Covid 19 blood samples of mild, severe, and healthy cases with 5 samples of different people each. NCBI datasource GSE164805. Files can be found at https://github.com/JanJanJan2018/covid19_2021analysis/upload and the official link to the source at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164805
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionPeripheral Blood Mononucleotide Cells or PBMC samples of healthy (5), mild (5), and severe (5).
samples <- read.csv('covid19caseTypeSamples.csv',sep=',', header=T, na.strings=c('',' ','NA'))
head(samples)## ID GSM5019817 GSM5019818 GSM5019819 GSM5019820
## 1 ASHG19LNC1A100055560V5 4.026114 2.332730 2.466728 2.540128
## 2 ASHG19AP1B142266208V5 6.098194 6.362773 6.314044 7.204741
## 3 ASHG19LNC1ABL100000340V5 7.672250 7.666406 7.803978 7.639394
## 4 ASHG19LNC1A114586415V5 3.979741 3.439878 3.213730 4.148296
## 5 ASHG19AP1B119650624V5 6.228602 6.292539 6.231822 6.672203
## 6 ASHG19AP1B127409724V5 8.774397 7.629270 8.488946 8.472281
## GSM5019821 GSM5019822 GSM5019823 GSM5019824 GSM5019825 GSM5019826 GSM5019827
## 1 2.535255 2.332686 2.350414 2.328666 2.339235 2.360941 2.814921
## 2 7.053378 6.657100 6.458480 6.677193 6.107985 6.446425 6.378113
## 3 7.279553 8.420305 7.845725 7.716493 8.412242 7.803641 8.704748
## 4 3.332558 3.855264 3.555929 2.328851 3.416486 3.359314 2.814921
## 5 6.753389 7.110841 6.708847 6.813066 6.922778 6.947409 5.893663
## 6 7.432321 7.933024 7.382453 6.737280 7.363980 7.691195 7.799064
## GSM5019828 GSM5019829 GSM5019830 GSM5019831
## 1 3.823082 2.620153 2.747991 2.333044
## 2 6.663142 7.671673 6.883828 7.530764
## 3 8.377483 7.920515 8.450972 8.088851
## 4 3.867367 3.350585 2.747991 3.258511
## 5 6.294101 6.141588 6.693083 7.286914
## 6 7.598433 5.253353 6.284809 5.310418colnames(samples)## [1] "ID" "GSM5019817" "GSM5019818" "GSM5019819" "GSM5019820"
## [6] "GSM5019821" "GSM5019822" "GSM5019823" "GSM5019824" "GSM5019825"
## [11] "GSM5019826" "GSM5019827" "GSM5019828" "GSM5019829" "GSM5019830"
## [16] "GSM5019831"meta information with gender and age of the sample ID number with the class type of healthy, mild, or severe
meta <- read.csv('covid19sampleMetaInformation.csv',sep=',',header=T,
na.strings=c('',' ','NA'))
row.names(meta) <- meta$sample_ID
meta <- meta[,-1]head(meta)## GSM5019817 GSM5019818 GSM5019819 GSM5019820 GSM5019821 GSM5019822
## case_type healthy_1 healthy_2 healthy_3 healthy_4 healthy_5 mild_1
## gender male male male male female male
## age 62 56 54 71 56 55
## GSM5019823 GSM5019824 GSM5019825 GSM5019826 GSM5019827 GSM5019828
## case_type mild_2 mild_3 mild_4 mild_5 severe_1 severe_2
## gender male male male female male male
## age 44 51 54 53 54 52
## GSM5019829 GSM5019830 GSM5019831
## case_type severe_3 severe_4 severe_5
## gender male male male
## age 73 51 60colnames(meta)## [1] "GSM5019817" "GSM5019818" "GSM5019819" "GSM5019820" "GSM5019821"
## [6] "GSM5019822" "GSM5019823" "GSM5019824" "GSM5019825" "GSM5019826"
## [11] "GSM5019827" "GSM5019828" "GSM5019829" "GSM5019830" "GSM5019831"Read in the platform data to merge the IDs of samples to their gene descriptions.
platform <- read.delim('GPL26963-20921.txt',sep='\t',header=T,
comment.char='#', na.strings=c('',' ','NA'))head(platform)## ID TRANSCRIPT_TYPE ACC ORF SOURCE BUILD CHROM STRAND
## 1 ASHGV40000072V5 lncRNA NR_027417 LOC644669 Refseq HG19 chr18 -
## 2 ASHGV40000162V5 lncRNA NR_037149 NME1-NME2 Refseq HG19 chr17 +
## 3 ASHGV40000243V5 lncRNA NR_130700 LOC728323 Refseq HG19 chr2 +
## 4 ASHGV40004835V5 lncRNA NR_130699 LOC728323 Refseq HG19 chr2 +
## 5 ASHGV40030421V5 lncRNA NR_130701 LOC728323 Refseq HG19 chr2 +
## 6 ASHGV40000318V5 lncRNA NR_046258 FAR2P2 Refseq HG19 chr2 -
## txStart txEnd GENE.DESCRIPTION
## 1 15313554 15325918 <NA>
## 2 49230896 49249105 <NA>
## 3 243030783 243102476 <NA>
## 4 243030783 243102476 <NA>
## 5 243030783 243102476 <NA>
## 6 131174325 131186119 <NA>
## SEQUENCE SPOT_ID
## 1 ATAGTAATCCAGAAGGAACATCTGAAGGAACACTTGATGAGGCTGCACCCTTGGCAGAAA <NA>
## 2 TTCTGCATACAAGTTGGCAGGACCATGGCCAACCTGGAGCGCACCTTCATCGCCATCAAG <NA>
## 3 CTGAGCACTGATACAAAGAAAGACAAACATCACCAAACCAATGCAGACCAAACCAATGCA <NA>
## 4 CAGCTGAGCACTGATACAAAGAAAGACAAACATCATATCTCTCTTGATTCTTAGTAACAA <NA>
## 5 TTAAATAGCGAAGATGGAGAAATACTCAATAATGAAGAGCATGAATATGCATCCAAAAAA <NA>
## 6 AGCAAAATGTGATTCCAGGTCTTGGCAACCTCTGAAATTCCAACTCCATTTGCGAGAGCT <NA>colnames(platform)## [1] "ID" "TRANSCRIPT_TYPE" "ACC" "ORF"
## [5] "SOURCE" "BUILD" "CHROM" "STRAND"
## [9] "txStart" "txEnd" "GENE.DESCRIPTION" "SEQUENCE"
## [13] "SPOT_ID"Keep only a few of the platform variables. The strand, chromosome number for linkage analysis on the same chromosome and strand direction as forward (+ assumed) and reverse (- assumed), and the sequence for copy number variations of the same gene, and also the ID to merge the gene information with the sample ID.The ACC is the ensemble transcript ID and the ORF variable or column is the gene name
genes <- platform[,c(1,3,4,7,8,12)]
head(genes)## ID ACC ORF CHROM STRAND
## 1 ASHGV40000072V5 NR_027417 LOC644669 chr18 -
## 2 ASHGV40000162V5 NR_037149 NME1-NME2 chr17 +
## 3 ASHGV40000243V5 NR_130700 LOC728323 chr2 +
## 4 ASHGV40004835V5 NR_130699 LOC728323 chr2 +
## 5 ASHGV40030421V5 NR_130701 LOC728323 chr2 +
## 6 ASHGV40000318V5 NR_046258 FAR2P2 chr2 -
## SEQUENCE
## 1 ATAGTAATCCAGAAGGAACATCTGAAGGAACACTTGATGAGGCTGCACCCTTGGCAGAAA
## 2 TTCTGCATACAAGTTGGCAGGACCATGGCCAACCTGGAGCGCACCTTCATCGCCATCAAG
## 3 CTGAGCACTGATACAAAGAAAGACAAACATCACCAAACCAATGCAGACCAAACCAATGCA
## 4 CAGCTGAGCACTGATACAAAGAAAGACAAACATCATATCTCTCTTGATTCTTAGTAACAA
## 5 TTAAATAGCGAAGATGGAGAAATACTCAATAATGAAGAGCATGAATATGCATCCAAAAAA
## 6 AGCAAAATGTGATTCCAGGTCTTGGCAACCTCTGAAATTCCAACTCCATTTGCGAGAGCTdata <- merge(platform, samples, by.x='ID', by.y='ID')
head(data)## ID TRANSCRIPT_TYPE ACC ORF SOURCE BUILD CHROM STRAND txStart
## 1 (+)E1A_r60_1 <NA> <NA> <NA> <NA> <NA> <NA> <NA> NA
## 2 (+)E1A_r60_3 <NA> <NA> <NA> <NA> <NA> <NA> <NA> NA
## 3 (+)E1A_r60_a104 <NA> <NA> <NA> <NA> <NA> <NA> <NA> NA
## 4 (+)E1A_r60_a107 <NA> <NA> <NA> <NA> <NA> <NA> <NA> NA
## 5 (+)E1A_r60_a135 <NA> <NA> <NA> <NA> <NA> <NA> <NA> NA
## 6 (+)E1A_r60_a20 <NA> <NA> <NA> <NA> <NA> <NA> <NA> NA
## txEnd GENE.DESCRIPTION SEQUENCE SPOT_ID GSM5019817 GSM5019818 GSM5019819
## 1 NA <NA> <NA> control 3.951274 2.554790 2.904286
## 2 NA <NA> <NA> control 3.574698 3.137513 3.313693
## 3 NA <NA> <NA> control 3.588675 2.364151 2.919153
## 4 NA <NA> <NA> control 3.950893 2.807319 3.162290
## 5 NA <NA> <NA> control 3.642766 2.360316 2.909418
## 6 NA <NA> <NA> control 4.270099 3.662905 3.758770
## GSM5019820 GSM5019821 GSM5019822 GSM5019823 GSM5019824 GSM5019825 GSM5019826
## 1 2.410318 2.582506 2.430097 2.403938 2.940644 2.460439 2.572454
## 2 3.424499 3.359705 3.554677 3.650878 3.599137 3.977917 3.962728
## 3 2.660142 2.397850 2.903925 2.805963 3.140166 2.677928 2.751035
## 4 3.103913 2.707994 4.670599 4.702492 4.516458 5.327897 4.633935
## 5 2.379767 2.406681 2.669327 2.636369 2.837708 2.605825 2.618590
## 6 3.864193 3.505396 3.457610 3.501079 3.414444 3.321733 3.462356
## GSM5019827 GSM5019828 GSM5019829 GSM5019830 GSM5019831
## 1 3.816681 3.679474 3.329814 3.630616 2.509811
## 2 4.019203 3.596089 3.514985 3.975853 3.404427
## 3 3.771064 3.801514 3.823361 3.735090 3.370800
## 4 5.040425 5.107250 5.340060 5.143806 5.349485
## 5 3.839998 3.694418 3.489002 3.742646 2.913778
## 6 4.014873 3.973877 3.915926 4.017910 3.856322lets make a gene table from only ORF and one from only ACC or the ensembl transcript IDs.
geneNames <- data[,c(4,14:28)]
GeneNames <- geneNames[complete.cases(geneNames),]
head(GeneNames)## ORF GSM5019817 GSM5019818 GSM5019819 GSM5019820 GSM5019821
## 62 CATG00000012021.1 11.891521 9.218327 8.343492 8.447615 9.293436
## 63 CATG00000038659.1 2.703713 4.632638 5.116481 4.649121 4.521387
## 64 CATG00000039101.1 4.520462 5.661540 5.372106 5.392326 5.763490
## 65 CATG00000002689.1 2.703713 5.199136 5.484770 5.639115 5.211397
## 66 CATG00000023380.1 10.059266 6.824806 6.182607 5.999354 7.029986
## 67 CATG00000035958.1 5.895658 4.208844 5.212020 4.963831 3.766763
## GSM5019822 GSM5019823 GSM5019824 GSM5019825 GSM5019826 GSM5019827 GSM5019828
## 62 15.196047 15.173212 14.998778 14.771526 14.078804 14.689620 14.880631
## 63 2.836406 3.108467 3.558454 3.429945 3.549286 2.814921 2.745772
## 64 4.781838 5.677510 5.760316 6.308934 5.436733 6.076964 5.801222
## 65 5.135699 4.926201 4.871242 4.782202 4.400629 4.224671 5.351747
## 66 8.924683 9.484880 9.074568 9.757172 8.212132 10.296325 10.457998
## 67 2.728640 3.041172 2.927675 3.618532 3.638655 5.992698 4.888696
## GSM5019829 GSM5019830 GSM5019831
## 62 14.963342 14.983678 15.224403
## 63 2.620153 2.747991 3.579230
## 64 6.214425 4.980677 6.320980
## 65 6.372759 4.614220 5.318465
## 66 11.056975 10.795667 10.723183
## 67 5.138310 5.875784 3.140396Ensemble <- data[,c(3,14:28)]
EnsembleNames <- Ensemble[complete.cases(Ensemble),]
head(EnsembleNames)## ACC GSM5019817 GSM5019818 GSM5019819 GSM5019820 GSM5019821
## 62 MICT00000079112 11.891521 9.218327 8.343492 8.447615 9.293436
## 63 HBMT00000701572 2.703713 4.632638 5.116481 4.649121 4.521387
## 64 ENCT00000204295 4.520462 5.661540 5.372106 5.392326 5.763490
## 65 ENCT00000068284 2.703713 5.199136 5.484770 5.639115 5.211397
## 66 ENCT00000143002 10.059266 6.824806 6.182607 5.999354 7.029986
## 67 ENCT00000192785 5.895658 4.208844 5.212020 4.963831 3.766763
## GSM5019822 GSM5019823 GSM5019824 GSM5019825 GSM5019826 GSM5019827 GSM5019828
## 62 15.196047 15.173212 14.998778 14.771526 14.078804 14.689620 14.880631
## 63 2.836406 3.108467 3.558454 3.429945 3.549286 2.814921 2.745772
## 64 4.781838 5.677510 5.760316 6.308934 5.436733 6.076964 5.801222
## 65 5.135699 4.926201 4.871242 4.782202 4.400629 4.224671 5.351747
## 66 8.924683 9.484880 9.074568 9.757172 8.212132 10.296325 10.457998
## 67 2.728640 3.041172 2.927675 3.618532 3.638655 5.992698 4.888696
## GSM5019829 GSM5019830 GSM5019831
## 62 14.963342 14.983678 15.224403
## 63 2.620153 2.747991 3.579230
## 64 6.214425 4.980677 6.320980
## 65 6.372759 4.614220 5.318465
## 66 11.056975 10.795667 10.723183
## 67 5.138310 5.875784 3.140396Lets add in the mean values of the healthy, mild, and severe cases.
metaT <- as.data.frame(t(meta))
case <- as.character(paste(metaT$case_type))
colnames(GeneNames)[2:16] <- case
GeneNames$healthyMean <- apply(GeneNames[,2:6],1,mean)
GeneNames$mildMean <- apply(GeneNames[,7:11],1,mean)
GeneNames$severeMean <- apply(GeneNames[,12:16],1,mean)Lets add in some fold change values of mild/healthy and severe/healthy. To see the proportion of change in the mild and severe case types compared to the healthy mean values per gene.
