917845 3.894580 5.467432
## mDLBCL.19 6.462646 6.074863 4.830440 7.098906 8.877298 4.129958 5.556917
## CHL.18 6.943623 6.834273 4.973301 7.058475 9.037384 3.554003 5.245798
## class
## pDLBCL IFNG-H
## CHL IFNG-L
## pDLBCL.1 IFNG-H
## mDLBCL IFNG-L
## CHL.1 IFNG-L
## mDLBCL.1 9p24.1-H
## pDLBCL.2 IFNG-L
## CHL.2 IFNG-L
## CHL.3 9p24.1-H
## CHL.4 9p24.1-H
## CHL.5 9p24.1-H
## mDLBCL.2 IFNG-L
## mDLBCL.3 IS
## CHL.6 IFNG-L
## CHL.7 IFNG-L
## pDLBCL.3 IFNG-L
## CHL.8 IFNG-L
## mDLBCL.4 IS
## mDLBCL.5 IS
## mDLBCL.6 IS
## mDLBCL.7 IS
## CHL.9 IFNG-L
## mDLBCL.8 IFNG-H
## CHL.10 9p24.1-H
## CHL.11 IFNG-L
## CHL.12 9p24.1-H
## CHL.13 9p24.1-H
## mDLBCL.9 IS
## mDLBCL.10 <NA>
## mDLBCL.11 IS
## mDLBCL.12 IFNG-L
## mDLBCL.13 IFNG-H
## mDLBCL.14 9p24.1-H
## pDLBCL.4 IFNG-L
## pDLBCL.5 IFNG-H
## mDLBCL.15 IFNG-L
## mDLBCL.16 IFNG-H
## CHL.14 IFNG-L
## pDLBCL.6 IFNG-H
## pDLBCL.7 IFNG-H
## CHL.15 IFNG-L
## CHL.16 IFNG-L
## CHL.17 9p24.1-H
## mDLBCL.17 IS
## mDLBCL.18 IS
## mDLBCL.19 IS
## CHL.18 IFNG-HThere is a problem in this grouping because there is an NA at row 29, so we need to change the group to be the label it is instead of removing it. It is labeled mDLBCL.
df_group$class[29] <- as.factor("IS")Lets now predict the class as one of the 4 groups using the research study genes.
training <- df_group[inTrain,]
testing <- df_group[-inTrain,]
table(training$class)##
## 9p24.1-H IFNG-H IFNG-L IS
## 6 4 17 10table(testing$class)##
## 9p24.1-H IFNG-H IFNG-L IS
## 3 5 1 1rf_group4 <- randomForest(training[1:14], training$class, mtry=5, ntree=5000, confusion=T)
rf_group4$confusion## 9p24.1-H IFNG-H IFNG-L IS class.error
## 9p24.1-H 0 0 3 3 1.0000000
## IFNG-H 0 0 1 3 1.0000000
## IFNG-L 0 0 13 4 0.2352941
## IS 0 0 6 4 0.6000000Using these genes the error was huge in predicting a 4 class problem, but random forest is always best with a 2 class or low class prediction, also with tuning the model it helps. None predicted accuratly for the 9p24.1-H or IFNG-H which are CHL and pDLBCL respectively. All CHL predicted as the transition state of IFNG-L or as mDLBCL or IS. The best performing class is the IFNG-L or transition state with 13/17 predicted accurately with 76% accuracy. The next best is the IS or mDLBCL class with 6/10 correctly predicted with 60% accuracy.
But lets see how well it predicts the hold out set.
prediction <- predict(rf_group4,testing)
results <- data.frame(predicted=prediction, actual=testing$class)
results## predicted actual
## pDLBCL IFNG-L IFNG-H
## CHL IFNG-L IFNG-L
## mDLBCL.1 IFNG-L 9p24.1-H
## mDLBCL.6 IS IS
## mDLBCL.8 IS IFNG-H
## CHL.10 IFNG-L 9p24.1-H
## mDLBCL.13 IFNG-L IFNG-H
## pDLBCL.7 IFNG-H IFNG-H
## CHL.17 IS 9p24.1-H
## CHL.18 IFNG-L IFNG-HThere were 3/10 correctly predicted with 30% accuracy in predicting the group of the lymphoma. The best performing group predicted correctly was the IFNG-L with 1/1 correctly predicted, and also for IS with 1/1 correctly predicted. None of the 9p24.1-H were predicted correctly with 0/3 score with 2/3 predicted as IFNG-L and the other as IS. The IFNG-H group had a score of 1/5 for 20% accuracy as 3/5 predicted as IFNG-L and 1/5 predicted as IS. This does show how the transition state of IFNG-L is a group that CHL and pDLBCL lymphomas transition to as that is the reason these 2 lymphomas were not predicted well.
Next we will explore the other genes by the topGenes2 table that are in the subset groups of this project using these research genes as well as the other genes specific to top genes in this project with top 10 over expressed in the group avg/group median and top 10 under expressed the same well and that also had a gene in the features table that matched up with the Affymetrix probe IDs extracted from.
topGenes2 <- write.csv(topGenes2, 'topGenes2.csv', row.names=F)You can get the topGenes2 table here
Thanks and keep checking in.
==============================================================
***** Part 5
In this part we will read in the the topGenes2 data and start our machine learning analysis on the groups and subgroup top genes. We have to grep each sample to each group in the importance column.
We will also see how well select genes can predict the gender or age group they seemed to be specific to.
Some other features to check out that we noted with the study genes.
BCL2 is the only gene that has over estimation in all males but not females.
PTPRD, it seems to be high or over estimated only in the CHL and pDLBCL for males and also females, but not in the mDLBCL for either gender.
BCL2 is only elevated in both age groups of CHL and only the older than 72 years of age group of both types DLBCL.
PDL2 is over estimated in mDLBCL and CHL both age groups
PDL1 is over estimated in the young with CHL or mDLBCL but the old with pDLBCL.
The PTPRD gene is over expressed only in younger than 72 years of age group with CHL or pDLBCL. We can use PTPRD to predict age
We can use CD247 (PDL1) and PDCD1LG2 (PDL2) genes to predict gender.
Lets see if we can predict gender by BCL2 gene and the PTPRD gene to predict CHL or pDLBCL as a class or mDLBCL.