GeneNames$FC_mildOverHealthy <- GeneNames$mildMean/GeneNames$healthyMean
GeneNames$FC_severeOverHealthy <- GeneNames$severeMean/GeneNames$healthyMeanLets see the range for these genes fold change values
range(GeneNames$FC_mildOverHealthy)## [1] 0.2890426 3.9827525range(GeneNames$FC_severeOverHealthy)## [1] 0.2613439 3.6320169From the above, some were reduced by more than half or a little over 70% while some genes were over expressed by close to 400% of the healthy mean values. Lets see what genes are in the top most expressed and bottom least expressed or suppressed groups.
suppressed <- GeneNames[GeneNames$FC_severeOverHealthy<0.4,]
overexpressed <- GeneNames[GeneNames$FC_severeOverHealthy>3,]suppressedList <- suppressed$ORF
overexpressedList <- overexpressed$ORF
print('suppressed genes:')## [1] "suppressed genes:"suppressedList## [1] AL645608.1 CPA3 FST TOX2
## [5] ZNF627 UCK1 AC002383.1 SPINT1-AS1
## [9] TRABD2A CATG00000011049.1 XIST TKFC
## [13] UBE2E2-AS1 TMEM74B UNC5B-AS1 RP11-504G3.4
## [17] G042086 AC104809.2 XLOC_000210 LOC102503427
## [21] G073686 G036736
## 44824 Levels: A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2ML1-AS1 A2ML1-AS2 ... ZZEF1print('overexpressed genes:')## [1] "overexpressed genes:"overexpressedList## [1] FAM170B CATG00000023238.1 KRT2 CLEC1A
## [5] EPCAM SPP1 OLAH CREB3L2
## [9] AC034268.2 AL136234.1 AMPH AC073525.1
## [13] PKN2-AS1 LINC00993 G007492 G066671
## [17] AC079062.1 XLOC_005549
## 44824 Levels: A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2ML1-AS1 A2ML1-AS2 ... ZZEF1Now lets use the dplyr package to group by the genes on original data and get the number of genes and copynumber sequence data if available extracting the most suppressed and most over expressed genes.
Genes <- genes[!is.na(genes$ORF),]
ORFgenes <- Genes %>% group_by(ORF) %>% count(ORF)
DuplicatedORFgenes <- ORFgenes[ORFgenes$n>1,]
colnames(DuplicatedORFgenes)[2] <- 'numberOfGenes'Lets see if any of these over or under expressed genes have any copy number variants or CVNs.
suppressedAndDuplicated <- merge(DuplicatedORFgenes,suppressed,
by.x='ORF',by.y='ORF')
suppressedAndDuplicated## ORF numberOfGenes healthy_1 healthy_2 healthy_3 healthy_4 healthy_5
## 1 AC104809.2 2 8.304387 7.709691 9.091352 9.255427 8.382099
## 2 AL645608.1 2 12.439624 5.948756 6.359245 6.715597 6.373147
## 3 SPINT1-AS1 5 7.800517 14.410816 13.113907 14.354393 15.428774
## 4 TKFC 2 3.706158 10.379152 7.494028 8.194997 11.794859
## 5 TMEM74B 2 4.317956 9.727566 7.075981 8.098729 11.368666
## 6 TRABD2A 2 8.303377 8.384967 10.236728 10.156279 8.084781
## 7 UBE2E2-AS1 3 5.820832 12.627983 10.937238 11.603584 13.288831
## 8 UNC5B-AS1 2 4.777421 7.085060 7.310813 7.464189 7.096564
## 9 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 10 ZNF627 2 12.062612 8.332354 9.429363 9.840050 8.688471
## mild_1 mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3
## 1 4.568608 2.568134 4.222530 2.564730 2.360941 2.814921 2.745772 2.620153
## 2 3.117029 3.128939 3.163898 3.642938 3.589933 2.814921 2.745772 2.620153
## 3 9.458467 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734
## 4 4.556318 4.940234 4.738495 4.248374 4.572020 2.814921 2.745772 2.620153
## 5 5.136620 5.243220 4.383264 4.511120 4.974582 2.814921 2.745772 3.768807
## 6 6.830477 5.825408 6.183036 6.988208 7.079069 5.734607 2.745772 2.620153
## 7 5.408135 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215
## 8 3.564236 2.785973 4.091255 3.684111 3.455844 2.814921 2.745772 2.620153
## 9 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 10 6.132492 6.436146 6.403680 6.021617 5.864689 4.322140 2.745772 2.620153
## severe_4 severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 1 2.747991 2.333044 8.548591 3.256989 2.652376 0.3809971
## 2 2.747991 3.886607 7.567274 3.328547 2.963089 0.4398608
## 3 2.747991 6.875624 13.021681 8.632600 5.030222 0.6629405
## 4 4.079229 4.169061 8.313839 4.611088 3.285827 0.5546281
## 5 2.747991 4.060894 8.117780 4.849761 3.227677 0.5974246
## 6 2.747991 3.494433 9.033226 6.581240 3.468591 0.7285591
## 7 2.747991 4.674968 10.855694 5.140508 3.653569 0.4735310
## 8 2.747991 2.487849 6.746809 3.516284 2.683337 0.5211773
## 9 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 10 2.747991 6.593356 9.670570 6.171725 3.805882 0.6381966
## FC_severeOverHealthy
## 1 0.3102706
## 2 0.3915662
## 3 0.3862959
## 4 0.3952238
## 5 0.3976059
## 6 0.3839814
## 7 0.3365579
## 8 0.3977194
## 9 0.2613439
## 10 0.3935530overexpressedAndDuplicated <- merge(DuplicatedORFgenes, overexpressed,
by.x='ORF',by.y='ORF')
overexpressedAndDuplicated## ORF numberOfGenes healthy_1 healthy_2 healthy_3 healthy_4 healthy_5
## 1 AC073525.1 3 2.703713 2.671017 2.466728 2.333917 2.757890
## 2 AC079062.1 3 3.677109 4.650799 2.466728 3.084533 4.310347
## 3 AMPH 3 2.703713 2.332730 2.466728 2.333917 2.335227
## 4 LINC00993 2 8.614976 2.445286 2.466728 2.333917 2.335227
## 5 PKN2-AS1 8 3.746769 4.163341 2.975420 3.470122 3.962219
## 6 SPP1 2 2.703713 2.823735 2.466728 2.333917 2.335227
## mild_1 mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3
## 1 6.293041 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306
## 2 5.548849 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568
## 3 2.332686 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878
## 4 10.534604 10.510957 9.536985 9.157969 7.090456 11.487453 10.679546 11.984561
## 5 4.114379 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009
## 6 2.332686 3.037681 3.608159 4.246722 2.360941 11.547730 12.742451 8.456738
## severe_4 severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 1 9.791646 8.276233 2.586653 5.563357 9.052546 2.150794
## 2 11.831606 12.395121 3.637903 7.175177 11.941830 1.972339
## 3 8.903431 7.459420 2.434463 5.174168 8.275405 2.125384
## 4 11.748312 10.778599 3.639227 9.366194 11.335694 2.573677
## 5 11.165575 11.104678 3.663574 6.110685 11.135171 1.667957
## 6 7.898226 5.348248 2.532664 3.117238 9.198678 1.230814
## FC_severeOverHealthy
## 1 3.499714
## 2 3.282614
## 3 3.399273
## 4 3.114863
## 5 3.039428
## 6 3.632017Lets make a list to get the sequence IDs of these genes if available.
overAndDuplicatedList <- overexpressedAndDuplicated$ORF
underAndDuplicatedList <- suppressedAndDuplicated$ORF
ORF_sequence <- data[,c(4,12)]
overexpressedAndDuplicated2 <- merge(ORF_sequence,
overexpressedAndDuplicated, by.x='ORF',by.y='ORF')
suppressedAndDuplicated2 <- merge(ORF_sequence,
suppressedAndDuplicated,
by.x='ORF',by.y='ORF')overexpressedAndDuplicated2## ORF SEQUENCE
## 1 AC073525.1 AATTTGTGTGTAATTATAATGTTCTATGTGTGGTGTTATCAAAAGAATCACTGTGTCTCT
## 2 AC073525.1 CTGTAGTCAATAACAGCAGCACCAGACAGCATATTAATTCTTTTACCATAAATTTGTGTG
## 3 AC073525.1 ATAGTCCTTGCTATTCATCTTTAATTCAATCTTTTCATGGAACTTCCAGAGAAGAAGCCA
## 4 AC079062.1 TCCTTTTGATGCAGTGCTGAGTAATGAGGTATTTCCCTGTCTAAAGATTTTAGAAGATGG
## 5 AC079062.1 CCCAAATCTTTATACCTTATGTCTGTGTCTCTTTTTAAATTAAAAGTAAAATTTAGGCCA
## 6 AC079062.1 TGTAGAACAATTTGGTAAGCATTGTCATCTTTACCCCATGAACACCATATTTTGTAGTCT
## 7 AMPH ACCAAGGTCTACATGATGGAATTCAAAAGGCTTCTGGTGGTTCATTTAATGGATTCACAC
## 8 AMPH CCAGAGATATGGATTGTTGTACCAAGAAATAGAGGCTGACAAAGACGAGGCTTCTGGTGG
## 9 AMPH GCAGACAGACCAGAGTATGATCTGCAACTTGGCTGAATCTGAACAGGCTCCACCCACAGA
## 10 LINC00993 AAAAAAAAGGGCTCTGCTTTGACCTGAAGTATTTTATCTATCCTCAGTCTCAGGACACTG
## 11 LINC00993 GTGTGTGACTTATAATGTGTGTATTGTATTAATAAAAGTATATAAACATGTAGTTTACAA
## 12 PKN2-AS1 TATGTCTATGGCTCATGTTGGCTATGGTATTTTGAACTTGATTTCTGAGGCTGCTGACAG
## 13 PKN2-AS1 TCCTCTGTTGAAAATAAAGGTCTACAAAGTGTCCGTTACCCTGGAGCTGTACAAGTCACA
## 14 PKN2-AS1 GCAGAGAAAGTGCACCATTCAAAAGTGGACAGCAACAGCAGTGCAGCCCCTTTCTGGACA
## 15 PKN2-AS1 ACCCCTGCCATCATTCAACACAATTGCACAGACGCTAATCTCTTCATGGGAAGGCATGCA
## 16 PKN2-AS1 AGTTGCCAGCGAATAAGAAGTGTCAAATAAGTGTCCACCACAAGAGCAAATATCCCTGGG
## 17 PKN2-AS1 TGCACTTCTTTGAACTCCCATTAATTTATCTTTATCAGCACCTAATTCATTGCTGTCACA
## 18 PKN2-AS1 AGCAGAGAAAGTGCGTAAATGTCTCAGTCACTGACTATAAGTACAAAGGGCCCAGAAGCT
## 19 PKN2-AS1 ACGATGGCTTCACCTGAGTATCCCCAGAGCCTGACGTTAGACAAAGACACAAACAATGGT
## 20 SPP1 GCTTAATGAAGACATTAAAAGAACTTTACAACAAATACCCAGATGCTGTGGCCACATGGC
## 21 SPP1 CTAAAAGCTTCAGGGTTATGTCTATGTTCATTCTATAGAAGAAATGCAAACTATCACTGT
## numberOfGenes healthy_1 healthy_2 healthy_3 healthy_4 healthy_5 mild_1
## 1 3 2.703713 2.671017 2.466728 2.333917 2.757890 6.293041
## 2 3 2.703713 2.671017 2.466728 2.333917 2.757890 6.293041
## 3 3 2.703713 2.671017 2.466728 2.333917 2.757890 6.293041
## 4 3 3.677109 4.650799 2.466728 3.084533 4.310347 5.548849
## 5 3 3.677109 4.650799 2.466728 3.084533 4.310347 5.548849
## 6 3 3.677109 4.650799 2.466728 3.084533 4.310347 5.548849
## 7 3 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## 8 3 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## 9 3 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## 10 2 8.614976 2.445286 2.466728 2.333917 2.335227 10.534604
## 11 2 8.614976 2.445286 2.466728 2.333917 2.335227 10.534604
## 12 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 13 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 14 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 15 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 16 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 17 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 18 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 19 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 20 2 2.703713 2.823735 2.466728 2.333917 2.335227 2.332686
## 21 2 2.703713 2.823735 2.466728 2.333917 2.335227 2.332686
## mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3 severe_4
## 1 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306 9.791646
## 2 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306 9.791646
## 3 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306 9.791646
## 4 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568 11.831606
## 5 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568 11.831606
## 6 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568 11.831606
## 7 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878 8.903431
## 8 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878 8.903431
## 9 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878 8.903431
## 10 10.510957 9.536985 9.157969 7.090456 11.487453 10.679546 11.984561 11.748312
## 11 10.510957 9.536985 9.157969 7.090456 11.487453 10.679546 11.984561 11.748312
## 12 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 13 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 14 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 15 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 16 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 17 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 18 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 19 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 20 3.037681 3.608159 4.246722 2.360941 11.547730 12.742451 8.456738 7.898226
## 21 3.037681 3.608159 4.246722 2.360941 11.547730 12.742451 8.456738 7.898226
## severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 1 8.276233 2.586653 5.563357 9.052546 2.150794
## 2 8.276233 2.586653 5.563357 9.052546 2.150794
## 3 8.276233 2.586653 5.563357 9.052546 2.150794
## 4 12.395121 3.637903 7.175177 11.941830 1.972339
## 5 12.395121 3.637903 7.175177 11.941830 1.972339
## 6 12.395121 3.637903 7.175177 11.941830 1.972339
## 7 7.459420 2.434463 5.174168 8.275405 2.125384
## 8 7.459420 2.434463 5.174168 8.275405 2.125384
## 9 7.459420 2.434463 5.174168 8.275405 2.125384
## 10 10.778599 3.639227 9.366194 11.335694 2.573677
## 11 10.778599 3.639227 9.366194 11.335694 2.573677
## 12 11.104678 3.663574 6.110685 11.135171 1.667957
## 13 11.104678 3.663574 6.110685 11.135171 1.667957
## 14 11.104678 3.663574 6.110685 11.135171 1.667957
## 15 11.104678 3.663574 6.110685 11.135171 1.667957
## 16 11.104678 3.663574 6.110685 11.135171 1.667957
## 17 11.104678 3.663574 6.110685 11.135171 1.667957
## 18 11.104678 3.663574 6.110685 11.135171 1.667957
## 19 11.104678 3.663574 6.110685 11.135171 1.667957
## 20 5.348248 2.532664 3.117238 9.198678 1.230814
## 21 5.348248 2.532664 3.117238 9.198678 1.230814
## FC_severeOverHealthy
## 1 3.499714
## 2 3.499714
## 3 3.499714
## 4 3.282614
## 5 3.282614
## 6 3.282614
## 7 3.399273
## 8 3.399273
## 9 3.399273
## 10 3.114863
## 11 3.114863
## 12 3.039428
## 13 3.039428
## 14 3.039428
## 15 3.039428
## 16 3.039428
## 17 3.039428
## 18 3.039428
## 19 3.039428
## 20 3.632017
## 21 3.632017Many of our overly expressed or up regulated genes have alternate genotypes or mutations in having more than one genetic sequence for each gene. There are only 6 genes that are overly expressed more than 3 fold the healthy cases for the severe cases, but some of these six genes have more than 2 CNVs and up to 8 CNVs. As we can see in the data table above.