We can test that out. We need the labels table.
library(rmarkdown)
library(randomForest)labels <- read.csv("compare_df_6labels_47samples.csv", header=T, row.names=1)
paged_table(labels)We also need the topGenes2 table.
topGenes <- read.csv("topGenes2.csv", header=T)
str(topGenes)## 'data.frame': 87 obs. of 96 variables:
## $ ID : chr "TC0300013532.hg.1" "TC1200008790.hg.1" "TC0400010896.hg.1" "TC0100014340.hg.1" ...
## $ pDLBCL : num 3.39 3 1.79 3.68 3.35 ...
## $ CHL : num 3.02 3.33 2.26 2.55 3.46 ...
## $ pDLBCL.1 : num 3.51 2.56 1.72 3.62 2.74 ...
## $ mDLBCL : num 6.55 5.31 1.85 3.43 2.78 ...
## $ CHL.1 : num 2.96 3.3 1.83 3.45 3.25 ...
## $ mDLBCL.1 : num 5.33 3.25 1.69 3.18 2.89 ...
## $ pDLBCL.2 : num 2.36 3.84 2.79 3.3 5.31 ...
## $ CHL.2 : num 2.69 5.35 1.51 3.04 3.06 ...
## $ CHL.3 : num 2.4 5.33 2.14 2.93 3.1 ...
## $ CHL.4 : num 3.04 4.73 2.6 3.12 3.26 ...
## $ CHL.5 : num 3.64 5.58 2.04 2.81 3.19 ...
## $ mDLBCL.2 : num 2.66 5.71 2 2.85 3.11 ...
## $ mDLBCL.3 : num 2.53 4.45 2.28 3.76 5.02 ...
## $ CHL.6 : num 2.44 5.32 1.98 2.38 3.4 ...
## $ CHL.7 : num 2.65 4.73 2.23 2.91 3.06 ...
## $ pDLBCL.3 : num 2.21 5.11 1.84 3.26 3.11 ...
## $ CHL.8 : num 2.58 3.84 2.64 2.84 3.81 ...
## $ mDLBCL.4 : num 2.39 4.29 1.61 2.95 2.94 ...
## $ mDLBCL.5 : num 2.14 5.46 1.95 2.49 3.59 ...
## $ mDLBCL.6 : num 2.6 4.91 2.07 2.71 3.27 ...
## $ mDLBCL.7 : num 2.63 4.45 1.43 2.79 3.33 ...
## $ CHL.9 : num 2.07 4.21 1.64 2.94 2.88 ...
## $ mDLBCL.8 : num 3.14 4.45 1.91 3.03 3.22 ...
## $ CHL.10 : num 2.18 3.62 1.56 3.29 3.1 ...
## $ CHL.11 : num 2.18 4.93 1.68 2.63 3.45 ...
## $ CHL.12 : num 2.21 5.36 1.73 2.84 3.51 ...
## $ CHL.13 : num 2.81 3.97 1.75 2.73 3.16 ...
## $ mDLBCL.9 : num 2.14 4.89 1.92 3.14 3.19 ...
## $ mDLBCL.10 : num 2.87 3.82 1.98 2.76 4.41 ...
## $ mDLBCL.11 : num 2.46 3.52 1.67 3.15 3.48 ...
## $ mDLBCL.12 : num 2.36 4.89 1.99 3.02 3.56 ...
## $ mDLBCL.13 : num 2.51 5.89 3.52 5.52 5.07 ...
## $ mDLBCL.14 : num 2.05 4.44 1.78 2.89 2.96 ...
## $ pDLBCL.4 : num 1.98 5.49 3.19 4.36 6.15 ...
## $ pDLBCL.5 : num 2 4.96 5.2 6.58 7.81 ...
## $ mDLBCL.15 : num 2.34 5.86 3.17 3.74 6.56 ...
## $ mDLBCL.16 : num 2.35 5.41 2.01 2.53 3.33 ...
## $ CHL.14 : num 2.1 3.26 1.95 3.18 3.33 ...
## $ pDLBCL.6 : num 2.44 5.32 1.52 2.68 3.06 ...
## $ pDLBCL.7 : num 2.11 6.16 1.79 2.66 2.99 ...
## $ CHL.15 : num 2.65 5.96 1.67 2.94 2.8 ...
## $ CHL.16 : num 2.67 5.93 1.75 2.92 3.44 ...
## $ CHL.17 : num 2.44 4.97 1.74 3.19 3.25 ...
## $ mDLBCL.17 : num 1.96 5.32 1.81 5.21 3.91 ...
## $ mDLBCL.18 : num 2.34 5.66 2.74 4.54 5.68 ...
## $ mDLBCL.19 : num 2.51 4.31 2.11 3.21 3.21 ...
## $ CHL.18 : num 2.64 6.22 1.88 2.41 3.18 ...
## $ CHL_mean : num 2.6 4.73 1.93 2.9 3.25 ...
## $ pDLBCL_mean : num 2.5 4.56 2.48 3.77 4.32 ...
## $ mDLBCL_mean : num 2.79 4.81 2.07 3.35 3.78 ...
## $ CHL_x_mean : num 2.48 5.21 1.74 2.88 3.18 ...
## $ mDLBCL_x_mean : num 3.25 4.51 2.23 3.81 4.08 ...
## $ pDLBCL_x_mean : num 2.14 4.85 3.26 4.38 5.6 ...
## $ CHL_y_mean : num 2.63 4.61 1.97 2.91 3.26 ...
## $ mDLBCL_y_mean : num 2.68 4.89 2.04 3.23 3.7 ...
## $ pDLBCL_y_mean : num 2.86 4.26 1.7 3.16 3.04 ...
## $ CHL_young72_mean : num 2.63 4.74 2.01 2.91 3.27 ...
## $ mDLBCL_young72_mean : num 3.11 5.05 2.15 3.23 4.09 ...
## $ pDLBCL_young72_mean : num 2.77 4.04 2.13 3.73 3.84 ...
## $ CHL_old : num 2.54 4.72 1.78 2.88 3.21 ...
## $ mDLBCL_old : num 2.66 4.71 2.04 3.39 3.64 ...
## $ pDLBCL_old : num 2.23 5.07 2.83 3.81 4.79 ...
## $ CHL_median : num 2.64 4.93 1.83 2.92 3.25 ...
## $ mDLBCL_median : num 2.48 4.89 1.97 3.09 3.33 ...
## $ pDLBCL_median : num 2.28 5.03 1.81 3.46 3.23 ...
## $ CHL_x_median : num 2.54 5.63 1.71 2.93 3.25 ...
## $ mDLBCL_x_median : num 2.58 4.45 1.98 3.47 4.17 ...
## $ pDLBCL_x_median : num 2.1 5.03 2.99 3.83 5.73 ...
## $ CHL_y_median : num 2.64 4.73 1.88 2.91 3.25 ...
## $ mDLBCL_y_median : num 2.37 4.9 1.97 3.03 3.3 ...
## $ pDLBCL_y_median : num 2.92 4.16 1.75 3.15 3.03 ...
## $ CHL_young72_median : num 2.65 4.83 1.92 2.93 3.25 ...
## $ mDLBCL_young72_median: num 2.49 5.38 1.98 3.29 3.54 ...
## $ pDLBCL_young72_median: num 2.8 4.06 1.81 3.65 3.23 ...
## $ CHL_old72_median : num 2.44 4.97 1.74 2.84 3.19 ...
## $ mDLBCL_old72_median : num 2.45 4.67 1.95 3.03 3.3 ...
## $ pDLBCL_old72_median : num 2.23 5.14 2.29 2.99 4.19 ...
## $ CHL_change : num 0.983 0.96 1.053 0.993 0.999 ...
## $ pDLBCL_change : num 1.094 0.905 1.367 1.09 1.335 ...
## $ mDLBCL_change : num 1.124 0.985 1.055 1.084 1.134 ...
## $ CHL_x_change : num 0.976 0.926 1.018 0.983 0.98 ...
## $ CHL_y_change : num 0.995 0.974 1.052 0.999 1.004 ...
## $ pDLBCL_x_change : num 1.016 0.963 1.089 1.143 0.976 ...
## $ pDLBCL_y_change : num 0.981 1.024 0.972 1.004 1.003 ...
## $ mDLBCL_x_change : num 1.26 1.014 1.123 1.098 0.977 ...
## $ mDLBCL_y_change : num 1.129 0.998 1.036 1.066 1.122 ...
## $ CHL_old72_change : num 1.043 0.949 1.024 1.016 1.007 ...
## $ CHL_young72_change : num 0.993 0.982 1.05 0.994 1.003 ...
## $ pDLBCL_old_change : num 0.997 0.986 1.235 1.273 1.145 ...
## $ pDLBCL_young72_change: num 0.99 0.996 1.177 1.022 1.188 ...
## $ mDLBCL_young72_change: num 1.248 0.938 1.089 0.984 1.157 ...
## $ mDLBCL_old72_change : num 1.09 1.01 1.05 1.12 1.1 ...
## $ SPOT_ID.1 : chr "NM_198152 // RefSeq // Homo sapiens urotensin 2B (UTS2B), mRNA. // chr3 // 100 // 100 // 0 // --- // 0 /// ENST"| __truncated__ "NM_001301175 // RefSeq // Homo sapiens ubiquitin specific peptidase 30 (USP30), transcript variant 2, mRNA. // "| __truncated__ "NM_001114387 // RefSeq // Homo sapiens transmembrane protease, serine 11A (TMPRSS11A), transcript variant 2, mR"| __truncated__ "NM_002353 // RefSeq // Homo sapiens tumor-associated calcium signal transducer 2 (TACSTD2), mRNA. // chr1 // 10"| __truncated__ ...
## $ Gene_ID : chr "UTS2B" "USP30" "TMPRSS11A" "TACSTD2" ...
## $ importance : chr "There were 8 genes found in the data of mDLBCL younger than 72 years of age genes to match any of the 20 probe "| __truncated__ "top gene pDLBCL avg/median group values" "top gene pDLBCL avg/median group values" "There were 7 genes found in the data of pDLBCL older than 72 years of age genes to match any of the 20 probe ID"| __truncated__ ...paged_table(topGenes[1:10,])lets get the samples that are male and female. These are integer values for index where a female or male is.
labels_t <- data.frame(t(labels))