The data table below shows we have as many as 10 genes that are under expressed or down regulated more than 60% in severe compared to healthy gene expression values based on the group mean values. The CNVs for some of these genes give mutations greater than 3 CNVs and up to 15 CNVs per gene.
suppressedAndDuplicated2## ORF SEQUENCE
## 1 AC104809.2 TTGCATAACAGAAGATGTATCAGGTCTTTGTCCTGGATCCTCGGAGGAAGCTTCTAAACC
## 2 AC104809.2 TTCTCCTTTGGAAGGATCTCTCTGGCCCATCTGGGGGAGGGCAGCCCAGAGACACGTGTG
## 3 AL645608.1 ACTCCAAACTACCCAGAGATAACAACACTCGGTTTAGGGCAGTATTTGCTCAGATTGGTG
## 4 AL645608.1 TTGGACATAAGCGTCTTCAGACTTTTCCCTGCGAGCAGAGCCGAGGCAGACCCTGTGAGG
## 5 SPINT1-AS1 ACACACCGTGATGACCTCCACATACCATATTTGATGACAGTCTTCCTTGAGCCAGCTGTG
## 6 SPINT1-AS1 GCCCCCAACTGAGAAGCTGGTGCCCTTGGTGTGGTGGAAGCAAGGTGCCATGTGATAAGT
## 7 SPINT1-AS1 AGCCATCCTCCTGCCTCAGCCTCCCAAAGTATTAGGATTACAGTGCCCTTGGTGTGGTGG
## 8 SPINT1-AS1 CCAACTGAGAAGCTGGGTGAAGCCATCTTGCATCTTTAGCCCCAGTCAAGTTACCTCAGC
## 9 SPINT1-AS1 CCCGGGTTACCTGCGCAGTGCCCTTGGTGTGGTGGAAGCAAGGTGCCATGTGATAAGTAA
## 10 TKFC CCAGGACCTGGCTCAGCTGCAGACCTCCAAGAAGCTGGTGAACTCGGTGGCTGGCTGTGC
## 11 TKFC CAAGACCCTTCCCGCTCTCCACCCTATTTCCTCCCCTGAAGAAGAGCAACAGCTCAAGCT
## 12 TMEM74B ATCCGGACACAGTGACAGCGCGGGAGATGGAACGACTGGAGATGTACTACGCCCGCCTAG
## 13 TMEM74B CCCGGCACAGCTGCCAAGGGGCCAAGGGATGAGCTGGGGCCCTCCTTCCCAATGGCATCT
## 14 TRABD2A TGAATGGGTTGAACTTTTCACAGGTCATCTTTGCTTTGAACCAGACCCTCCTGCAGCAGG
## 15 TRABD2A AGCTTTGTGACTTCAGGTCATTTCATGGGCAACAACACAGTGCTGGATGTTTTGCGGCGT
## 16 UBE2E2-AS1 CGCAGACGCGTGGGGCTCGCATGTACCCAAGACAGGAAAACTTCACGTTGGCCTGGAAAC
## 17 UBE2E2-AS1 GCCTTTTGGCTCGCCCTGGCCCAGAATGCGCACCAGCCGGTAGAGAGGAGCTTCGGGCCG
## 18 UBE2E2-AS1 TTCTTGCTCTGTTGCCCAGGCTGAAGTCCAGTGGTGCAATCCCAGCTCACTGCAACCTCC
## 19 UNC5B-AS1 CCGCGAAGGGCATCCCCGAAGACCGGGAGGAACGCCGCGGGGACCTGTGGCTTAGCGCGC
## 20 UNC5B-AS1 GGCCGCTAAGATGGAAAAGCATCCCCGAAGACCGGGAGGAACGCCGCGGGGACCTGTGGC
## 21 XIST GTACCACACTGAGGTGAGGACTTAAAAATGATAAGACGAGTTCCCTATTTTATAAGAAAA
## 22 XIST ACCTGCCAGCAACAGCTTCCTTCTTTGAGCTTAGACACTTCATTTTCCTAGTCCATCCCT
## 23 XIST AGGAACACCTACCCCTTGGCTAATGCTGGGATGCCACCTATAGAAAAGTCAGAGGGTCCA
## 24 XIST TGCCTTCCTCTGCCTTGTCTTAAAGACTGGATTGGGAGAAAATTGATATTCTCACTACCA
## 25 XIST TCAGTTGCATACAGTTGTGCCTTTTATCAGGACTCCTGTACTTATCAAAGCAGAGAGTGC
## 26 XIST CTGGAGAAAAAGGTGGAGATGGGGCATGAGGATCCTCCAGGGGAAAAGCTCACTACCACT
## 27 XIST GGGCCACGTGTATGTCTCCCAGTGGGCGGTACACCAGGTGTTTTCAAGGACATTCTGAGC
## 28 XIST CTTTCTCTTAGATGCCACCTATAGAAAAGTCAGAGGGTCCAGATCCCATTGAAGATACCA
## 29 XIST GGCTTGGGATGCCATGGTGTATAATACAACAAGTGAGAGCTCTTCATTGTTCCTATCTGC
## 30 XIST ACCGGTGCTTTGGTAGCCTACTGAACCCTGTCTTTCTTCTTAAGGACATTCTGAGCATGT
## 31 XIST CCCCTGTCACAAAGCCTACCTAGATGGATAGAGGACCCAAGCGAAAAAGTTTCTGGCATC
## 32 XIST CCCCTGTCACAAAGCCTACCTAGATGGATAGAGGACCCAAGCGAAAAAGGAGCAGACATT
## 33 XIST CATTTACAAGGTTTTTTCTGGCATCACTACCACTACTGATTAAACAAGAATAAGAGAACA
## 34 XIST AGAAGCACCTGCCAGCAACAGCTTCCTTCTTTGAGCTTAGGTAACCAGGAAAGAGCTAGT
## 35 XIST TCAATCCACATGAAGAAAAGGATCTTCCTCAGAAGAATAGGCTTGTTGTTTTACAGTGTT
## 36 ZNF627 CTGGGCAACACGAGACGGGGCCTTACTCTGCTGCCTAGGCTGGAGTACAGTGGCACAATC
## 37 ZNF627 AGATGGGCCCGGGAGAGGAGGGCAGGGCCTGCGCCTCCCTACGGAGCCTTTGTTTCTGGC
## numberOfGenes healthy_1 healthy_2 healthy_3 healthy_4 healthy_5 mild_1
## 1 2 8.304387 7.709691 9.091352 9.255427 8.382099 4.568608
## 2 2 8.304387 7.709691 9.091352 9.255427 8.382099 4.568608
## 3 2 12.439624 5.948756 6.359245 6.715597 6.373147 3.117029
## 4 2 12.439624 5.948756 6.359245 6.715597 6.373147 3.117029
## 5 5 7.800517 14.410816 13.113907 14.354393 15.428774 9.458467
## 6 5 7.800517 14.410816 13.113907 14.354393 15.428774 9.458467
## 7 5 7.800517 14.410816 13.113907 14.354393 15.428774 9.458467
## 8 5 7.800517 14.410816 13.113907 14.354393 15.428774 9.458467
## 9 5 7.800517 14.410816 13.113907 14.354393 15.428774 9.458467
## 10 2 3.706158 10.379152 7.494028 8.194997 11.794859 4.556318
## 11 2 3.706158 10.379152 7.494028 8.194997 11.794859 4.556318
## 12 2 4.317956 9.727566 7.075981 8.098729 11.368666 5.136620
## 13 2 4.317956 9.727566 7.075981 8.098729 11.368666 5.136620
## 14 2 8.303377 8.384967 10.236728 10.156279 8.084781 6.830477
## 15 2 8.303377 8.384967 10.236728 10.156279 8.084781 6.830477
## 16 3 5.820832 12.627983 10.937238 11.603584 13.288831 5.408135
## 17 3 5.820832 12.627983 10.937238 11.603584 13.288831 5.408135
## 18 3 5.820832 12.627983 10.937238 11.603584 13.288831 5.408135
## 19 2 4.777421 7.085060 7.310813 7.464189 7.096564 3.564236
## 20 2 4.777421 7.085060 7.310813 7.464189 7.096564 3.564236
## 21 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 22 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 23 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 24 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 25 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 26 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 27 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 28 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 29 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 30 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 31 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 32 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 33 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 34 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 35 15 10.328164 7.744841 14.071082 14.067985 4.532861 12.100095
## 36 2 12.062612 8.332354 9.429363 9.840050 8.688471 6.132492
## 37 2 12.062612 8.332354 9.429363 9.840050 8.688471 6.132492
## mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3 severe_4
## 1 2.568134 4.222530 2.564730 2.360941 2.814921 2.745772 2.620153 2.747991
## 2 2.568134 4.222530 2.564730 2.360941 2.814921 2.745772 2.620153 2.747991
## 3 3.128939 3.163898 3.642938 3.589933 2.814921 2.745772 2.620153 2.747991
## 4 3.128939 3.163898 3.642938 3.589933 2.814921 2.745772 2.620153 2.747991
## 5 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734 2.747991
## 6 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734 2.747991
## 7 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734 2.747991
## 8 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734 2.747991
## 9 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734 2.747991
## 10 4.940234 4.738495 4.248374 4.572020 2.814921 2.745772 2.620153 4.079229
## 11 4.940234 4.738495 4.248374 4.572020 2.814921 2.745772 2.620153 4.079229
## 12 5.243220 4.383264 4.511120 4.974582 2.814921 2.745772 3.768807 2.747991
## 13 5.243220 4.383264 4.511120 4.974582 2.814921 2.745772 3.768807 2.747991
## 14 5.825408 6.183036 6.988208 7.079069 5.734607 2.745772 2.620153 2.747991
## 15 5.825408 6.183036 6.988208 7.079069 5.734607 2.745772 2.620153 2.747991
## 16 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215 2.747991
## 17 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215 2.747991
## 18 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215 2.747991
## 19 2.785973 4.091255 3.684111 3.455844 2.814921 2.745772 2.620153 2.747991
## 20 2.785973 4.091255 3.684111 3.455844 2.814921 2.745772 2.620153 2.747991
## 21 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 22 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 23 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 24 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 25 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 26 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 27 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 28 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 29 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 30 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 31 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 32 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 33 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 34 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 35 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153 2.747991
## 36 6.436146 6.403680 6.021617 5.864689 4.322140 2.745772 2.620153 2.747991
## 37 6.436146 6.403680 6.021617 5.864689 4.322140 2.745772 2.620153 2.747991
## severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 1 2.333044 8.548591 3.256989 2.652376 0.3809971
## 2 2.333044 8.548591 3.256989 2.652376 0.3809971
## 3 3.886607 7.567274 3.328547 2.963089 0.4398608
## 4 3.886607 7.567274 3.328547 2.963089 0.4398608
## 5 6.875624 13.021681 8.632600 5.030222 0.6629405
## 6 6.875624 13.021681 8.632600 5.030222 0.6629405
## 7 6.875624 13.021681 8.632600 5.030222 0.6629405
## 8 6.875624 13.021681 8.632600 5.030222 0.6629405
## 9 6.875624 13.021681 8.632600 5.030222 0.6629405
## 10 4.169061 8.313839 4.611088 3.285827 0.5546281
## 11 4.169061 8.313839 4.611088 3.285827 0.5546281
## 12 4.060894 8.117780 4.849761 3.227677 0.5974246
## 13 4.060894 8.117780 4.849761 3.227677 0.5974246
## 14 3.494433 9.033226 6.581240 3.468591 0.7285591
## 15 3.494433 9.033226 6.581240 3.468591 0.7285591
## 16 4.674968 10.855694 5.140508 3.653569 0.4735310
## 17 4.674968 10.855694 5.140508 3.653569 0.4735310
## 18 4.674968 10.855694 5.140508 3.653569 0.4735310
## 19 2.487849 6.746809 3.516284 2.683337 0.5211773
## 20 2.487849 6.746809 3.516284 2.683337 0.5211773
## 21 2.333044 10.148987 6.790507 2.652376 0.6690822
## 22 2.333044 10.148987 6.790507 2.652376 0.6690822
## 23 2.333044 10.148987 6.790507 2.652376 0.6690822
## 24 2.333044 10.148987 6.790507 2.652376 0.6690822
## 25 2.333044 10.148987 6.790507 2.652376 0.6690822
## 26 2.333044 10.148987 6.790507 2.652376 0.6690822
## 27 2.333044 10.148987 6.790507 2.652376 0.6690822
## 28 2.333044 10.148987 6.790507 2.652376 0.6690822
## 29 2.333044 10.148987 6.790507 2.652376 0.6690822
## 30 2.333044 10.148987 6.790507 2.652376 0.6690822
## 31 2.333044 10.148987 6.790507 2.652376 0.6690822
## 32 2.333044 10.148987 6.790507 2.652376 0.6690822
## 33 2.333044 10.148987 6.790507 2.652376 0.6690822
## 34 2.333044 10.148987 6.790507 2.652376 0.6690822
## 35 2.333044 10.148987 6.790507 2.652376 0.6690822
## 36 6.593356 9.670570 6.171725 3.805882 0.6381966
## 37 6.593356 9.670570 6.171725 3.805882 0.6381966
## FC_severeOverHealthy
## 1 0.3102706
## 2 0.3102706
## 3 0.3915662
## 4 0.3915662
## 5 0.3862959
## 6 0.3862959
## 7 0.3862959
## 8 0.3862959
## 9 0.3862959
## 10 0.3952238
## 11 0.3952238
## 12 0.3976059
## 13 0.3976059
## 14 0.3839814
## 15 0.3839814
## 16 0.3365579
## 17 0.3365579
## 18 0.3365579
## 19 0.3977194
## 20 0.3977194
## 21 0.2613439
## 22 0.2613439
## 23 0.2613439
## 24 0.2613439
## 25 0.2613439
## 26 0.2613439
## 27 0.2613439
## 28 0.2613439
## 29 0.2613439
## 30 0.2613439
## 31 0.2613439
## 32 0.2613439
## 33 0.2613439
## 34 0.2613439
## 35 0.2613439
## 36 0.3935530
## 37 0.3935530This data could show the target genes affected by Covid-19 in PBMC data. There could also be linked gene analysis of these genes. If these up and down regulated genes are on the same strand of the same chromosome, they are considered a linked group, and also depending on how far away these genes are from each other on the same strand, this could be a clue to where gene therapeutics need to target to prevent these mutations from forming in people infected with severe strains of covid-19.
Lets see if any of these CNVs are on the same strand of any chromosome to compare a group of linked genes using the data table created earlier called genes and merging by sequence.