females <- grep('female', labels_t$gender)
males <- grep('^male*', labels_t$gender)
gender <- "gender"
gender[females] <- "female"
gender[males] <- "male"
gender## [1] "male" "male" "male" "male" "male" "female" "female" "male"
## [9] "male" "male" "male" "male" "female" "female" "male" "female"
## [17] "male" "male" "male" "male" "female" "male" "male" "female"
## [25] "male" "male" "male" "male" "male" "male" "male" "female"
## [33] "male" "female" "female" "male" "male" "male" "male" "male"
## [41] "female" "female" "male" "male" "male" "male" "male"Lets get the samples that are by type of diagnosis to use PTPRD gene to predict a class of CHL or pDLBCL and a different class of mDLBCL.
CHL <- grep('CHL',labels_t$diagnosis)
pDLBCL <- grep('pDLBCL', labels_t$diagnosis)
mDLBCL <- grep('mDLBCL', labels_t$diagnosis)
diagnosis <- 'diagnosis'
diagnosis[c(CHL,pDLBCL)] <- 'CHL or pDLBCL'
diagnosis[mDLBCL] <- 'mDLBCL'
diagnosis## [1] "CHL or pDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "mDLBCL"
## [5] "CHL or pDLBCL" "mDLBCL" "CHL or pDLBCL" "CHL or pDLBCL"
## [9] "CHL or pDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "mDLBCL"
## [13] "mDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "CHL or pDLBCL"
## [17] "CHL or pDLBCL" "mDLBCL" "mDLBCL" "mDLBCL"
## [21] "mDLBCL" "CHL or pDLBCL" "mDLBCL" "CHL or pDLBCL"
## [25] "CHL or pDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "mDLBCL"
## [29] "mDLBCL" "mDLBCL" "mDLBCL" "mDLBCL"
## [33] "mDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "mDLBCL"
## [37] "mDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "CHL or pDLBCL"
## [41] "CHL or pDLBCL" "CHL or pDLBCL" "CHL or pDLBCL" "mDLBCL"
## [45] "mDLBCL" "mDLBCL" "CHL or pDLBCL"table(diagnosis)## diagnosis
## CHL or pDLBCL mDLBCL
## 27 20We are going to see if the PTPRD gene can predict diagnosis with a 2 class model, and if the BCL2 gene can predict gender of a 2 class model within all samples.
colnames(topGenes)## [1] "ID" "pDLBCL" "CHL"
## [4] "pDLBCL.1" "mDLBCL" "CHL.1"
## [7] "mDLBCL.1" "pDLBCL.2" "CHL.2"
## [10] "CHL.3" "CHL.4" "CHL.5"
## [13] "mDLBCL.2" "mDLBCL.3" "CHL.6"
## [16] "CHL.7" "pDLBCL.3" "CHL.8"
## [19] "mDLBCL.4" "mDLBCL.5" "mDLBCL.6"
## [22] "mDLBCL.7" "CHL.9" "mDLBCL.8"
## [25] "CHL.10" "CHL.11" "CHL.12"
## [28] "CHL.13" "mDLBCL.9" "mDLBCL.10"
## [31] "mDLBCL.11" "mDLBCL.12" "mDLBCL.13"
## [34] "mDLBCL.14" "pDLBCL.4" "pDLBCL.5"
## [37] "mDLBCL.15" "mDLBCL.16" "CHL.14"
## [40] "pDLBCL.6" "pDLBCL.7" "CHL.15"
## [43] "CHL.16" "CHL.17" "mDLBCL.17"
## [46] "mDLBCL.18" "mDLBCL.19" "CHL.18"
## [49] "CHL_mean" "pDLBCL_mean" "mDLBCL_mean"
## [52] "CHL_x_mean" "mDLBCL_x_mean" "pDLBCL_x_mean"
## [55] "CHL_y_mean" "mDLBCL_y_mean" "pDLBCL_y_mean"
## [58] "CHL_young72_mean" "mDLBCL_young72_mean" "pDLBCL_young72_mean"
## [61] "CHL_old" "mDLBCL_old" "pDLBCL_old"
## [64] "CHL_median" "mDLBCL_median" "pDLBCL_median"
## [67] "CHL_x_median" "mDLBCL_x_median" "pDLBCL_x_median"
## [70] "CHL_y_median" "mDLBCL_y_median" "pDLBCL_y_median"
## [73] "CHL_young72_median" "mDLBCL_young72_median" "pDLBCL_young72_median"
## [76] "CHL_old72_median" "mDLBCL_old72_median" "pDLBCL_old72_median"
## [79] "CHL_change" "pDLBCL_change" "mDLBCL_change"
## [82] "CHL_x_change" "CHL_y_change" "pDLBCL_x_change"
## [85] "pDLBCL_y_change" "mDLBCL_x_change" "mDLBCL_y_change"
## [88] "CHL_old72_change" "CHL_young72_change" "pDLBCL_old_change"
## [91] "pDLBCL_young72_change" "mDLBCL_young72_change" "mDLBCL_old72_change"
## [94] "SPOT_ID.1" "Gene_ID" "importance"BCL2 <- topGenes[grep('BCL2', topGenes$Gene_ID),c(2:48,95)]
PTPRD<- topGenes[grep('PTPRD', topGenes$Gene_ID),c(2:48,95)]PTPRD## pDLBCL CHL pDLBCL.1 mDLBCL CHL.1 mDLBCL.1 pDLBCL.2 CHL.2
## 22 3.685317 3.67643 3.148372 3.455512 4.022412 3.541898 3.398471 3.771869
## CHL.3 CHL.4 CHL.5 mDLBCL.2 mDLBCL.3 CHL.6 CHL.7 pDLBCL.3
## 22 3.356006 3.531764 4.031001 3.221535 3.692095 3.412819 3.451064 2.983141
## CHL.8 mDLBCL.4 mDLBCL.5 mDLBCL.6 mDLBCL.7 CHL.9 mDLBCL.8 CHL.10
## 22 4.32982 3.077683 3.609745 3.551329 3.633576 3.063946 3.638433 3.289788
## CHL.11 CHL.12 CHL.13 mDLBCL.9 mDLBCL.10 mDLBCL.11 mDLBCL.12 mDLBCL.13
## 22 3.486482 3.592392 3.67398 3.394398 4.003065 3.024652 2.729431 3.280114
## mDLBCL.14 pDLBCL.4 pDLBCL.5 mDLBCL.15 mDLBCL.16 CHL.14 pDLBCL.6 pDLBCL.7
## 22 3.446065 3.11189 3.248538 2.647033 3.586893 3.981202 3.500345 3.130425
## CHL.15 CHL.16 CHL.17 mDLBCL.17 mDLBCL.18 mDLBCL.19 CHL.18 Gene_ID
## 22 3.229043 3.55118 3.628847 3.120526 3.477699 3.912454 3.289102 PTPRDPTPRD_t <- data.frame(t(PTPRD[1:47]))
colnames(PTPRD_t) <- "PTPRD"
PTPRD_t$class <- as.factor(diagnosis)
paged_table(PTPRD_t)test the 2 class model with PTPRD gene that is another gene along 9p24.1 loci of high variation in CHL.