linkedSuppressed <- merge(genes,
suppressedAndDuplicated2,
by.x='SEQUENCE',by.y='SEQUENCE')
linkedSuppressed <- linkedSuppressed[order(linkedSuppressed$CHROM),]
linkedSuppressed## SEQUENCE
## 4 ACTCCAAACTACCCAGAGATAACAACACTCGGTTTAGGGCAGTATTTGCTCAGATTGGTG
## 37 TTGGACATAAGCGTCTTCAGACTTTTCCCTGCGAGCAGAGCCGAGGCAGACCCTGTGAGG
## 19 CCGCGAAGGGCATCCCCGAAGACCGGGAGGAACGCCGCGGGGACCTGTGGCTTAGCGCGC
## 26 GGCCGCTAAGATGGAAAAGCATCCCCGAAGACCGGGAGGAACGCCGCGGGGACCTGTGGC
## 11 CAAGACCCTTCCCGCTCTCCACCCTATTTCCTCCCCTGAAGAAGAGCAACAGCTCAAGCT
## 14 CCAGGACCTGGCTCAGCTGCAGACCTCCAAGAAGCTGGTGAACTCGGTGGCTGGCTGTGC
## 1 ACACACCGTGATGACCTCCACATACCATATTTGATGACAGTCTTCCTTGAGCCAGCTGTG
## 7 AGCCATCCTCCTGCCTCAGCCTCCCAAAGTATTAGGATTACAGTGCCCTTGGTGTGGTGG
## 13 CCAACTGAGAAGCTGGGTGAAGCCATCTTGCATCTTTAGCCCCAGTCAAGTTACCTCAGC
## 18 CCCGGGTTACCTGCGCAGTGCCCTTGGTGTGGTGGAAGCAAGGTGCCATGTGATAAGTAA
## 24 GCCCCCAACTGAGAAGCTGGTGCCCTTGGTGTGGTGGAAGCAAGGTGCCATGTGATAAGT
## 6 AGATGGGCCCGGGAGAGGAGGGCAGGGCCTGCGCCTCCCTACGGAGCCTTTGTTTCTGGC
## 22 CTGGGCAACACGAGACGGGGCCTTACTCTGCTGCCTAGGCTGGAGTACAGTGGCACAATC
## 8 AGCTTTGTGACTTCAGGTCATTTCATGGGCAACAACACAGTGCTGGATGTTTTGCGGCGT
## 32 TGAATGGGTTGAACTTTTCACAGGTCATCTTTGCTTTGAACCAGACCCTCCTGCAGCAGG
## 34 TTCTCCTTTGGAAGGATCTCTCTGGCCCATCTGGGGGAGGGCAGCCCAGAGACACGTGTG
## 36 TTGCATAACAGAAGATGTATCAGGTCTTTGTCCTGGATCCTCGGAGGAAGCTTCTAAACC
## 10 ATCCGGACACAGTGACAGCGCGGGAGATGGAACGACTGGAGATGTACTACGCCCGCCTAG
## 17 CCCGGCACAGCTGCCAAGGGGCCAAGGGATGAGCTGGGGCCCTCCTTCCCAATGGCATCT
## 20 CGCAGACGCGTGGGGCTCGCATGTACCCAAGACAGGAAAACTTCACGTTGGCCTGGAAAC
## 25 GCCTTTTGGCTCGCCCTGGCCCAGAATGCGCACCAGCCGGTAGAGAGGAGCTTCGGGCCG
## 35 TTCTTGCTCTGTTGCCCAGGCTGAAGTCCAGTGGTGCAATCCCAGCTCACTGCAACCTCC
## 2 ACCGGTGCTTTGGTAGCCTACTGAACCCTGTCTTTCTTCTTAAGGACATTCTGAGCATGT
## 3 ACCTGCCAGCAACAGCTTCCTTCTTTGAGCTTAGACACTTCATTTTCCTAGTCCATCCCT
## 5 AGAAGCACCTGCCAGCAACAGCTTCCTTCTTTGAGCTTAGGTAACCAGGAAAGAGCTAGT
## 9 AGGAACACCTACCCCTTGGCTAATGCTGGGATGCCACCTATAGAAAAGTCAGAGGGTCCA
## 12 CATTTACAAGGTTTTTTCTGGCATCACTACCACTACTGATTAAACAAGAATAAGAGAACA
## 15 CCCCTGTCACAAAGCCTACCTAGATGGATAGAGGACCCAAGCGAAAAAGGAGCAGACATT
## 16 CCCCTGTCACAAAGCCTACCTAGATGGATAGAGGACCCAAGCGAAAAAGTTTCTGGCATC
## 21 CTGGAGAAAAAGGTGGAGATGGGGCATGAGGATCCTCCAGGGGAAAAGCTCACTACCACT
## 23 CTTTCTCTTAGATGCCACCTATAGAAAAGTCAGAGGGTCCAGATCCCATTGAAGATACCA
## 27 GGCTTGGGATGCCATGGTGTATAATACAACAAGTGAGAGCTCTTCATTGTTCCTATCTGC
## 28 GGGCCACGTGTATGTCTCCCAGTGGGCGGTACACCAGGTGTTTTCAAGGACATTCTGAGC
## 29 GTACCACACTGAGGTGAGGACTTAAAAATGATAAGACGAGTTCCCTATTTTATAAGAAAA
## 30 TCAATCCACATGAAGAAAAGGATCTTCCTCAGAAGAATAGGCTTGTTGTTTTACAGTGTT
## 31 TCAGTTGCATACAGTTGTGCCTTTTATCAGGACTCCTGTACTTATCAAAGCAGAGAGTGC
## 33 TGCCTTCCTCTGCCTTGTCTTAAAGACTGGATTGGGAGAAAATTGATATTCTCACTACCA
## ID ACC ORF.x CHROM STRAND
## 4 ASHGV40022214V5 ENST00000458555 AL645608.1 chr1 -
## 37 ASHG19AP1B100113816V5 ENST00000598827 AL645608.1 chr1 -
## 19 ASHGV40003889V5 ENST00000447119 UNC5B-AS1 chr10 -
## 26 ASHG19LNC1A112541842V5 ENST00000449737 UNC5B-AS1 chr10 -
## 11 ASHG19AP1B100062052V5 ENST00000394900 TKFC chr11 +
## 14 ASHG19LNC1A109913934V5 ENST00000530057 TKFC chr11 +
## 1 ASHG19LNC1A100897032V5 ENST00000563217 SPINT1-AS1 chr15 -
## 7 ASHG19LNC1A102477428V5 ENST00000568419 SPINT1-AS1 chr15 -
## 13 ASHG19LNC1A103273246V5 ENST00000568525 SPINT1-AS1 chr15 -
## 18 ASHG19LNC1A106435303V5 ENST00000565315 SPINT1-AS1 chr15 -
## 24 ASHG19LNC1A108820494V5 ENST00000564302 SPINT1-AS1 chr15 -
## 6 ASHG19AP1B140931179V5 ENST00000361113 ZNF627 chr19 +
## 22 ASHG19LNC1A106739687V5 ENST00000588651 ZNF627 chr19 +
## 8 ASHG19LNC1A101589007V5 ENST00000479944 TRABD2A chr2 -
## 32 ASHG19AP1B106995025V5 ENST00000409520 TRABD2A chr2 -
## 34 ASHGV40001229V5 ENST00000457369 AC104809.2 chr2 -
## 36 ASHGV40028330V5 ENST00000418218 AC104809.2 chr2 -
## 10 ASHG19AP1B105290038V5 ENST00000381894 TMEM74B chr20 -
## 17 ASHG19LNC1A113541636V5 ENST00000481747 TMEM74B chr20 -
## 20 ASHG19LNC1A107985017V5 ENST00000430018 UBE2E2-AS1 chr3 -
## 25 ASHG19LNC1A111080969V5 ENST00000421375 UBE2E2-AS1 chr3 -
## 35 ASHG19LNC1ABL100001006V5 compmerge.7801.pooled.chr3 UBE2E2-AS1 chr3 -
## 2 ASHG19LNC1A105198991V5 ENST00000602495 XIST chrX -
## 3 ASHG19LNC1A100840254V5 ENST00000417942 XIST chrX -
## 5 ASHG19LNC1A107574203V5 ENST00000648091 XIST chrX -
## 9 ASHG19LNC1A101632754V5 ENST00000635841 XIST chrX -
## 12 ASHG19LNC1A109726396V5 ENST00000650548 XIST chrX -
## 15 ASHG19LNC1A102817147V5 ENST00000416330 XIST chrX -
## 16 ASHG19LNC1A107974766V5 ENST00000421322 XIST chrX -
## 21 ASHG19LNC1A109563269V5 ENST00000650637 XIST chrX -
## 23 ASHG19LNC1A107175310V5 ENST00000602863 XIST chrX -
## 27 ASHG19LNC1A109563186V5 ENST00000648927 XIST chrX -
## 28 ASHG19LNC1A102028185V5 ENST00000434839 XIST chrX -
## 29 ASHGV40054144V5 ENST00000429829 XIST chrX -
## 30 ASHG19LNC1A112431175V5 ENST00000602587 XIST chrX -
## 31 ASHG19LNC1A108770478V5 ENST00000650627 XIST chrX -
## 33 ASHG19LNC1A106781691V5 ENST00000647913 XIST chrX -
## ORF.y numberOfGenes healthy_1 healthy_2 healthy_3 healthy_4 healthy_5
## 4 AL645608.1 2 12.439624 5.948756 6.359245 6.715597 6.373147
## 37 AL645608.1 2 12.439624 5.948756 6.359245 6.715597 6.373147
## 19 UNC5B-AS1 2 4.777421 7.085060 7.310813 7.464189 7.096564
## 26 UNC5B-AS1 2 4.777421 7.085060 7.310813 7.464189 7.096564
## 11 TKFC 2 3.706158 10.379152 7.494028 8.194997 11.794859
## 14 TKFC 2 3.706158 10.379152 7.494028 8.194997 11.794859
## 1 SPINT1-AS1 5 7.800517 14.410816 13.113907 14.354393 15.428774
## 7 SPINT1-AS1 5 7.800517 14.410816 13.113907 14.354393 15.428774
## 13 SPINT1-AS1 5 7.800517 14.410816 13.113907 14.354393 15.428774
## 18 SPINT1-AS1 5 7.800517 14.410816 13.113907 14.354393 15.428774
## 24 SPINT1-AS1 5 7.800517 14.410816 13.113907 14.354393 15.428774
## 6 ZNF627 2 12.062612 8.332354 9.429363 9.840050 8.688471
## 22 ZNF627 2 12.062612 8.332354 9.429363 9.840050 8.688471
## 8 TRABD2A 2 8.303377 8.384967 10.236728 10.156279 8.084781
## 32 TRABD2A 2 8.303377 8.384967 10.236728 10.156279 8.084781
## 34 AC104809.2 2 8.304387 7.709691 9.091352 9.255427 8.382099
## 36 AC104809.2 2 8.304387 7.709691 9.091352 9.255427 8.382099
## 10 TMEM74B 2 4.317956 9.727566 7.075981 8.098729 11.368666
## 17 TMEM74B 2 4.317956 9.727566 7.075981 8.098729 11.368666
## 20 UBE2E2-AS1 3 5.820832 12.627983 10.937238 11.603584 13.288831
## 25 UBE2E2-AS1 3 5.820832 12.627983 10.937238 11.603584 13.288831
## 35 UBE2E2-AS1 3 5.820832 12.627983 10.937238 11.603584 13.288831
## 2 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 3 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 5 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 9 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 12 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 15 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 16 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 21 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 23 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 27 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 28 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 29 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 30 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 31 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## 33 XIST 15 10.328164 7.744841 14.071082 14.067985 4.532861
## mild_1 mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3
## 4 3.117029 3.128939 3.163898 3.642938 3.589933 2.814921 2.745772 2.620153
## 37 3.117029 3.128939 3.163898 3.642938 3.589933 2.814921 2.745772 2.620153
## 19 3.564236 2.785973 4.091255 3.684111 3.455844 2.814921 2.745772 2.620153
## 26 3.564236 2.785973 4.091255 3.684111 3.455844 2.814921 2.745772 2.620153
## 11 4.556318 4.940234 4.738495 4.248374 4.572020 2.814921 2.745772 2.620153
## 14 4.556318 4.940234 4.738495 4.248374 4.572020 2.814921 2.745772 2.620153
## 1 9.458467 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734
## 7 9.458467 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734
## 13 9.458467 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734
## 18 9.458467 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734
## 24 9.458467 10.569911 8.771150 7.053824 7.309647 4.907036 5.596723 5.023734
## 6 6.132492 6.436146 6.403680 6.021617 5.864689 4.322140 2.745772 2.620153
## 22 6.132492 6.436146 6.403680 6.021617 5.864689 4.322140 2.745772 2.620153
## 8 6.830477 5.825408 6.183036 6.988208 7.079069 5.734607 2.745772 2.620153
## 32 6.830477 5.825408 6.183036 6.988208 7.079069 5.734607 2.745772 2.620153
## 34 4.568608 2.568134 4.222530 2.564730 2.360941 2.814921 2.745772 2.620153
## 36 4.568608 2.568134 4.222530 2.564730 2.360941 2.814921 2.745772 2.620153
## 10 5.136620 5.243220 4.383264 4.511120 4.974582 2.814921 2.745772 3.768807
## 17 5.136620 5.243220 4.383264 4.511120 4.974582 2.814921 2.745772 3.768807
## 20 5.408135 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215
## 25 5.408135 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215
## 35 5.408135 5.882807 5.220627 4.691287 4.499683 3.857133 3.692539 3.295215
## 2 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 3 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 5 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 9 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 12 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 15 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 16 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 21 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 23 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 27 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 28 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 29 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 30 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 31 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## 33 12.100095 5.525440 7.803481 4.374068 4.149449 2.814921 2.745772 2.620153
## severe_4 severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 4 2.747991 3.886607 7.567274 3.328547 2.963089 0.4398608
## 37 2.747991 3.886607 7.567274 3.328547 2.963089 0.4398608
## 19 2.747991 2.487849 6.746809 3.516284 2.683337 0.5211773
## 26 2.747991 2.487849 6.746809 3.516284 2.683337 0.5211773
## 11 4.079229 4.169061 8.313839 4.611088 3.285827 0.5546281
## 14 4.079229 4.169061 8.313839 4.611088 3.285827 0.5546281
## 1 2.747991 6.875624 13.021681 8.632600 5.030222 0.6629405
## 7 2.747991 6.875624 13.021681 8.632600 5.030222 0.6629405
## 13 2.747991 6.875624 13.021681 8.632600 5.030222 0.6629405
## 18 2.747991 6.875624 13.021681 8.632600 5.030222 0.6629405
## 24 2.747991 6.875624 13.021681 8.632600 5.030222 0.6629405
## 6 2.747991 6.593356 9.670570 6.171725 3.805882 0.6381966
## 22 2.747991 6.593356 9.670570 6.171725 3.805882 0.6381966
## 8 2.747991 3.494433 9.033226 6.581240 3.468591 0.7285591
## 32 2.747991 3.494433 9.033226 6.581240 3.468591 0.7285591
## 34 2.747991 2.333044 8.548591 3.256989 2.652376 0.3809971
## 36 2.747991 2.333044 8.548591 3.256989 2.652376 0.3809971
## 10 2.747991 4.060894 8.117780 4.849761 3.227677 0.5974246
## 17 2.747991 4.060894 8.117780 4.849761 3.227677 0.5974246
## 20 2.747991 4.674968 10.855694 5.140508 3.653569 0.4735310
## 25 2.747991 4.674968 10.855694 5.140508 3.653569 0.4735310
## 35 2.747991 4.674968 10.855694 5.140508 3.653569 0.4735310
## 2 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 3 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 5 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 9 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 12 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 15 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 16 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 21 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 23 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 27 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 28 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 29 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 30 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 31 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## 33 2.747991 2.333044 10.148987 6.790507 2.652376 0.6690822
## FC_severeOverHealthy
## 4 0.3915662
## 37 0.3915662
## 19 0.3977194
## 26 0.3977194
## 11 0.3952238
## 14 0.3952238
## 1 0.3862959
## 7 0.3862959
## 13 0.3862959
## 18 0.3862959
## 24 0.3862959
## 6 0.3935530
## 22 0.3935530
## 8 0.3839814
## 32 0.3839814
## 34 0.3102706
## 36 0.3102706
## 10 0.3976059
## 17 0.3976059
## 20 0.3365579
## 25 0.3365579
## 35 0.3365579
## 2 0.2613439
## 3 0.2613439
## 5 0.2613439
## 9 0.2613439
## 12 0.2613439
## 15 0.2613439
## 16 0.2613439
## 21 0.2613439
## 23 0.2613439
## 27 0.2613439
## 28 0.2613439
## 29 0.2613439
## 30 0.2613439
## 31 0.2613439
## 33 0.2613439The only genes that are on the same strand of the same chromosome on our data of suppressed and duplicated genes are the TRABD2A and AC104809.2 genes on the reverse strand of chromosome 2. All other suppressed and duplicated genes are on different chromosomes and/or different strands of same chromosome. Just by looking at the data table above. There could be a linkage group on chromosome 2 for the reverse strand.