set.seed(123)
inTrain <- sample(1:47,.8*47)
training <- PTPRD_t[inTrain,]
testing <- PTPRD_t[-inTrain,]
table(training$class)##
## CHL or pDLBCL mDLBCL
## 21 16table(testing$class)##
## CHL or pDLBCL mDLBCL
## 6 4rf_PTPRD <- randomForest(training[1],training$class, ntree=5000, confusion=T)
rf_PTPRD$confusion## CHL or pDLBCL mDLBCL class.error
## CHL or pDLBCL 8 13 0.6190476
## mDLBCL 13 3 0.8125000Not very good at predicting the class in a 2 class model with high error. Lets see how well the model does on predicting the hold out set.
prediction_PTPRD <- predict(rf_PTPRD,testing)
result <- data.frame(predicted=prediction_PTPRD, actual=testing$class)
result## predicted actual
## pDLBCL mDLBCL CHL or pDLBCL
## CHL CHL or pDLBCL CHL or pDLBCL
## mDLBCL.1 CHL or pDLBCL mDLBCL
## mDLBCL.6 CHL or pDLBCL mDLBCL
## mDLBCL.8 mDLBCL mDLBCL
## CHL.10 CHL or pDLBCL CHL or pDLBCL
## mDLBCL.13 CHL or pDLBCL mDLBCL
## pDLBCL.7 mDLBCL CHL or pDLBCL
## CHL.17 mDLBCL CHL or pDLBCL
## CHL.18 CHL or pDLBCL CHL or pDLBCLNot very good as well, There were 6/10 incorrect for 40% accuracy over all. That is 3/6 for 50% accuracy in the CHL or pDLBCL class, and a 1/4 for 25% accuracy in the mDLBCL class.
Turns out that the PTPRD gene isn’t very good at predicting the class of lymphoma.
Lets now see if BCL2 is good at predicting gender.
BCL2_t <- data.frame(t(BCL2[1:47]))
colnames(BCL2_t) <- 'BCL2'
BCL2_t$class <- as.factor(gender)
paged_table(BCL2_t)table(BCL2_t$class)##
## female male
## 12 35There are nearly 3 x the males as there are females.
set.seed(123)
inTrain <- sample(1:47, .8*47)
training <- BCL2_t[inTrain,]
testing <- BCL2_t[-inTrain,]
table(training$class)##
## female male
## 9 28table(testing$class)##
## female male
## 3 7rf_BCL2 <- randomForest(training[1],training$class, mtry=1, ntree=5000, confusion=T)
rf_BCL2$confusion## female male class.error
## female 2 7 0.7777778
## male 6 22 0.2142857The female had a 22% accuracy while the males were predicted with 78% accuracy in the training model. Lets see how well it predicts the hold out 20% of samples by gender.
predict_gender <- predict(rf_BCL2, testing)
result <- data.frame(prediction=predict_gender, actual=testing$class)
result## prediction actual
## pDLBCL male male
## CHL male male
## mDLBCL.1 male female
## mDLBCL.6 female male
## mDLBCL.8 male male
## CHL.10 male female
## mDLBCL.13 male female
## pDLBCL.7 male male
## CHL.17 male male
## CHL.18 male maleNot too bad. It scored 6/10 correct with 60% accuracy in predicting gender, while 4/10 were incorrectly predicted. females were all incorrectly predicted with 0/3 or 0% accuracy, while 6/7 males were predicted correctly with 85% accuracy. It could be that BCL2 is a gene more associated with age. But could also be that there were 3x more males to train model on than females with 1/3 as many male samples.
Now we can leave the study genes alone that looked like they might be more relevant to gender or age group within or exclusive to the standard classification of large B-cell lymphoma.
Lets see by gender if we can get better at predicting class of lymphoma if we use only the males or females. And the same for the age group.
df <- topGenes[,c(2:48,95)]
males_df <- df[,c(males,48)]
CHL_m <- grep('CHL', colnames(males_df))
pDLBCL_m <- grep('pDLBCL', colnames(males_df))
mDLBCL_m <- grep('mDLBCL', colnames(males_df))
dx_m <- 'dx'
dx_m[CHL_m] <- 'CHL'
dx_m[pDLBCL_m] <- 'pDLBCL'
dx_m[mDLBCL_m] <- 'mDLBCL'
dx_m## [1] "pDLBCL" "CHL" "pDLBCL" "mDLBCL" "CHL" "CHL" "CHL" "CHL"
## [9] "CHL" "mDLBCL" "CHL" "CHL" "mDLBCL" "mDLBCL" "mDLBCL" "CHL"
## [17] "mDLBCL" "CHL" "CHL" "CHL" "mDLBCL" "mDLBCL" "mDLBCL" "mDLBCL"
## [25] "mDLBCL" "mDLBCL" "mDLBCL" "CHL" "pDLBCL" "pDLBCL" "CHL" "mDLBCL"
## [33] "mDLBCL" "mDLBCL" "CHL"paged_table(males_df)Lets grep genes for list of genes in ‘and males’ from topGenes$importance
male_gene_index <- grep('and male', topGenes$importance)
genes_m <- topGenes$Gene_ID[male_gene_index]
genes_m## [1] "SPRR1B" "SMPX" "MAL2" "LOC389834" "FABP4" "DSG3"
## [7] "CT45A6" "CT45A10" "CLDN10" "CHIT1"The male data set of genes of importance to predict diagnosis of the 3 standard classes.