linkedOverExpressed <- merge(genes,overexpressedAndDuplicated2,
by.x='SEQUENCE',by.y='SEQUENCE')
linkedOverExpressed <- linkedOverExpressed[order(linkedOverExpressed$CHROM),]
linkedOverExpressed## SEQUENCE
## 4 ACCCCTGCCATCATTCAACACAATTGCACAGACGCTAATCTCTTCATGGGAAGGCATGCA
## 5 ACGATGGCTTCACCTGAGTATCCCCAGAGCCTGACGTTAGACAAAGACACAAACAATGGT
## 6 AGCAGAGAAAGTGCGTAAATGTCTCAGTCACTGACTATAAGTACAAAGGGCCCAGAAGCT
## 7 AGTTGCCAGCGAATAAGAAGTGTCAAATAAGTGTCCACCACAAGAGCAAATATCCCTGGG
## 14 GCAGAGAAAGTGCACCATTCAAAAGTGGACAGCAACAGCAGTGCAGCCCCTTTCTGGACA
## 17 TATGTCTATGGCTCATGTTGGCTATGGTATTTTGAACTTGATTTCTGAGGCTGCTGACAG
## 18 TCCTCTGTTGAAAATAAAGGTCTACAAAGTGTCCGTTACCCTGGAGCTGTACAAGTCACA
## 20 TGCACTTCTTTGAACTCCCATTAATTTATCTTTATCAGCACCTAATTCATTGCTGTCACA
## 1 AAAAAAAAGGGCTCTGCTTTGACCTGAAGTATTTTATCTATCCTCAGTCTCAGGACACTG
## 16 GTGTGTGACTTATAATGTGTGTATTGTATTAATAAAAGTATATAAACATGTAGTTTACAA
## 2 AATTTGTGTGTAATTATAATGTTCTATGTGTGGTGTTATCAAAAGAATCACTGTGTCTCT
## 8 ATAGTCCTTGCTATTCATCTTTAATTCAATCTTTTCATGGAACTTCCAGAGAAGAAGCCA
## 12 CTGTAGTCAATAACAGCAGCACCAGACAGCATATTAATTCTTTTACCATAAATTTGTGTG
## 10 CCCAAATCTTTATACCTTATGTCTGTGTCTCTTTTTAAATTAAAAGTAAAATTTAGGCCA
## 19 TCCTTTTGATGCAGTGCTGAGTAATGAGGTATTTCCCTGTCTAAAGATTTTAGAAGATGG
## 21 TGTAGAACAATTTGGTAAGCATTGTCATCTTTACCCCATGAACACCATATTTTGTAGTCT
## 11 CTAAAAGCTTCAGGGTTATGTCTATGTTCATTCTATAGAAGAAATGCAAACTATCACTGT
## 15 GCTTAATGAAGACATTAAAAGAACTTTACAACAAATACCCAGATGCTGTGGCCACATGGC
## 3 ACCAAGGTCTACATGATGGAATTCAAAAGGCTTCTGGTGGTTCATTTAATGGATTCACAC
## 9 CCAGAGATATGGATTGTTGTACCAAGAAATAGAGGCTGACAAAGACGAGGCTTCTGGTGG
## 13 GCAGACAGACCAGAGTATGATCTGCAACTTGGCTGAATCTGAACAGGCTCCACCCACAGA
## ID ACC ORF.x CHROM STRAND ORF.y
## 4 ASHG19LNC1A102048698V5 ENST00000642677 PKN2-AS1 chr1 - PKN2-AS1
## 5 ASHG19LNC1A107993380V5 ENST00000645890 PKN2-AS1 chr1 - PKN2-AS1
## 6 ASHG19LNC1A100466408V5 ENST00000644540 PKN2-AS1 chr1 - PKN2-AS1
## 7 ASHGV40009549V5 ENST00000458097 PKN2-AS1 chr1 - PKN2-AS1
## 14 ASHG19LNC1A106003695V5 ENST00000645056 PKN2-AS1 chr1 - PKN2-AS1
## 17 ASHG19LNC1A108789827V5 ENST00000437598 PKN2-AS1 chr1 - PKN2-AS1
## 18 ASHG19LNC1A105608119V5 ENST00000425750 PKN2-AS1 chr1 - PKN2-AS1
## 20 ASHG19LNC1A100861958V5 ENST00000643720 PKN2-AS1 chr1 - PKN2-AS1
## 1 ASHG19LNC1ABL100000221V5 HSALNT0289079 LINC00993 chr10 + LINC00993
## 16 ASHGV40005533V5 NR_104061 LINC00993 chr10 + LINC00993
## 2 ASHG19LNC1A105245011V5 ENST00000547040 AC073525.1 chr12 + AC073525.1
## 8 ASHG19LNC1A109214365V5 ENST00000550049 AC073525.1 chr12 + AC073525.1
## 12 ASHGV40011710V5 ENST00000549762 AC073525.1 chr12 + AC073525.1
## 10 ASHGV40056463V5 ENST00000581011 AC079062.1 chr18 - AC079062.1
## 19 ASHG19LNC1A105645213V5 ENST00000584544 AC079062.1 chr18 - AC079062.1
## 21 ASHG19LNC1A103274970V5 ENST00000581862 AC079062.1 chr18 - AC079062.1
## 11 ASHG19AP1B126895679V5 ENST00000395080 SPP1 chr4 + SPP1
## 15 ASHG19LNC1A100597206V5 ENST00000509659 SPP1 chr4 + SPP1
## 3 ASHG19LNC1A105290217V5 ENST00000467580 AMPH chr7 - AMPH
## 9 ASHG19LNC1A103709111V5 ENST00000471913 AMPH chr7 - AMPH
## 13 ASHG19AP1B101564289V5 ENST00000356264 AMPH chr7 - AMPH
## numberOfGenes healthy_1 healthy_2 healthy_3 healthy_4 healthy_5 mild_1
## 4 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 5 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 6 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 7 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 14 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 17 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 18 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 20 8 3.746769 4.163341 2.975420 3.470122 3.962219 4.114379
## 1 2 8.614976 2.445286 2.466728 2.333917 2.335227 10.534604
## 16 2 8.614976 2.445286 2.466728 2.333917 2.335227 10.534604
## 2 3 2.703713 2.671017 2.466728 2.333917 2.757890 6.293041
## 8 3 2.703713 2.671017 2.466728 2.333917 2.757890 6.293041
## 12 3 2.703713 2.671017 2.466728 2.333917 2.757890 6.293041
## 10 3 3.677109 4.650799 2.466728 3.084533 4.310347 5.548849
## 19 3 3.677109 4.650799 2.466728 3.084533 4.310347 5.548849
## 21 3 3.677109 4.650799 2.466728 3.084533 4.310347 5.548849
## 11 2 2.703713 2.823735 2.466728 2.333917 2.335227 2.332686
## 15 2 2.703713 2.823735 2.466728 2.333917 2.335227 2.332686
## 3 3 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## 9 3 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## 13 3 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3 severe_4
## 4 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 5 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 6 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 7 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 14 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 17 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 18 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 20 6.266343 7.892024 7.933767 4.346910 9.781261 11.060330 12.564009 11.165575
## 1 10.510957 9.536985 9.157969 7.090456 11.487453 10.679546 11.984561 11.748312
## 16 10.510957 9.536985 9.157969 7.090456 11.487453 10.679546 11.984561 11.748312
## 2 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306 9.791646
## 8 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306 9.791646
## 12 6.447829 5.306062 5.169035 4.600816 7.758208 8.991335 10.445306 9.791646
## 10 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568 11.831606
## 19 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568 11.831606
## 21 7.208202 8.290226 9.096499 5.732109 10.946679 12.092176 12.443568 11.831606
## 11 3.037681 3.608159 4.246722 2.360941 11.547730 12.742451 8.456738 7.898226
## 15 3.037681 3.608159 4.246722 2.360941 11.547730 12.742451 8.456738 7.898226
## 3 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878 8.903431
## 9 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878 8.903431
## 13 3.233616 7.822054 8.973390 3.509091 7.981420 8.742877 8.289878 8.903431
## severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 4 11.104678 3.663574 6.110685 11.135171 1.667957
## 5 11.104678 3.663574 6.110685 11.135171 1.667957
## 6 11.104678 3.663574 6.110685 11.135171 1.667957
## 7 11.104678 3.663574 6.110685 11.135171 1.667957
## 14 11.104678 3.663574 6.110685 11.135171 1.667957
## 17 11.104678 3.663574 6.110685 11.135171 1.667957
## 18 11.104678 3.663574 6.110685 11.135171 1.667957
## 20 11.104678 3.663574 6.110685 11.135171 1.667957
## 1 10.778599 3.639227 9.366194 11.335694 2.573677
## 16 10.778599 3.639227 9.366194 11.335694 2.573677
## 2 8.276233 2.586653 5.563357 9.052546 2.150794
## 8 8.276233 2.586653 5.563357 9.052546 2.150794
## 12 8.276233 2.586653 5.563357 9.052546 2.150794
## 10 12.395121 3.637903 7.175177 11.941830 1.972339
## 19 12.395121 3.637903 7.175177 11.941830 1.972339
## 21 12.395121 3.637903 7.175177 11.941830 1.972339
## 11 5.348248 2.532664 3.117238 9.198678 1.230814
## 15 5.348248 2.532664 3.117238 9.198678 1.230814
## 3 7.459420 2.434463 5.174168 8.275405 2.125384
## 9 7.459420 2.434463 5.174168 8.275405 2.125384
## 13 7.459420 2.434463 5.174168 8.275405 2.125384
## FC_severeOverHealthy
## 4 3.039428
## 5 3.039428
## 6 3.039428
## 7 3.039428
## 14 3.039428
## 17 3.039428
## 18 3.039428
## 20 3.039428
## 1 3.114863
## 16 3.114863
## 2 3.499714
## 8 3.499714
## 12 3.499714
## 10 3.282614
## 19 3.282614
## 21 3.282614
## 11 3.632017
## 15 3.632017
## 3 3.399273
## 9 3.399273
## 13 3.399273Looking at the table above, there are no linked genes in our over expressed and duplicate genes list of genes with more than 1 copy number variation and being more than 3 fold expressed in severe compared to healthy cases.
Lets look at those two genes in our suppressed list that could possibly be linked, and find out how far away they are on the reverse strand of chromosome 2 for the TRABD2A and AC104809.2 genes
linkedPossibility <- subset(data, data$ORF=='TRABD2A' | data$ORF=='AC104809.2')
linkedPossibility## ID TRANSCRIPT_TYPE ACC ORF SOURCE
## 8242 ASHG19AP1B106995025V5 protein_coding ENST00000409520 TRABD2A GENCODE
## 33325 ASHG19LNC1A101589007V5 lncRNA ENST00000479944 TRABD2A GENCODE
## 47820 ASHGV40001229V5 lncRNA ENST00000457369 AC104809.2 GENCODE
## 53533 ASHGV40028330V5 lncRNA ENST00000418218 AC104809.2 GENCODE
## BUILD CHROM STRAND txStart txEnd
## 8242 HG19 chr2 - 85048790 85108369
## 33325 HG19 chr2 - 85048790 85062628
## 47820 HG19 chr2 - 241894441 241898771
## 53533 HG19 chr2 - 241894034 241906868
## GENE.DESCRIPTION
## 8242 TraB domain containing 2A [Source:HGNC Symbol;Acc:HGNC:27013]
## 33325 TraB domain containing 2A [Source:HGNC Symbol;Acc:HGNC:27013]
## 47820 uncharacterized LOC200772 [Source:NCBI gene;Acc:200772]
## 53533 uncharacterized LOC200772 [Source:NCBI gene;Acc:200772]
## SEQUENCE SPOT_ID
## 8242 TGAATGGGTTGAACTTTTCACAGGTCATCTTTGCTTTGAACCAGACCCTCCTGCAGCAGG <NA>
## 33325 AGCTTTGTGACTTCAGGTCATTTCATGGGCAACAACACAGTGCTGGATGTTTTGCGGCGT <NA>
## 47820 TTCTCCTTTGGAAGGATCTCTCTGGCCCATCTGGGGGAGGGCAGCCCAGAGACACGTGTG <NA>
## 53533 TTGCATAACAGAAGATGTATCAGGTCTTTGTCCTGGATCCTCGGAGGAAGCTTCTAAACC <NA>
## GSM5019817 GSM5019818 GSM5019819 GSM5019820 GSM5019821 GSM5019822
## 8242 7.378635 6.953671 7.801827 7.864007 6.907068 7.239426
## 33325 8.303377 8.384967 10.236728 10.156279 8.084781 6.830477
## 47820 6.560193 6.372759 6.818216 7.066998 6.807693 4.354209
## 53533 8.304387 7.709691 9.091352 9.255427 8.382099 4.568608
## GSM5019823 GSM5019824 GSM5019825 GSM5019826 GSM5019827 GSM5019828
## 8242 6.093318 5.939712 6.481947 7.140843 6.202466 3.844681
## 33325 5.825408 6.183036 6.988208 7.079069 5.734607 2.745772
## 47820 4.030067 4.100551 3.799968 4.372259 2.814921 3.617909
## 53533 2.568134 4.222530 2.564730 2.360941 2.814921 2.745772
## GSM5019829 GSM5019830 GSM5019831
## 8242 3.419549 4.082650 4.029360
## 33325 2.620153 2.747991 3.494433
## 47820 2.620153 2.747991 3.471045
## 53533 2.620153 2.747991 2.333044We can see from the data table below that the TRABD2A gene starts at 85048790 kb pair and ends at 85108369. While the AC104809.2 gene starts at 241894441 kb pair and ends at 241906868.
print('space between the end of TRABD2A and beginning of AC104809.2:')## [1] "space between the end of TRABD2A and beginning of AC104809.2:"241894434-85108369## [1] 156786065print('length of TRABD2A genes:')## [1] "length of TRABD2A genes:"85108369-85048790## [1] 5957985062628-85048790## [1] 13838print('length of AC104809.2 genes:')## [1] "length of AC104809.2 genes:"241898771-241894441## [1] 4330241906868-241894034## [1] 12834This is a space of 156786065 kb pairs between the two genes. The length of the TRABD2A gene is 59,579 kb pairs long for CNV1 and 13,838 kb pairs long for CNV 2.The CNV 1 of AC104809.2 is 4,330 kb pairs long and 12,834 kb pairs long for its CNV 2.
If we take the space between these two genes on the reverse strand of chromosome 2, we can see the number of genes that could possibly fit in this space span of 156,786,065 kb pair length.
156786065/((12834+4330)/2)## [1] 18269.18156786065/((59579+13838)/2)## [1] 4271.111There is a possibility of 4,271 genes similar to TRABD2A existing in this space of the same chromosome 2 reverse strand, and 18,269 genes similar to the AC104809.2 gene. This doesn’t appear to show significance of these two genes being linked as a group in affected genes of the covid-19 virus. Because literally thousands of genes could be inbetween these two genes and aren’t in our groups of genes more than doubled 3 fold or under expressed by more than 60% and also having any amount of CNVs.
We can look at a list of those genes right now.
GenesChrom2Reverse <- subset(Genes, Genes$CHROM=='chr2' & Genes$STRAND=='-')
GenesCh2Rev_unique <- unique(GenesChrom2Reverse$ORF)
head(GenesCh2Rev_unique,200)## [1] FAR2P2 LOC654342 RAB6C-AS1 LOC100286922 BRE-AS1
## [6] LOC100505736 BIRC6-AS2 FAM95A LOC442028 LOC100287010
## [11] LOC389033 LOC401010 MGC16025 FAR2P1 LDAH
## [16] FLJ33534 LINC01116 MIR4435-2HG LINC01106 PCBP1-AS1
## [21] NRXN1 LINC00471 AC016757.1 AC012358.1 AC012456.1
## [26] LINC01854 ACOXL-AS1 LINC01121 LINC00487 AC016747.1
## [31] AC019080.1 AC079354.1 AC005104.1 AC093690.1 AC012506.2
## [36] LINC01946 AC009226.1 AC068481.1 AC104809.1 CCNT2-AS1
## [41] AC009487.1 HAGLR LINC01280 AC009313.1 AC010884.1
## [46] TGFA-IT1 AC106900.1 AC016716.2 AC083900.1 AC078883.1
## [51] LINC01594 AC015977.2 LINC01107 AC013733.1 AC064875.1
## [56] LINC01831 NRIR LINC01907 CFLAR-AS1 LINC01876
## [61] AC093642.1 AC007463.1 AC016722.1 MIR217HG AC073409.1
## [66] AC007966.1 AC092164.1 AC078883.2 LINC01247 AC012065.1
## [71] AC073636.1 AC017101.1 CERS6-AS1 LINC01940 RAPGEF4-AS1
## [76] LINC01820 AC092839.1 LINC01494 RNF144A-AS1 AC012070.1
## [81] LINC01890 LINC01185 U51244.1 AC006460.1 AC009411.1
## [86] LINC01939 AC073641.1 AC104653.1 AC096554.1 AC105398.1
## [91] AC010975.1 AC017048.1 LINC01822 LINC01159 AC140481.1
## [96] STEAP3-AS1 FLJ31356 AC108025.1 AC016738.2 AC007163.1
## [101] LINC00276 AC092162.2 LINC02580 AC159540.1 RGPD4-AS1
## [106] AC021188.1 MEIS1-AS2 LINC00309 AC099344.1 AC103563.2
## [111] AC011747.1 LINC01593 AC010745.3 LINC01816 AC011247.1
## [116] AC108868.1 LINC01249 AC007557.2 AC007098.1 AC013402.2
## [121] AGBL5-AS1 FSIP2-AS1 LINC01891 LINC01090 LINC01819
## [126] UTAT33 AC012594.1 AC079354.3 PGM5P4-AS1 HS1BP3-IT1
## [131] LINC01807 AC012485.2 AC009495.2 AC018467.1 AC098820.1
## [136] LINC01628 AC097717.1 ITGA6-AS1 LINC00342 AC133785.1
## [141] AC007743.1 AC104809.2 PANTR1 MYCNOS AC093732.1
## [146] AC016907.2 AC007179.2 AC020601.1 AC009505.1 AC016683.1
## [151] LINC01114 AC013476.1 AC017053.1 AC007405.1 LINC01914
## [156] LINC01250 AC067960.1 AC106869.1 LINC01103 LINC01827
## [161] AC018685.2 DPP10-AS1 AC012074.1 ID2-AS1 AC016723.1
## [166] AC114808.1 AC013270.1 LINC01815 AJ239322.1 LINC00298
## [171] AC009299.3 AC010148.1 LINC00607 RMDN2-AS1 AC007405.2
## [176] AC061961.1 LINC01814 LINC01920 AC013727.2 MIR7515HG
## [181] AC097662.1 AC007881.2 LINC01945 LINC01923 AC114808.2
## [186] AC019118.2 LINC01829 LINC00299 ANKRD44-IT1 LINC01812
## [191] AC073254.1 AC020594.1 LINC01792 LINC01797 HOXD-AS2
## [196] LINC01304 AC073257.2 LINC02245 LINC01115 AC011995.2
## 44824 Levels: A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2ML1-AS1 A2ML1-AS2 ... ZZEF1There are 44,824 unique genes located in that space of chromosome 2 on the reverse strand.Here are the first 100 of those genes.
head(GenesChrom2Reverse[GenesChrom2Reverse$ORF %in% GenesCh2Rev_unique,],100)## ID ACC ORF CHROM STRAND
## 6 ASHGV40000318V5 NR_046258 FAR2P2 chr2 -
## 7 ASHGV40004004V5 NR_046259 FAR2P2 chr2 -
## 8 ASHGV40056696V5 NR_046260 FAR2P2 chr2 -
## 45 ASHGV40002743V5 NR_027238 LOC654342 chr2 -
## 97 ASHGV40003779V5 NR_036537 RAB6C-AS1 chr2 -
## 101 ASHGV40003810V5 NR_037695 LOC100286922 chr2 -
## 102 ASHGV40003811V5 NR_037696 LOC100286922 chr2 -
## 103 ASHGV40028220V5 NR_037694 LOC100286922 chr2 -
## 236 ASHGV40026530V5 NR_028308 BRE-AS1 chr2 -
## 237 ASHGV40026532V5 NR_120504 LOC100505736 chr2 -
## 238 ASHGV40026580V5 NR_125793 BIRC6-AS2 chr2 -
## 239 ASHGV40027071V5 NR_038409 FAM95A chr2 -
## 240 ASHGV40027073V5 NR_037597 LOC442028 chr2 -
## 241 ASHGV40027193V5 NR_037885 LOC100287010 chr2 -
## 242 ASHGV40027413V5 NR_026740 LOC389033 chr2 -
## 245 ASHGV40027435V5 NR_002826 LOC401010 chr2 -
## 247 ASHGV40028295V5 NR_026664 MGC16025 chr2 -
## 412 ASHGV40056693V5 NR_026758 FAR2P1 chr2 -
## 465 ASHGV40000183V5 NR_104233 LDAH chr2 -
## 498 ASHGV40001928V5 NR_040080 FLJ33534 chr2 -
## 520 ASHGV40056709V5 ENST00000295549 LINC01116 chr2 -
## 551 ASHGV40027266V5 NR_015395 MIR4435-2HG chr2 -
## 552 ASHGV40003487V5 ENST00000409569 MIR4435-2HG chr2 -
## 566 ASHGV40003986V5 NR_046111 LINC01106 chr2 -
## 567 ASHGV40056679V5 NR_027244 LINC01106 chr2 -
## 568 ASHGV40056680V5 ENST00000448359 LINC01106 chr2 -
## 611 ASHGV40026898V5 ENST00000435880 PCBP1-AS1 chr2 -
## 612 ASHGV40001043V5 ENST00000447773 NRXN1 chr2 -
## 626 ASHGV40028197V5 ENST00000313064 LINC00471 chr2 -
## 658 ASHGV40028275V5 ENST00000470346 AC016757.1 chr2 -
## 730 ASHGV40026761V5 ENST00000366153 AC012358.1 chr2 -
## 734 ASHGV40026360V5 ENST00000430048 AC012456.1 chr2 -
## 773 ASHGV40056692V5 NR_122042 LINC01854 chr2 -
## 774 ASHGV40004680V5 NR_122041 LINC01854 chr2 -
## 775 ASHGV40027261V5 NR_122074 ACOXL-AS1 chr2 -
## 776 ASHGV40000455V5 ENST00000418615 ACOXL-AS1 chr2 -
## 804 ASHGV40003701V5 ENST00000378479 LINC01121 chr2 -
## 823 ASHGV40026283V5 ENST00000382045 LINC00487 chr2 -
## 839 ASHGV40026811V5 ENST00000420918 AC016747.1 chr2 -
## 851 ASHGV40003568V5 ENST00000397057 AC019080.1 chr2 -
## 926 ASHGV40027933V5 ENST00000409819 AC079354.1 chr2 -
## 937 ASHGV40000363V5 ENST00000414896 AC005104.1 chr2 -
## 956 ASHGV40026533V5 ENST00000418963 AC093690.1 chr2 -
## 966 ASHGV40026458V5 ENST00000426527 AC012506.2 chr2 -
## 970 ASHGV40026568V5 ENST00000416279 LINC01946 chr2 -
## 983 ASHGV40027982V5 NR_110283 AC009226.1 chr2 -
## 984 ASHGV40027981V5 ENST00000432413 AC009226.1 chr2 -
## 1023 ASHGV40004389V5 ENST00000415520 AC068481.1 chr2 -
## 1024 ASHGV40000663V5 ENST00000428379 AC068481.1 chr2 -
## 1047 ASHGV40000603V5 ENST00000425110 AC104809.1 chr2 -
## 1056 ASHGV40000670V5 ENST00000428857 CCNT2-AS1 chr2 -
## 1057 ASHGV40027465V5 NR_036549 CCNT2-AS1 chr2 -
## 1066 ASHGV40000854V5 ENST00000437683 AC009487.1 chr2 -
## 1090 ASHGV40004419V5 ENST00000452365 HAGLR chr2 -
## 1091 ASHGV40003727V5 ENST00000644334 HAGLR chr2 -
## 1092 ASHGV40004418V5 ENST00000416928 HAGLR chr2 -
## 1126 ASHGV40004407V5 ENST00000449783 LINC01280 chr2 -
## 1140 ASHGV40027630V5 ENST00000425470 AC009313.1 chr2 -
## 1147 ASHGV40027203V5 ENST00000456519 AC010884.1 chr2 -
## 1164 ASHGV40026909V5 NR_046798 TGFA-IT1 chr2 -
## 1169 ASHGV40000456V5 ENST00000418620 AC106900.1 chr2 -
## 1186 ASHGV40000457V5 ENST00000418621 AC016716.2 chr2 -
## 1242 ASHGV40027988V5 ENST00000421964 AC083900.1 chr2 -
## 1253 ASHGV40000991V5 ENST00000444919 AC078883.1 chr2 -
## 1254 ASHGV40000840V5 ENST00000436922 AC078883.1 chr2 -
## 1276 ASHGV40027232V5 ENST00000445083 LINC01594 chr2 -
## 1288 ASHGV40000508V5 ENST00000420852 AC015977.2 chr2 -
## 1314 ASHGV40003816V5 ENST00000446979 LINC01107 chr2 -
## 1331 ASHGV40027792V5 ENST00000449835 AC013733.1 chr2 -
## 1344 ASHGV40026367V5 ENST00000425974 AC064875.1 chr2 -
## 1368 ASHGV40001078V5 ENST00000449772 LINC01831 chr2 -
## 1404 ASHGV40004803V5 ENST00000414795 NRIR chr2 -
## 1405 ASHGV40026285V5 ENST00000366140 NRIR chr2 -
## 1433 ASHGV40028189V5 ENST00000415174 LINC01907 chr2 -
## 1459 ASHGV40056718V5 ENST00000415011 CFLAR-AS1 chr2 -
## 1469 ASHGV40027591V5 NR_110249 LINC01876 chr2 -
## 1470 ASHGV40001051V5 ENST00000448255 LINC01876 chr2 -
## 1473 ASHGV40000289V5 ENST00000412193 AC093642.1 chr2 -
## 1488 ASHGV40004390V5 ENST00000416534 AC007463.1 chr2 -
## 1494 ASHGV40056624V5 ENST00000453936 AC016722.1 chr2 -
## 1513 ASHGV40026775V5 ENST00000446139 MIR217HG chr2 -
## 1516 ASHGV40056687V5 ENST00000451749 AC073409.1 chr2 -
## 1523 ASHGV40027809V5 NR_110214 AC007966.1 chr2 -
## 1524 ASHGV40004379V5 NR_110216 AC007966.1 chr2 -
## 1544 ASHGV40026544V5 ENST00000452212 AC092164.1 chr2 -
## 1570 ASHGV40027704V5 ENST00000441212 AC078883.2 chr2 -
## 1580 ASHGV40026276V5 ENST00000448901 LINC01247 chr2 -
## 1589 ASHGV40000937V5 ENST00000441870 AC012065.1 chr2 -
## 1598 ASHGV40056711V5 ENST00000432925 AC073636.1 chr2 -
## 1617 ASHGV40027818V5 ENST00000453665 AC017101.1 chr2 -
## 1674 ASHGV40027675V5 ENST00000425636 CERS6-AS1 chr2 -
## 1675 ASHGV40002607V5 ENST00000599361 CERS6-AS1 chr2 -
## 1691 ASHGV40003763V5 ENST00000455228 LINC01940 chr2 -
## 1714 ASHGV40000694V5 ENST00000430128 RAPGEF4-AS1 chr2 -
## 1715 ASHGV40001192V5 ENST00000455435 RAPGEF4-AS1 chr2 -
## 1716 ASHGV40027709V5 ENST00000435328 RAPGEF4-AS1 chr2 -
## 1733 ASHGV40000450V5 ENST00000418415 LINC01820 chr2 -
## 1737 ASHGV40026752V5 ENST00000433475 AC092839.1 chr2 -
## 1747 ASHGV40028068V5 ENST00000419511 LINC01494 chr2 -
## 1755 ASHGV40026289V5 ENST00000418970 RNF144A-AS1 chr2 -
## SEQUENCE
## 6 AGCAAAATGTGATTCCAGGTCTTGGCAACCTCTGAAATTCCAACTCCATTTGCGAGAGCT
## 7 ACGGACACCGGCTGGGAAAGGGTTTCTTCTGTCCATAAAAGCTACTCCAATGGCTGTGGG
## 8 TTTTGCTGTGCTGGGACCTGTGCATGCCAGACAAGGCCAAGCTGGCTGAAAGAGCAACCA
## 45 CTGTGAAAGGACTGCTGGCCAGACCCCCAAGCTAGCCCGCCAGGCCTCCATAGAGCTGCC
## 97 TGACGAAAAAGGAAATAGCAATGTTTTTTGAGTATGGCAAGTGTTTCCAAGCATTCAGAA
## 101 AAGGACCCCTTCGAGATTTCGTTCCTTTGGCTCCCTGGGAAGTGGGGGCCTTTCTTCCTT
## 102 GGAGGAAGCGGATTTCGTTCCTTTGGCTCCCTGGGAAGTGGGGGCCTTTCTTCCTTCTGC
## 103 CGGATAGGACCTCTGTTTGTCTTTCGATCATTGTAAATATCTGTATGCAATTTGCTATTT
## 236 GCCAAATGAAAATTGTTGAGTTAGGTCAGTAAGATTGAGTAGACAGATCCTTCTGATTTT
## 237 TGTCTGTTACAGAGAGATCTGACTTGACTTTTGGGCCCTCCTGGTATATGGACTTGTACT
## 238 AGGGTAACTCCCTTGCTCTAAGAGCAATTACTATATGATGCTTCCAGTTTGAGGAATAAA
## 239 TTAATCCTGAGATGGCTTCAGGGGCTGGTCCTTCTCCATGGCCCCCTCCACATATCTCAG
## 240 CAGCCACTGGAACCAGCTCTGCACAGCTCAGACCTGAGTGATGAGGACACAGCTTCGCAG
## 241 TAAAGACTTCTGGGAAGTGTAGTTTGCATTGTTATCCCACTGTTCTAGAGGGCAGGGATG
## 242 GGCCCCTGCTTTGCGCGCTGGCCGGGCTGGCCCTGCTCTGTGCCGTGGGCGCTTTGGCCG
## 245 CAGCGGCTGGCCCAGGGGCCAGAGGATGAGCTGGAGGATCTACAGCTCTCAGAGGAGGAC
## 247 TTCAGGGGAATCTGAGAAAAGTTTGAAGAAAGAAAATTCCACTCGGCCAGCCAACCTTGG
## 412 TTTTGCTGTGCTGGGACCTGTGCATGCCAGGCAAGGCCAAGATGGCTCAAAGAGCAACCA
## 465 CAAGAAGATTCTTACAACATCAGAGGATTCAAACGCTCAAGAAATTAAGGACATTTATGG
## 498 GGTGTCTCAGCAGCAGCCTTGTGGCTGTGCCTCTTCTGTGCCCTCCGAGTTCTAGGCTGA
## 520 GGAAATGACCCGAACTGCCAGCCTGCGCCTTTGCAGCCGGCCCTCGCTTTGCTGAAGACG
## 551 TTATAAATCTTCAATACATCCTGTCCCCCTAAAACGGCATCTGGGTCTTTTGAGGGTTAA
## 552 CCTCTCCCTGAATAACTGGGAGATGAAACAGGAAGCTCTATGACACACTTGATCGAATAT
## 566 GCACGCATAGCTGCCCCAGATCCCGGAAGAAAATCTCTCCCACACCACTGTAGTCAGAGA
## 567 TAAAATTTTTTTCCAAAATAAAATAAACAAAAGGGGCTTTTTGCAACCCAATTCCTATCT
## 568 CCCTAAATATAAAAAAAAGTTGAAGGAGGCAGAAGGGAGAGTGATGCACGATGGGCAAGG
## 611 AGAATGAAAAGGGAGTGAAATTTCCCGTGATCTTTCCACAAATGACCAGCTTGGGGAGTG
## 612 GCCTCCAGAGGCTGGTCTGCGATTTGCTTTGGCTGACAGAATATGATGAAGTGATGTTAT
## 626 AGTCTTTCCCCAAAGGAGGTAGAAGATGGGGAAGATGAGATGTCAGAAGCTAAGGACAAT
## 658 GAGTGACTTATTTGTGTTTTCCTCAAAGCTAGAGGGGACCCCCAATCTGTTTGTTTCCAG
## 730 ACCAAGAGCACTATATAATAATCAGAAGCAGCAGCCAGCAGTTATCTACTGACAAACTCG
## 734 ATGAGGTGACCCAAGTCACCAGAGGAAAAGTGTCTGTCCCCAATCTCCACATTAAATTTG
## 773 GTGCAGTATCAGGAATGTGATATGCGACATACACTTAGCACATGCTGGTTCCTTTCTCTT
## 774 AACTTGGAAGCAGATTATTTTCTGGAGTCTGTAGGCAACTCACTCCTGGTCCTGTTCTCT
## 775 CACCTCTGTTCCTGGCTGTCAAGATGATAATAATAATTACCATCCTTTCACTCACAAATG
## 776 GTGATCCCAGTGCCTCACTGCTTCCAGTTGCTGGAGGATATGTGGTGCTGCACTGACAAA
## 804 GCCTGCACAGGATACAGGCGTAACAAAGACAAGGATGAAATAAGTCCTGTGATGGAGAGA
## 823 ATGCTCTCTGTTCCCTGTGAGAAGAAGGGGTTTCTTTTCTTCTGGGATGATTCATCCCTT
## 839 TGGCTGAACCAAATGTTTCCTCAAAACTCACATTTTTTCCCACCATTTCAGAAGCTGCCT
## 851 TCTGATACAGCCAAACTCCACGCCACCTGGTTTGCTCAACAGCAAAAGACACGGCCGGGT
## 926 ATGTTCAATATCCCAACATGACCAAAAGGGTCAAATTCCAGCTCTAGTCTTCACATCTTT
## 937 GGAGAACCCGGTTGAAAATGAAGCTCAGAGAAAATAAGCAAACACCTGTCACTGCTTCCT
## 956 TATAGGCTGGATATGGTCACTCTGATGGCTTATTTGGAGGAAGTAATTTTAAATAGGTTT
## 966 AGTAAAACAACAAGTTTCTGTTAATTTAGGGCCAACCCATGAGTAAACAGATAGAGCCTG
## 970 AGCTGCTTACCCCTCACTGGGTTGTGGCATGAACAATAAATACACTTTTAAGATACTGAA
## 983 TAAGCTATGTACTATTGAAGGAGCTTTAGCCGCTGCAAATCTTATCCTTCCTCCCTCCAG
## 984 TTCAGTGTCGAAATTGGTATGGAGACGTGGATGGAGATTTGAGTCTTAGGAATTTGGGAA
## 1023 TCAAAGCCAGCAAAAGAAGAGTTTCTAGAGAAAGGAGAGGATTGATGGGTTCACTGGTGC
## 1024 TCAAAGCCAGGTACTCTGCTCAGTGTGGGGACTCTAGGAGTGACATAGACACAGATGTTT
## 1047 CACCTGCCAGGTGAGGACACAGAAGCATGCGTGGGCCAGCGCCTCTCCCAGCCGCGCCCC