males_dx_df <- males_df[males_df$Gene_ID %in% genes_m,]
males_dx_df## pDLBCL CHL pDLBCL.1 mDLBCL CHL.1 CHL.2 CHL.3 CHL.4
## 10 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 11 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 12 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 13 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 14 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 15 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 16 2.127182 2.788845 2.115515 2.305325 2.191573 2.005831 2.210159 2.185680
## 35 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 36 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 37 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 38 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 39 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 40 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 42 2.205227 2.763608 4.581370 3.330021 3.416666 3.257589 4.726385 3.378047
## 53 3.326863 2.709651 4.343689 2.320567 3.256265 2.106494 2.495920 2.629729
## 54 3.326863 2.709651 4.343689 2.320567 3.256265 2.106494 2.495920 2.629729
## 55 3.326863 2.709651 4.343689 2.320567 3.256265 2.106494 2.495920 2.629729
## 57 3.231147 2.498076 2.099723 1.925029 2.183705 2.090934 2.366762 2.516796
## 58 3.231147 2.498076 2.099723 1.925029 2.183705 2.090934 2.366762 2.516796
## 59 3.231147 2.498076 2.099723 1.925029 2.183705 2.090934 2.366762 2.516796
## 60 3.231147 2.498076 2.099723 1.925029 2.183705 2.090934 2.366762 2.516796
## 64 2.154457 2.088324 2.003630 1.840714 2.681566 1.651746 1.885876 2.007413
## 65 2.154457 2.088324 2.003630 1.840714 2.681566 1.651746 1.885876 2.007413
## 66 2.154457 2.088324 2.003630 1.840714 2.681566 1.651746 1.885876 2.007413
## 67 2.032138 1.850398 1.951956 1.826161 2.092506 1.812784 1.883707 1.923404
## 68 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 69 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 70 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 71 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 72 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 73 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 74 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 77 3.380794 3.635628 3.882431 4.293454 3.373098 7.227211 3.830759 4.864639
## CHL.5 mDLBCL.2 CHL.7 CHL.8 mDLBCL.4 mDLBCL.5 mDLBCL.6 CHL.9
## 10 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 11 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 12 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 13 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 14 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 15 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 16 2.006926 2.616547 2.273527 2.173246 2.175879 2.317447 2.647874 2.182016
## 35 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 36 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 37 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 38 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 39 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 40 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 42 3.271699 3.414658 2.732309 5.116151 4.316409 3.417756 4.541609 4.176644
## 53 3.101723 2.164108 2.029822 2.960409 8.133783 4.324922 2.072142 2.943281
## 54 3.101723 2.164108 2.029822 2.960409 8.133783 4.324922 2.072142 2.943281
## 55 3.101723 2.164108 2.029822 2.960409 8.133783 4.324922 2.072142 2.943281
## 57 2.982946 2.742360 2.321052 2.362872 3.270014 2.317579 2.142324 2.236284
## 58 2.982946 2.742360 2.321052 2.362872 3.270014 2.317579 2.142324 2.236284
## 59 2.982946 2.742360 2.321052 2.362872 3.270014 2.317579 2.142324 2.236284
## 60 2.982946 2.742360 2.321052 2.362872 3.270014 2.317579 2.142324 2.236284
## 64 2.090433 1.816739 2.177835 2.039986 2.055238 2.076733 1.965607 1.863729
## 65 2.090433 1.816739 2.177835 2.039986 2.055238 2.076733 1.965607 1.863729
## 66 2.090433 1.816739 2.177835 2.039986 2.055238 2.076733 1.965607 1.863729
## 67 1.946816 1.869453 1.692387 2.056874 1.898575 2.222977 2.296827 1.822425
## 68 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 69 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 70 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 71 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 72 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 73 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 74 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 77 2.838445 7.170012 5.561294 3.625181 3.818218 4.726057 5.893514 3.851825
## mDLBCL.8 CHL.11 CHL.12 CHL.13 mDLBCL.9 mDLBCL.10 mDLBCL.11 mDLBCL.12
## 10 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 11 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 12 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 13 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 14 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 15 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 16 2.301481 2.521647 2.230016 2.366452 2.123432 2.455331 2.081947 2.246569
## 35 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 36 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 37 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 38 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 39 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 40 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 42 4.550476 3.079089 4.669479 4.756083 2.395022 4.620422 3.699957 3.192031
## 53 2.679304 3.052082 6.836376 2.671998 5.904312 2.828835 2.462488 2.318022
## 54 2.679304 3.052082 6.836376 2.671998 5.904312 2.828835 2.462488 2.318022
## 55 2.679304 3.052082 6.836376 2.671998 5.904312 2.828835 2.462488 2.318022
## 57 3.005478 2.089293 1.976170 2.634121 2.263726 2.556427 2.214243 2.252333
## 58 3.005478 2.089293 1.976170 2.634121 2.263726 2.556427 2.214243 2.252333
## 59 3.005478 2.089293 1.976170 2.634121 2.263726 2.556427 2.214243 2.252333
## 60 3.005478 2.089293 1.976170 2.634121 2.263726 2.556427 2.214243 2.252333
## 64 2.260826 1.915579 1.655303 1.910050 1.951227 2.659688 1.857070 1.821691
## 65 2.260826 1.915579 1.655303 1.910050 1.951227 2.659688 1.857070 1.821691
## 66 2.260826 1.915579 1.655303 1.910050 1.951227 2.659688 1.857070 1.821691
## 67 1.916119 1.923644 1.897072 1.688631 1.913212 2.775583 1.664943 1.767089
## 68 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 69 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 70 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 71 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 72 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 73 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 74 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 77 3.786893 7.545068 3.734721 5.743182 6.984887 3.131724 3.553398 4.016649
## mDLBCL.14 mDLBCL.15 mDLBCL.16 CHL.14 pDLBCL.6 pDLBCL.7 CHL.17 mDLBCL.17
## 10 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 11 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 12 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 13 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 14 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 15 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 16 2.191737 2.195214 2.149873 2.361694 4.324170 2.138477 