## 1056 CCACTCATGGCAATCACAGGAATATATAAAACATGAGCAGAAAGAGGCCTTTGGAGAAAT
## 1057 ACATATATTGAGGTTCTGGAGTGATTCATCCTACCCTCATACATAAATGTTTGTGCTAAC
## 1066 ATCCTGCGGGATTGTTTCAGAAACCCCTAGGAAAAAGCCGCGCACGCAGTAATCATGAAA
## 1090 CACTGGAAAGAGAGGAGGTGGGGACGGATATGGTATTTGTAGGGCAGCGCTGTGAACAAT
## 1091 CGTACTCCAGATCTGGGGACCCTTCACCTGCCTCTACTACTGCAAATGATTGGATATTCG
## 1092 TGCTTCCCAGATCTGGGGACCCTTCACCTGCCTCTACTACTGCAAATGATTGGATATTCG
## 1126 TCTTCCATCTGCCAGAGGCTAAGCTGCAGGAGGTACGTGGCCATAAGAAACCCGTGACAC
## 1140 GAAGTAAAATAGACCTGTATTCCTGTCATTCTCTTTCTCATTTTCTTCCTCCTCACCAAA
## 1147 TGCATGAACGACAATTAAAGCACCACTTGAAAAGTCTGTTTTCCTCACATATTTGTTTTC
## 1164 ATTGGCTGGCTATTTTTATTCCTGTCTGAAAGCCAGGGATGGAAAACCCTGAGAGGTTTG
## 1169 AAGTTTTGTAATCTGCTAATTGACAGGGGACATCGTCTCACTATATTGCCCCAGGCTGGA
## 1186 AGAGATGTAAATTTATAATTGAGGGCCACAAGGAATCAGGGAGCTGGAGGAGACTGCGTT
## 1242 CCTTCCCCTTGATGTAAATCTCAAGTGTTTAAAAGGAGGAATGAGTCTAAATCATAGAAA
## 1253 CTGCCGAGTGGCAAGAAAAACCTATTGGATGGTTACATGAGGACACAGCAAGAAAGCCCT
## 1254 CTGCCGAGTGGGTCAGAGAGCTTCAGGAGTCCCCGCTTGCCAAACAGTAGTACGTAAATA
## 1276 TACTAGAATGTTCTCTGCCATCCACTAAGCATTGAATCCCTCCAGACACTGTTACAACAG
## 1288 CCAGCTGCAGGAAAGTAATTTGGGCAAGAATGACTTTTCTTCATCCTGTAGATGAGGACG
## 1314 AATGGACCAAGATAGGAGCTAAAGGTGCTTGTGAGATTCCACGCATCATACTAGAGGTGT
## 1331 AATGACCCTCATTTTGGGGGTCAGAAAGGAAGCATGGACATTCACTCATCTCTATATGAA
## 1344 TCTGTAGTTCATTTCATTTCCCCAGATTTGTTATCATCCACCATCACTCATACAAGCCTA
## 1368 TCCTGGAAACAAACCTACTCTCAGAAAACCCATTGAAGTCCCTGTTTTACAACTAACATA
## 1404 TTATATATCTCGAAGAGGTTATATGGGCACATTGTGAGATGGTGGCCTCCCATGAGCCAA
## 1405 TCCATGCGTGCACTCTCTCTCTTCCCCTCCCTGCCCTTGCCTCCTTGCGTCTGCATAAAG
## 1433 TATGATGTGTAAATGTGGGGGAGGTTCAATGAGAGGTGGCCCAGAATACTTGTATAGGAA
## 1459 GAGACTGAGGCCAACGACCAAAGCAAAGGACAGCAGAACTGACTGACACAGCTCAGAAAA
## 1469 ATTTGGTATCAGTACCCTCAGTAAATCAGAGTTGCTGTGACCTGGGCTTTGATGTAAGGG
## 1470 TAAGATGTGTATTCCTGAGCCTGAGTCTACTGACAAATATACCACATCCCCAGAGTAAGT
## 1473 AGGAAAAATGCTCCACGTTTAGCTCCATGAACTTCAGACTTAAACAGCATCACTGGCTCC
## 1488 AAGACCTCTACGGAAAGATAAAGTTCTCGGAGATTGGTTGGCCTACAGTATCTAAGCGGT
## 1494 CTACCCCAAGGCCTGCCAGAATGAAAATAAAGAACAAAGACAACAAAGAAAACAGCCGAC
## 1513 TTGGCCAGGGAAGAGCTCTAATATCACACATTAATAACCTTACCTTTGTAACATGTAAAT
## 1516 GTGTAGAAAAAACAAGAAAATTGTGTACCTAACTCTCCATGGTAACCTCTCTCACTTTTT
## 1523 GCCTCGCGACCCGTGTGTGGCGATCCCTGCCCCGCTCCCCAGCAGGCCTGCGGCCGCCAG
## 1524 TAAGCTTTGTTGAACAGAGTTGGAGGGAATCATTGCTGTGAGAAGCTGACAGTGGTGGAT
## 1544 TGACTGTGAGAAGAAAAGCAAAAGCAAAAATGCGAAGCGTAGCTATGATGCTATTTTAGT
## 1570 CCAGCAAACACGCCCGGAGGGAAGAACCGGCGGAAAGCACTTTGTTTAAAACAGAAAAAA
## 1580 GCTTCTCCAAGTACTTGATTGCTTGAAATTGGACTATAGTAGCTTCAAGAAACACTTATA
## 1589 TGTATAGCAGGTAACCATTTGTGTCCTGGATGTCTGTCCACCCAAGAGGCCATGACTTTG
## 1598 ACCACCCCACAATGGCAGGAGACACCATGAGATGTTTTCTACTGTAGAAACTTTCTCATT
## 1617 CATGGAAGAGTTTGTAACGTAACCAGTGAAATGAAGCATCCATTTTAGAGAAAAGGAAAT
## 1674 CTGCAAACCCCATTTTAATTAGCCCCAAAGAACTGTGCCCTAAAATGTAAAATGAAATAA
## 1675 GGCTGTGGAGGTAATCTTATTTTCCTAAGGGTAGTTTCATGATGACAGTGTCAAAAAATT
## 1691 TCGAAGGCTAATCTCATCTAGAAACACCTTTACAGCACCACCGTCCAAAGTGGAGATGAT
## 1714 ATGAACTCCACTCAGGGTAAGCCTGCCTTGTTCCTGGAGCCCTCTTCCTCTGGCTGCAAT
## 1715 AACTCCACTCAGGCCTTGTTCCTGGAGCCCTCTTCCTCTGGCTGCAATCCAGAGCAAGTT
## 1716 GCTTAAGAAATCCAGGCACTTGAGAGCCACTGTAAGTAAACTCTAATTCCCACAGCAGAA
## 1733 TACAGAAGAGGTCTATGGTTTCTTAGACACGCGTGGATTCTCACAGCCACCACCACAGAC
## 1737 TGAGCTACCACAGGTCATAACCATTAGGAAAGAAACTGGAATGTTACCATGCCAGGCTTT
## 1747 TCTGGAACTTCCCACATCTCCACGTGCCCTCACCTTCAGTGAGAGTCTGAGAAGAAGCCG
## 1755 GCATGGAAGGTGACTACTCATGACTGCAACTTAGAGAACAAGGGTTATAATAAAAATAAALets compare these list of genes we made earlier with a study of six different research studies gathered last year on alzheimer, flu vaccines and antibiotics, tetanis vaccinations, hemochromatosis, myocardial infarction males, and overweight females using green tea extract to lose weight.
otherStudies <- read.csv('all_6_studies.csv', sep=',', header=T,
na.strings=c('',' ','NA'))head(otherStudies)## GENE_SYMBOL Tetanis_Means Alz_Females_AD1_Mean Alz_Females_control1_Mean
## 1 A1BG 22.5144403 6.630 6.647
## 2 A1CF 22.9031540 6.521 6.495
## 3 A2M 0.2789759 10.719 10.231
## 4 A2ML1 21.1270650 6.795 6.571
## 5 AAAS 24.6740221 6.873 6.875
## 6 AACS 21.2603715 7.753 7.946
## Alz_males_AD1_Mean Alz_males_control1_Mean Alz_FC_fem_ctrl_AD
## 1 6.602 6.619 0.998
## 2 6.501 6.506 1.004
## 3 10.626 10.377 1.048
## 4 6.791 6.568 1.034
## 5 6.904 6.828 1.000
## 6 7.771 7.907 0.976
## Alz_FC_male_ctrl_AD FC_MI_males HealthyMI_Male_Means MI_Male_Means FC_t1
## 1 0.997 1.0070609 5.653239 5.693156 1.0201514
## 2 0.999 1.0120300 2.616675 2.648154 0.9619983
## 3 1.024 1.0193310 3.568283 3.637261 1.0350745
## 4 1.034 1.0143156 3.014349 3.057501 1.0353801
## 5 1.011 0.9996461 7.043090 7.040597 0.9648626
## 6 0.983 1.0018558 5.423620 5.433685 0.9485759
## FC_t3 FC_t7 FC_t21 FC_nt1 FC_nt3 FC_nt7 FC_nt21
## 1 0.9854788 1.0103582 1.0051797 0.9792245 1.0458806 0.9965033 0.9167685
## 2 1.0271201 0.9809052 0.9904443 0.9994338 0.9561409 1.0465855 1.0123896
## 3 0.9863961 0.9610774 0.9941113 1.0260937 1.0013217 1.0091036 1.0198015
## 4 1.0013636 0.9895909 0.9773165 0.9770602 0.9667186 1.0000093 1.0030886
## 5 1.0615646 0.9563912 0.9983206 1.0909490 0.9806961 0.9945219 0.9938919
## 6 1.0247688 1.0556220 0.9404336 1.0075403 0.9839949 1.0119647 0.9231889
## FCB_1 FCB_3 FCB_7 FCB_21 T0_Mean T1_Mean T3_Mean T7_Mean
## 1 0.9639935 1.0082221 1.0046967 0.9210742 4.217513 4.302502 4.240024 4.283943
## 2 0.9358623 0.8948162 0.9365016 0.9481045 3.290115 3.165085 3.250923 3.188847
## 3 0.7442716 0.7452552 0.7520397 0.7669312 3.206508 3.318974 3.273823 3.146397
## 4 0.8597981 0.8311828 0.8311906 0.8337578 2.799989 2.899052 2.903006 2.872788
## 5 0.9600159 0.9414838 0.9363262 0.9306070 4.520001 4.361180 4.629674 4.427780
## 6 0.8493087 0.8357154 0.8457145 0.7807543 6.280743 5.957762 6.105329 6.444919
## T21_Mean NT0_Mean NT1_Mean NT3_Mean NT7_Mean NT21_Mean FC_egcg_quer FC_egcg
## 1 4.306132 4.151913 4.065655 4.252190 4.237321 3.884642 0.984 0.985
## 2 3.158375 3.080839 3.079095 2.944048 3.081198 3.119373 0.991 1.017
## 3 3.127869 2.325823 2.386512 2.389667 2.411421 2.459171 1.003 0.999
## 4 2.807623 2.463947 2.407425 2.327302 2.327324 2.334512 1.009 1.016
## 5 4.420344 3.977521 4.339273 4.255508 4.232195 4.206345 1.001 0.999
## 6 6.061019 5.294369 5.334290 5.248914 5.311716 4.903717 0.998 1.005
## DE_EGCG DE_Quercentin Pre_Means Post_EGCG_Means Post_EGCG_Quercentin_Means
## 1 0.086 0.092 5.789 5.703 5.697
## 2 -0.084 0.045 4.959 5.043 4.914
## 3 0.006 -0.016 5.221 5.215 5.236
## 4 -0.073 -0.040 4.443 4.516 4.483
## 5 0.008 -0.011 8.117 8.109 8.128
## 6 -0.036 0.012 6.799 6.835 6.787
## hemo_G1M_Mean hemo_G2M_Mean hemo_G3M_Mean hemo_G1F_Mean hemo_G2F_Mean
## 1 4.522635 4.748975 4.725348 4.824635 4.955795
## 2 2.291845 2.334910 2.147122 2.256710 2.415030
## 3 4.281935 4.509535 4.189510 4.254255 4.422700
## 4 2.973803 3.272673 3.054648 3.222355 3.461075
## 5 5.491507 5.396690 5.421036 5.213965 5.247970
## 6 5.498480 5.392593 5.515120 5.470545 5.347540
## hemo_G3F_Mean hemo_healthyFemale_Mean hemo_healthyMale_Mean hemo_Female_Mean
## 1 4.63670 4.816690 4.706227 4.839512
## 2 2.59693 2.546950 2.229808 2.388082
## 3 4.36168 3.998705 4.323837 4.343118
## 4 2.89653 3.357760 3.048290 3.252678
## 5 5.57909 5.287245 5.522265 5.300592
## 6 5.74754 5.471870 5.673802 5.476742
## hemo_Male_Mean hemo_FC_1m hemo_FC_2m hemo_FC_3m hemo_FC_1F hemo_FC_2F
## 1 4.670245 0.9609895 1.0090832 1.0040628 1.0016495 1.0288798
## 2 2.249433 1.0278219 1.0471352 0.9629181 0.8860441 0.9482047
## 3 4.316418 0.9903090 1.0429474 0.9689333 1.0639082 1.1060331
## 4 3.096857 0.9755642 1.0736093 1.0020858 0.9596740 1.0307690
## 5 5.435228 0.9944303 0.9772602 0.9816689 0.9861402 0.9925717
## 6 5.472299 0.9690996 0.9504371 0.9720324 0.9997579 0.9772783
## hemo_FC_3F hemo_FC_malesOverall hemo_FC_femalesOverall tetanis_GSM1443061
## 1 0.9626320 0.9923542 1.0047381 22.2254758
## 2 1.0196235 1.0088015 0.9376242 23.7878439
## 3 1.0907731 0.9982840 1.0861311 0.4436067
## 4 0.8626376 1.0159325 0.9687047 22.0408389
## 5 1.0551979 0.9842390 1.0025244 20.4283581
## 6 1.0503795 0.9644853 1.0008904 20.3136924
## tetanis_GSM1443062 tetanis_GSM1443063 tetanis_GSM1443064 tetanis_GSM1443065
## 1 22.383648 22.3137073 23.0564055 23.3328267
## 2 23.252106 22.0297034 22.0690760 23.7295220
## 3 0.275007 0.1890338 0.2750070 0.2387869
## 4 20.594164 21.3072342 22.3235782 0.9781956
## 5 22.423258 21.0154695 27.1071361 22.4659325
## 6 23.350445 0.5945485 0.4005379 0.4329594
## tetanis_GSM1443066 Alz_GSM2973262 Alz_GSM2973263 Alz_GSM2973264
## 1 20.0299356 6.736 6.649 6.612
## 2 0.4436067 6.545 6.480 6.588
## 3 0.2387869 11.253 10.758 10.790
## 4 0.6780719 6.816 6.819 6.779
## 5 20.0652334 6.654 7.013 6.696
## 6 21.5513548 7.579 7.964 7.532
## Alz_GSM2973265 Alz_GSM2973266 Alz_GSM2973267 Alz_GSM2973268 Alz_GSM2973269
## 1 6.560 6.575 6.471 6.601 6.680
## 2 6.483 6.466 6.443 6.448 6.511
## 3 11.280 10.550 11.016 10.375 10.232
## 4 6.931 6.630 7.164 6.498 6.492
## 5 6.919 6.852 6.603 7.000 6.767
## 6 