2.169210 2.250016
## 35 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 36 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 37 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 38 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 39 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 40 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 42 3.589921 4.103315 3.296677 2.540951 4.194828 4.775434 5.113265 2.929154
## 53 2.717477 2.774380 5.162850 2.610332 2.285040 3.017648 3.893279 3.168983
## 54 2.717477 2.774380 5.162850 2.610332 2.285040 3.017648 3.893279 3.168983
## 55 2.717477 2.774380 5.162850 2.610332 2.285040 3.017648 3.893279 3.168983
## 57 2.309280 5.858629 2.451799 2.559516 2.425482 2.273718 2.262537 3.537996
## 58 2.309280 5.858629 2.451799 2.559516 2.425482 2.273718 2.262537 3.537996
## 59 2.309280 5.858629 2.451799 2.559516 2.425482 2.273718 2.262537 3.537996
## 60 2.309280 5.858629 2.451799 2.559516 2.425482 2.273718 2.262537 3.537996
## 64 2.163669 1.847283 8.501844 1.996380 1.829853 1.963556 1.733200 1.668057
## 65 2.163669 1.847283 8.501844 1.996380 1.829853 1.963556 1.733200 1.668057
## 66 2.163669 1.847283 8.501844 1.996380 1.829853 1.963556 1.733200 1.668057
## 67 2.122229 2.192730 6.989247 1.590206 1.772256 1.910803 1.678924 1.838411
## 68 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 69 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 70 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 71 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 72 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 73 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 74 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 77 3.741841 4.220294 6.819141 3.649414 4.733757 3.542088 4.945895 3.566518
## mDLBCL.18 mDLBCL.19 CHL.18 Gene_ID
## 10 7.354649 3.027889 2.920757 SPRR1B
## 11 7.354649 3.027889 2.920757 SPRR1B
## 12 7.354649 3.027889 2.920757 SPRR1B
## 13 7.354649 3.027889 2.920757 SPRR1B
## 14 7.354649 3.027889 2.920757 SPRR1B
## 15 7.354649 3.027889 2.920757 SPRR1B
## 16 2.203880 2.064499 2.287019 SMPX
## 35 5.041233 3.994581 1.797710 MAL2
## 36 5.041233 3.994581 1.797710 MAL2
## 37 5.041233 3.994581 1.797710 MAL2
## 38 5.041233 3.994581 1.797710 MAL2
## 39 5.041233 3.994581 1.797710 MAL2
## 40 5.041233 3.994581 1.797710 MAL2
## 42 2.662405 4.044133 4.609380 LOC389834
## 53 2.633441 2.592530 2.795749 FABP4
## 54 2.633441 2.592530 2.795749 FABP4
## 55 2.633441 2.592530 2.795749 FABP4
## 57 6.522668 2.378329 2.074662 DSG3
## 58 6.522668 2.378329 2.074662 DSG3
## 59 6.522668 2.378329 2.074662 DSG3
## 60 6.522668 2.378329 2.074662 DSG3
## 64 1.835034 2.896035 1.905412 CT45A6
## 65 1.835034 2.896035 1.905412 CT45A6
## 66 1.835034 2.896035 1.905412 CT45A6
## 67 1.672015 2.331127 1.955676 CT45A10
## 68 4.413599 3.117395 2.730450 CLDN10
## 69 4.413599 3.117395 2.730450 CLDN10
## 70 4.413599 3.117395 2.730450 CLDN10
## 71 4.413599 3.117395 2.730450 CLDN10
## 72 4.413599 3.117395 2.730450 CLDN10
## 73 4.413599 3.117395 2.730450 CLDN10
## 74 4.413599 3.117395 2.730450 CLDN10
## 77 4.414295 3.257368 7.358518 CHIT1males_DF <- males_dx_df[!duplicated(males_dx_df$Gene_ID),]
males_DF## pDLBCL CHL pDLBCL.1 mDLBCL CHL.1 CHL.2 CHL.3 CHL.4
## 10 2.924230 3.272495 3.133263 3.118928 2.869639 3.151751 2.464758 2.683687
## 16 2.127182 2.788845 2.115515 2.305325 2.191573 2.005831 2.210159 2.185680
## 35 1.890996 2.975367 2.128983 1.633711 2.030586 1.854145 1.863012 1.694038
## 42 2.205227 2.763608 4.581370 3.330021 3.416666 3.257589 4.726385 3.378047
## 53 3.326863 2.709651 4.343689 2.320567 3.256265 2.106494 2.495920 2.629729
## 57 3.231147 2.498076 2.099723 1.925029 2.183705 2.090934 2.366762 2.516796
## 64 2.154457 2.088324 2.003630 1.840714 2.681566 1.651746 1.885876 2.007413
## 67 2.032138 1.850398 1.951956 1.826161 2.092506 1.812784 1.883707 1.923404
## 68 3.426300 3.508524 3.276908 2.942805 4.173509 3.400262 2.909614 3.068524
## 77 3.380794 3.635628 3.882431 4.293454 3.373098 7.227211 3.830759 4.864639
## CHL.5 mDLBCL.2 CHL.7 CHL.8 mDLBCL.4 mDLBCL.5 mDLBCL.6 CHL.9
## 10 2.666463 2.706390 3.283510 3.634387 2.826371 2.743203 2.755176 2.645335
## 16 2.006926 2.616547 2.273527 2.173246 2.175879 2.317447 2.647874 2.182016
## 35 2.676579 1.960693 1.803915 2.111299 1.957177 1.784722 1.676013 1.964451
## 42 3.271699 3.414658 2.732309 5.116151 4.316409 3.417756 4.541609 4.176644
## 53 3.101723 2.164108 2.029822 2.960409 8.133783 4.324922 2.072142 2.943281
## 57 2.982946 2.742360 2.321052 2.362872 3.270014 2.317579 2.142324 2.236284
## 64 2.090433 1.816739 2.177835 2.039986 2.055238 2.076733 1.965607 1.863729
## 67 1.946816 1.869453 1.692387 2.056874 1.898575 2.222977 2.296827 1.822425
## 68 3.524943 2.983981 2.801732 3.298979 3.179837 2.920549 3.096044 3.157164
## 77 2.838445 7.170012 5.561294 3.625181 3.818218 4.726057 5.893514 3.851825
## mDLBCL.8 CHL.11 CHL.12 CHL.13 mDLBCL.9 mDLBCL.10 mDLBCL.11 mDLBCL.12
## 10 2.847968 2.926479 2.967611 2.889223 2.912622 6.387654 2.730479 2.638690
## 16 2.301481 2.521647 2.230016 2.366452 2.123432 2.455331 2.081947 2.246569
## 35 1.812762 1.806734 1.650264 1.843799 2.344507 3.004668 2.128840 1.879105
## 42 4.550476 3.079089 4.669479 4.756083 2.395022 4.620422 3.699957 3.192031
## 53 2.679304 3.052082 6.836376 2.671998 5.904312 2.828835 2.462488 2.318022
## 57 3.005478 2.089293 1.976170 2.634121 2.263726 2.556427 2.214243 2.252333
## 64 2.260826 1.915579 1.655303 1.910050 1.951227 2.659688 1.857070 1.821691
## 67 1.916119 1.923644 1.897072 1.688631 1.913212 2.775583 1.664943 1.767089
## 68 3.074838 2.783793 3.051870 2.947354 2.974613 2.991029 2.951059 5.146060
## 77 3.786893 7.545068 3.734721 5.743182 6.984887 3.131724 3.553398 4.016649
## mDLBCL.14 mDLBCL.15 mDLBCL.16 CHL.14 pDLBCL.6 pDLBCL.7 CHL.17 mDLBCL.17
## 10 3.044227 7.408137 3.460930 3.881796 2.568014 2.787795 3.461040 4.147761
## 16 2.191737 2.195214 2.149873 2.361694 4.324170 2.138477 2.169210 2.250016
## 35 2.167296 5.255127 1.764277 1.652628 1.855264 1.535954 1.982091 3.926928
## 42 3.589921 4.103315 3.296677 2.540951 4.194828 4.775434 5.113265 2.929154
## 53 2.717477 2.774380 5.162850 2.610332 2.285040 3.017648 3.893279 3.168983
## 57 2.309280 5.858629 2.451799 2.559516 2.425482 2.273718 2.262537 3.537996
## 64 2.163669 1.847283 8.501844 1.996380 1.829853 1.963556 1.733200 1.668057
## 67 2.122229 2.192730 6.989247 1.590206 1.772256 1.910803 1.678924 1.838411
## 68 2.991923 8.367649 3.030007 3.324361 2.791785 2.734316 3.126265 5.351248
## 77 3.741841 4.220294 6.819141 3.649414 4.733757 3.542088 4.945895 3.566518
## mDLBCL.18 mDLBCL.19 CHL.18 Gene_ID
## 10 7.354649 3.027889 2.920757 SPRR1B
## 16 2.203880 2.064499 2.287019 SMPX
## 35 5.041233 3.994581 1.797710 MAL2
## 42 2.662405 4.044133 4.609380 LOC389834
## 53 2.633441 2.592530 2.795749 FABP4
## 57 6.522668 2.378329 2.074662 DSG3
## 64 1.835034 2.896035 1.905412 CT45A6
## 67 1.672015 2.331127 1.955676 CT45A10
## 68 4.413599 3.117395 2.730450 CLDN10
## 77 4.414295 3.257368 7.358518 CHIT1males_DF_t <- data.frame(t(males_DF[,1:35]))
colnames(males_DF_t) <- males_DF$Gene_ID
males_DF_t$class <- as.factor(dx_m)
paged_table(males_DF_t)Now lets see how well the top genes over or under estimated in males can predict the standard class of 3 classes of lymphoma.
set.seed(123)
inTrain <- sample(1:35,.8*35)
training <- males_DF_t[inTrain,]
testing <- males_DF_t[-inTrain,]
table(training$class)##
## CHL mDLBCL pDLBCL
## 11 13 4table(testing$class)##
## CHL mDLBCL pDLBCL
## 4 3 0rf_males <- randomForest(training[1:10], training$class, mtry=3, ntree=5000, confusion=T)
rf_males$confusion## CHL mDLBCL pDLBCL class.error
## CHL 4 7 0 0.6363636
## mDLBCL 5 7 1 0.4615385
## pDLBCL 3 1 0 1.0000000Not very good for the pDLBCL class with 0% accuracy, but better at CHL with 36% accuracy, and even better with the mDLBCL class with 53% accuracy.
Lets see how well these genes predict the hold out 20% samples.
predicted_males <- predict(rf_males,testing)
result <- data.frame(predicted= predicted_males, actual=testing$class)
result## predicted actual
## CHL mDLBCL CHL
## CHL.2 mDLBCL CHL
## CHL.8 CHL CHL
## CHL.9 CHL CHL
## mDLBCL.8 CHL mDLBCL
## mDLBCL.12 mDLBCL mDLBCL
## mDLBCL.19 mDLBCL mDLBCLThe pDLBCL class was missing from the testing set. It had 7 samples to predict correctly but only predicted 4/7 correct, just over 50% accuracy. It predicted 2/3 mDLBCL correct with 66% accuracy, and 2/4 CHL for 50% accuracy. The male genes are not good genes to predict class of lymphoma, but it could also be using this measure of avg/median could be a terrible tool to use in finding top genes. Another way would be the more common PCA or principal component analysis. But we haven’t gotten too far along in testing these genes.
Lets see how well these genes can predict the class in all samples of males and females. We can recycle the df dataframe of 87 rows and 48 columns of 47 samples same order and the gene ID column.
DF47_maleGenes <- df[df$Gene_ID %in% genes_m,]
DF47_mg <- DF47_maleGenes[!duplicated(DF47_maleGenes$Gene_ID),]
DF47_mg_t <- data.frame(t(DF47_mg[,1:47]))
colnames(DF47_mg_t) <- DF47_mg$Gene_ID
DF47_mg_t$class <- 'diagnosis'
DF47_mg_t$class[CHL] <- "CHL"
DF47_mg_t$class[pDLBCL] <- "pDLBCL"
DF47_mg_t$class[mDLBCL] <- "mDLBCL"
DF47_mg_t$class <- as.factor(DF47_mg_t$class)
paged_table(DF47_mg_t)set.seed(123)
inTrain <- sample(1:47, .8*47)
training <- DF47_mg_t[inTrain,]
testing <- DF47_mg_t[-inTrain,]
table(training$class)##
## CHL mDLBCL pDLBCL
## 15 16 6table(testing$class)##
## CHL mDLBCL pDLBCL
## 4 4 2rf_mg47 <- randomForest(training[1:10], training$class, mtry=3, ntree=5000, confusion=T)
rf_mg47$confusion## CHL mDLBCL pDLBCL class.error
## CHL 6 9 0 0.6
## mDLBCL 8 8 0 0.5
## pDLBCL 2 4 0 1.0prediction_mg47 <- predict(rf_mg47, testing)
result <- data.frame(predicted=prediction_mg47, actual=testing$class)
result## predicted actual
## pDLBCL CHL pDLBCL
## CHL mDLBCL CHL
## mDLBCL.1 CHL mDLBCL
## mDLBCL.6 CHL mDLBCL
## mDLBCL.8 CHL mDLBCL
## CHL.10 CHL CHL
## mDLBCL.13 mDLBCL mDLBCL
## pDLBCL.7 CHL pDLBCL
## CHL.17 CHL CHL
## CHL.18 CHL CHLThese genes are terrible for prediction in training and the model. So we can forget about the male top genes This model had 10 samples to predict but only predicted 4/10 correct with 40% accuracy, but it does show that the pDLBCL samples were incorrectly predicted as CHL in males for all pDLBCL samples, and that only half the CHL samples were predicted correctly. But the mDLBCL classes also predicted more samples of that class as CHL too.
From here, I think we should switch it up and no longer use the demographics of the age or gender to make predictions of how well the genes from those demographics with higher or lower values of group average divided by group median.
We can also see if the genes not duplicated in the groups and subgroups can predict the class of 3 and then 4, or how the duplicated genes can predict the class of 3 and then 4. Lets look at the duplicated genes again and non duplicated. Some genes are in 5 groups.
duplicates <- df[duplicated(df$Gene_ID),"Gene_ID"]
du <- unique(duplicates)
du## [1] "SPRR2A" "SPRR1B" "S100A7" "MUC7" "MAL2" "GCNT4" "FABP4" "DSG3"
## [9] "DMKN" "CT45A6" "CLDN10" "CLCA2"notDuplicated <- df[-which(df$Gene_ID %in% du),"Gene_ID"]
noDu <- unique(notDuplicated)
noDu## [1] "UTS2B" "USP30" "TMPRSS11A" "TACSTD2" "SPRR2D"
## [6] "SMPX" "SCRG1" "S100A12" "RGS13" "PTPRD"
## [11] "PDCD1LG2" "PAX5" "NOP10" "NM_201998" "NM_014117"
## [16] "NM_001040033" "NM_001033556" "MUM1" "MGST1" "MGAM2"
## [21] "LUM" "LOC389834" "KRT4" "KLRB1" "KIAA0825"
## [26] "JCHAIN" "IL7R" "IL23R" "IFNG" "IDO1"
## [31] "ERP44" "DDX3Y" "CT45A10" "CHIT1" "CD5"
## [36] "CD274" "CCL13" "BCL6" "BCL2" "85444"
## [41] "51633" "LDHA" "LDHC" "LDHD"The duplicates is an idea to try but the not duplicated genes never shows the right amount, because we should have 87 genes but we get 43 genes that aren’t in the list of 31 duplicated genes because that adds to 74. There are 13 genes not accounted for.
For the remainder we will check the duplicate genes on predicting 3 and 4 classes of lymphoma, and then work down with predicting the class for females only, we did the males already, then the class by age of 72 or younger vs older than 72 years of age. So really just testing females only on class, then young on class, and old on class. Then we will test the separate genders on the new 4 classes, followed by the separate age groups on class of the 4 new classes.
So far the study genes scored the best on the 3 class model with 70% accuracy, but only 30% accuracy on the 4 new class model. We haven’t done any predictions on the 4 class model yet. We only got to the males on class with only male genes to predict class in the samples that were only males.
We also saw that BCL2 scored 60% accuracy in predicting gender out of all samples, but PTPRD scored 60% in predicting a 2 class model of combine CHL or pDLBCL vs mDLBCL regardless of gender or age.
du_dx <- topGenes[topGenes$Gene_ID %in% du,c(2:48,95)]
du_dx <- du_dx[!duplicated(du_dx$Gene_ID),]
paged_table(du_dx)Lets see how well the duplicated genes in all the genes of the data are at predicting the 3 class then the 4 class model.
Lets add the class vector of the 3 classes to the labels_t table because we will be using it.
labels_t$class3 <- '3 classes'
labels_t$class3[CHL] <- "CHL"
labels_t$class3[mDLBCL] <- "mDLBCL"
labels_t$class3[pDLBCL] <- "pDLBCL"
paged_table(labels_t)du_dx_t <- data.frame(t(du_dx[1:47]))
colnames(du_dx_t) <- du_dx$Gene_ID
du_dx_t$class <- as.factor(labels_t$class3)
paged_table(du_dx_t)We have our matrix of duplicated genes, now lets see how well they perform.
set.seed(123)
inTrain <- sample(1:47, .8*47)
training <- du_dx_t[inTrain,]
testing <- du_dx_t[-inTrain,]
table(training$class)##
## CHL mDLBCL pDLBCL
## 15 16 6table(testing$class)##
## CHL mDLBCL pDLBCL
## 4 4 2rf_duplicates <- randomForest(training[1:12], training$class, mtry=4, ntree=5000, confusion=T)
rf_duplicates$confusion## CHL mDLBCL pDLBCL class.error
## CHL 10 5 0 0.3333333
## mDLBCL 6 9 1 0.4375000
## pDLBCL 0 6 0 1.0000000In training, the model scored very poor on all 6 pDLBCL samples all misclassified as mDLBCL. There were 10/15 CHL samples classified correctly but the other 5 were misclassified as mDLBCL. The mDLBCL class identified 9/17 samples correctly but 6/17 as CHL and 1/17 as pDLBCL.
Lets see how well the hold out validation set is predicted.
prediction_duplicates <- predict(rf_duplicates,testing)
results <- data.frame(predicted = prediction_duplicates, actual = testing$class)
results## predicted actual
## pDLBCL mDLBCL pDLBCL
## CHL mDLBCL CHL
## mDLBCL.1 CHL mDLBCL
## mDLBCL.6 CHL mDLBCL
## mDLBCL.8 mDLBCL mDLBCL
## CHL.10 CHL CHL
## mDLBCL.13 mDLBCL mDLBCL
## pDLBCL.7 CHL pDLBCL
## CHL.17 CHL CHL
## CHL.18 CHL CHLThe model scored terribly. There were 10 samples to predict and only 4/10 predicted correctly. The mDLBCL had 2/4 correct with the other 2 incorrectly identified as CHL. The CHL had 3/4 correctly identified, but the 1/4 was incorrectly predicted to be mDLBCL. The pDLBCL was 0/2 predicted correct and each of the samples incorrectly identified as mDLBCL and the other as CHL.
The duplicate genes aren’t good at identifying the 3 classes of lymphoma, but lets see how well they do in predicting the 4 classes of the proposed groups of lymphoma.
du_dx_t$class <- as.factor(labels_t$group)
du_dx_t$class[29] <- as.factor("IS") #the machine won't take NAs and it was mDLBCL that is IS in new class
paged_table(du_dx_t)set.seed(123)
inTrain <- sample(1:47, .8*47)
training <- du_dx_t[inTrain,]
testing <- du_dx_t[-inTrain,]
table(training$class)##
## 9p24.1-H IFNG-H IFNG-L IS
## 6 4 17 10table(testing$class)##
## 9p24.1-H IFNG-H IFNG-L IS
## 3 5 1 1rf_du_class4 <- randomForest(training[1:12], training$class, mtry=4, ntree=5000, confusion=T)
rf_du_class4$confusion## 9p24.1-H IFNG-H IFNG-L IS class.error
## 9p24.1-H 0 0 4 2 1.0000000
## IFNG-H 0 0 3 1 1.0000000
## IFNG-L 1 0 14 2 0.1764706
## IS 0 1 7 2 0.8000000The training went terribly with the 9p24.1-H and IFNG-H both 0% accuracy and IS with 20% accuracy while IFNG-L scored 82% accuracy. This is the new class as a transition from pDLBCL to CHL. Lets see if it predicts better than this.
prediction_duClass4 <- predict(rf_du_class4,testing)
results <- data.frame(predicted = prediction_duClass4, actual = testing$class)
results## predicted actual
## pDLBCL IFNG-L IFNG-H
## CHL IS IFNG-L
## mDLBCL.1 IFNG-L 9p24.1-H
## mDLBCL.6 IFNG-L IS
## mDLBCL.8 IFNG-L IFNG-H
## CHL.10 IFNG-L 9p24.1-H
## mDLBCL.13 IFNG-L IFNG-H
## pDLBCL.7 IFNG-L IFNG-H
## CHL.17 IFNG-L 9p24.1-H
## CHL.18 IFNG-L IFNG-HWith the testing set the model predicted all the be IFNG-L or the transition class except 1 as the IS class for mDLBCL in immune senescence. It scored 0%. The IFNG-L class that there was only 1 of was misidentified as IS.
I was expecting some amazing results with this but the problem could be using the avg/median per group as a variability factor. Not any of these gene sets scored well on the class predictions, even the genes that were in the study.
The best model has been the study genes used in predicting the 3 class model with 70% accuracy and the 4 class model with 30% accuracy.
I re-ran all the code to get those genes from the study that performed the best in the 3 class model with 70% while others were 0-60% accuracy. It scored terrible in the 4 class model though, and so did the other gene sets.
genes_rs## [1] "PTPRD" "PDCD1LG2" "PAX5" "MUM1" "IFNG" "IDO1"
## [7] "ERP44" "CD5" "CD274" "BCL6" "BCL2" "LDHA"
## [13] "LDHC" "LDHD"Those are the genes to identify the 3 classes of lymphoma as CHL, mDLBCL, or pDLBCL. But when used as the genes from the research study, they do not predict the 4 class model well at all using a standard random forest classifier algorith.
I will leave this research analysis here. We know now that there is overlap between the large B-cell lymphomas with EBV in CHL, mDLBCL, and pDLBCL. It is likely there is a transition state because the genes of the study scored poor on the 4 class model that turns the 3 classes of these lymphomas into 4 classes. The EBV infection is a factor in all these samples and the study bases the finding from the immune senescence of aging that can turn deadly in the immune escape that lets the active EBV go undetected to do damage. We can say these lymphomas are EBV associated, and leave off the LDH genes that were not used to determine class in the study but for determining the latency type of EBV in the type of lymphoma from basic blood work.
We will add in only the genes that the study represented and reasoning in the next part.