7.575 7.828 7.763 7.721 7.851
## Alz_GSM2973270 Alz_GSM2973271 Alz_GSM2973272 Alz_GSM2973273 Alz_GSM2973274
## 1 6.620 6.695 6.636 6.549 6.631
## 2 6.537 6.486 6.481 6.471 6.557
## 3 11.219 10.559 11.929 10.030 11.262
## 4 6.941 6.536 6.569 6.748 7.007
## 5 7.041 6.719 7.130 6.641 6.798
## 6 7.693 7.656 7.168 7.945 7.643
## Alz_GSM2973275 Alz_GSM2973276 Alz_GSM2973277 Alz_GSM2973278 Alz_GSM2973279
## 1 6.638 6.610 6.629 6.633 6.575
## 2 6.501 6.522 6.561 6.483 6.495
## 3 10.870 10.028 10.711 10.903 10.508
## 4 7.001 6.707 6.659 6.758 6.719
## 5 7.414 7.448 6.721 7.281 6.612
## 6 7.517 7.640 7.619 7.287 7.772
## Alz_GSM2973280 Alz_GSM2973281 Alz_GSM2973282 Alz_GSM2973283 Alz_GSM2973284
## 1 6.686 6.594 6.571 6.662 6.610
## 2 6.545 6.541 6.462 6.500 6.488
## 3 10.889 10.479 10.737 10.755 9.645
## 4 6.915 6.992 6.746 6.725 6.604
## 5 6.763 6.654 6.956 6.645 6.597
## 6 7.657 7.693 7.449 7.926 8.040
## Alz_GSM2973285 Alz_GSM2973286 Alz_GSM2973287 Alz_GSM2973288 Alz_GSM2973289
## 1 6.586 6.590 6.587 6.598 6.680
## 2 6.540 6.522 6.523 6.470 6.530
## 3 10.631 9.751 11.035 10.142 10.214
## 4 6.540 6.504 6.989 6.693 6.658
## 5 6.594 6.856 6.879 6.744 6.890
## 6 7.645 7.879 7.600 8.110 8.053
## Alz_GSM2973290 Alz_GSM2973291 Alz_GSM2973292 Alz_GSM2973293 Alz_GSM2973294
## 1 6.551 6.680 6.569 6.676 6.580
## 2 6.473 6.518 6.507 6.517 6.465
## 3 10.348 10.304 9.772 11.610 10.145
## 4 6.683 6.547 6.521 6.591 6.536
## 5 6.866 6.778 6.907 6.981 7.039
## 6 8.405 8.068 7.578 7.603 8.300
## Alz_GSM2973295 Alz_GSM2973296 Alz_GSM2973297 Alz_GSM2973298 Alz_GSM2973299
## 1 6.559 6.617 6.894 6.557 6.570
## 2 6.556 6.482 6.476 6.525 6.504
## 3 9.673 11.446 10.918 10.640 10.878
## 4 6.559 6.559 6.666 6.903 6.570
## 5 6.756 7.035 7.097 6.749 6.896
## 6 8.035 7.817 7.296 7.639 7.533
## Alz_GSM2973300 Alz_GSM2973301 Alz_GSM2973302 Alz_GSM2973303 Alz_GSM2973304
## 1 6.896 6.618 6.638 6.594 6.678
## 2 6.471 6.440 6.523 6.503 6.528
## 3 11.223 9.633 10.446 11.354 10.838
## 4 6.530 6.749 7.304 6.596 6.826
## 5 6.872 6.779 6.739 6.934 7.056
## 6 7.453 8.124 7.700 7.661 7.470
## Alz_GSM2973305 Alz_GSM2973306 Alz_GSM2973307 Alz_GSM2973308 Alz_GSM2973309
## 1 6.592 6.636 6.648 6.622 6.577
## 2 6.487 6.526 6.541 6.500 6.479
## 3 9.562 10.928 10.706 10.236 10.858
## 4 6.502 6.765 7.201 6.636 6.895
## 5 6.865 6.647 7.092 6.790 6.809
## 6 8.161 7.995 7.431 8.184 7.630
## Alz_GSM2973310 Alz_GSM2973311 Alz_GSM2973312 Alz_GSM2973313 Alz_GSM2973314
## 1 6.715 6.777 6.606 6.632 6.615
## 2 6.590 6.486 6.523 6.515 6.494
## 3 11.231 10.371 9.716 9.869 10.132
## 4 6.997 6.588 6.515 6.653 6.560
## 5 6.704 7.227 7.214 6.902 7.241
## 6 7.646 8.063 7.857 7.971 8.042
## Alz_GSM2973315 Alz_GSM2973316 Alz_GSM2973317 Alz_GSM2973318 Alz_GSM2973319
## 1 6.610 6.642 6.647 6.583 6.641
## 2 6.504 6.494 6.522 6.490 6.613
## 3 10.695 10.372 10.453 10.354 10.450
## 4 6.854 6.470 6.590 6.684 6.803
## 5 6.974 6.882 6.819 6.893 6.794
## 6 7.839 8.073 7.907 8.087 7.866
## Alz_GSM2973320 Alz_GSM2973321 Alz_GSM2973322 Alz_GSM2973323 Alz_GSM2973324
## 1 6.559 6.603 6.668 6.644 6.610
## 2 6.502 6.495 6.483 6.540 6.473
## 3 9.839 9.939 10.398 10.141 9.838
## 4 6.535 6.611 6.610 6.432 6.538
## 5 6.892 6.853 7.039 6.723 6.770
## 6 8.056 8.031 8.042 8.387 8.139
## Alz_GSM2973325 Alz_GSM2973326 Alz_GSM2973327 Alz_GSM2973328 Alz_GSM2973329
## 1 6.570 6.587 6.673 6.566 6.645
## 2 6.468 6.551 6.534 6.514 6.499
## 3 10.110 11.115 9.570 11.067 9.929
## 4 6.476 6.566 6.497 6.825 6.521
## 5 7.003 7.070 6.926 6.840 6.811
## 6 7.861 7.953 7.640 7.896 7.972
## Alz_GSM2973330 Alz_GSM2973331 Alz_GSM2973332 Alz_GSM2973333 Alz_GSM2973334
## 1 6.667 6.552 6.558 6.601 6.649
## 2 6.541 6.492 6.479 6.535 6.488
## 3 9.643 10.062 11.117 10.779 10.415
## 4 6.578 6.527 6.740 6.741 6.464
## 5 6.895 6.740 6.985 6.869 6.665
## 6 7.991 8.069 8.038 8.148 7.930
## Alz_GSM2973335 Alz_GSM2973336 Alz_GSM2973337 Alz_GSM2973338 Alz_GSM2973339
## 1 6.661 6.617 6.542 6.547 6.612
## 2 6.516 6.546 6.458 6.470 6.522
## 3 10.890 11.026 10.927 9.637 10.613
## 4 6.557 7.165 7.070 6.436 6.803
## 5 6.818 6.669 6.496 6.883 6.927
## 6 7.931 7.801 7.574 8.119 7.864
## healthy_MI_Males_GSM4205364 healthy_MI_Males_GSM4205363
## 1 5.644049 5.679968
## 2 2.587690 2.586130
## 3 3.505137 3.588333
## 4 3.012391 2.997897
## 5 6.818183 7.215283
## 6 5.462818 5.451481
## healthy_MI_Males_GSM4205362 healthy_MI_Males_GSM4205361
## 1 5.625976 5.642286
## 2 2.596597 2.675930
## 3 3.518868 3.501965
## 4 3.021105 2.995948
## 5 7.099169 7.178522
## 6 5.399922 5.467114
## healthy_MI_Males_GSM4205360 healthy_MI_Males_GSM4205359 MI_Males_GSM4205358
## 1 5.678646 5.648512 5.641943
## 2 2.603796 2.649909 2.579765
## 3 3.726193 3.569199 3.635810
## 4 3.020613 3.038138 3.058363
## 5 7.064535 6.882851 7.085247
## 6 5.442549 5.317838 5.462760
## MI_Males_GSM4205357 MI_Males_GSM4205356 MI_Males_GSM4205355
## 1 5.721131 5.702217 5.670234
## 2 2.660311 2.675201 2.630861
## 3 3.774389 3.816698 3.545313
## 4 3.079992 3.084890 3.062900
## 5 6.842610 6.922287 7.140438
## 6 5.389249 5.423109 5.372327
## MI_Males_GSM4205354 MI_Males_GSM4205353 flu_GSM3409106_29_day_0
## 1 5.674048 5.749366 4.022284
## 2 2.669436 2.673351 3.189060
## 3 3.506585 3.544774 3.270110
## 4 3.041532 3.017330 2.888058
## 5 7.143140 7.109862 4.319929
## 6 5.519533 5.435134 6.487653
## flu_GSM3409107_29_day_1 flu_GSM3409108_29_day_3 flu_GSM3409004_29_day_7
## 1 4.244277 4.247060 4.368895
## 2 3.060868 3.437499 2.998192
## 3 3.412057 3.338492 3.061911
## 4 2.949764 2.865191 3.055791
## 5 4.274290 4.856434 4.384850
## 6 5.971451 6.582995 6.810864
## flu_GSM3409105_29_day_21_screening flu_GSM3409006_30._day_0
## 1 4.125401 4.256802
## 2 3.238962 3.092595
## 3 3.195047 3.117491
## 4 3.008899 2.748343
## 5 4.340757 4.680657
## 6 6.157318 6.178077
## flu_GSM3409007_30_day_1 flu_GSM3409008_30_day_3 flu_GSM3409009_30_day_7
## 1 3.930059 4.058096 4.064191
## 2 3.384631 3.238654 3.390659
## 3 3.196030 3.448284 3.103494
## 4 2.770064 2.987480 2.731479
## 5 4.538579 4.693672 4.370276
## 6 5.981701 5.851573 6.441340
## flu_GSM3409005_30_day_21_screening flu_GSM3409013_05_.day_0
## 1 4.215869 4.373453
## 2 2.980764 3.588691
## 3 2.973532 3.231922
## 4 2.769358 2.763565
## 5 4.262211 4.559417
## 6 6.013923 6.176500
## flu_GSM3409014_05_day_1 flu_GSM3409015_05_day_3 flu_GSM3409016_05_day_7
## 1 4.733170 4.414916 4.418743
## 2 3.049756 3.076615 3.177690
## 3 3.348835 3.034694 3.273787
## 4 2.977330 2.856346 2.831094
## 5 4.270671 4.338917 4.528213
## 6 5.920134 5.881419 6.082554
## flu_GSM3409012_05_day_21_screening flu_GSM3409161_33_day_0_no
## 1 4.577126 4.021917
## 2 3.255400 3.134153
## 3 3.215029 2.364401
## 4 2.644611 2.403953
## 5 4.658063 4.303755
## 6 6.011815 4.922308
## flu_GSM3409162_33_day_1_no flu_GSM3409163_33_day_3_no
## 1 4.231631 4.380898
## 2 3.146671 2.892426
## 3 2.516229 2.427865
## 4 2.427249 2.267024
## 5 4.466718 4.384636
## 6 5.002461 5.125761
## flu_GSM3409111_33._day_7_no flu_GSM3409160_33_day_21_screening_no
## 1 4.280365 4.119270
## 2 2.922931 2.957037
## 3 2.413767 2.281591
## 4 2.232214 2.324163
## 5 4.218476 4.113159
## 6 5.332674 5.335858
## flu_GSM3409124_36_day_0_no flu_GSM3409125_36_day_1_no
## 1 4.398104 3.736454
## 2 2.959022 2.914839
## 3 2.302118 2.290962
## 4 2.319035 2.418693
## 5 4.157258 4.337557
## 6 5.548462 5.451671
## flu_GSM3409126_36_day_3_no flu_GSM3409127_36_day_7_no
## 1 4.272086 4.211709
## 2 2.773035 3.316505
## 3 2.379305 2.552877
## 4 2.284622 2.503466
## 5 4.217106 4.207981
## 6 5.161908 4.998220
## flu_GSM3409123_36_day_21_screening_no flu_GSM3409135_38_day_0_no
## 1 3.697911 4.035720
## 2 2.901267 3.149342
## 3 2.529445 2.310950
## 4 2.356809 2.668853
## 5 4.378726 3.471550
## 6 4.706771 5.412336
## flu_GSM3409136_38_day_1_no flu_GSM3409137_38_day_3_no
## 1 4.228881 4.103586
## 2 3.175774 3.166684
## 3 2.352346 2.361830
## 4 2.376332 2.430261
## 5 4.213542 4.164780
## 6 5.548737 5.459073
## flu_GSM3409138_38_day_7_no flu_GSM3409134_38_day_21_screening_no
## 1 4.219890 3.836747
## 2 3.004159 3.499815
## 3 2.267620 2.566476
## 4 2.246292 2.322565
## 5 4.270130 4.127149
## 6 5.604253 4.668522
## EGCG_pre_GSM1923000 EGCG_pre_GSM1923004 EGCG_pre_GSM1923010
## 1 5.706 5.800 5.740
## 2 4.979 5.016 4.941
## 3 5.121 5.563 5.222
## 4 4.324 4.749 4.400
## 5 8.084 8.129 7.989
## 6 7.103 6.857 6.808
## EGCG_pre_GSM1923012 EGCG_pre_GSM1923007 EGCG_pre_GSM1923020
## 1 6.015 5.832 5.782
## 2 5.273 4.731 4.909
## 3 5.173 5.222 5.135
## 4 4.662 4.149 4.162
## 5 8.325 8.297 8.054
## 6 6.724 6.449 6.567
## EGCG_pre_GSM192998 EGCG_pre_GSM1922995 EGCG_pre_GSM1923002
## 1 5.706 5.586 5.662
## 2 4.876 4.776 4.931
## 3 5.004 5.222 4.902
## 4 4.543 4.413 4.722
## 5 8.130 8.069 8.134
## 6 6.871 7.024 6.713
## EGCG_pre_GSM1923008 EGCG_pre_GSM1923015 EGCG_pre_GSM1923018
## 1 5.909 5.765 5.944
## 2 5.032 4.933 4.788
## 3 5.206 5.536 5.223
## 4 4.499 4.312 4.345
## 5 7.652 8.358 8.428
## 6 6.936 6.955 6.801
## EGCG_pre_GSM1923022 EGCG_pre_GSM1923017 EGCG_post_EG_GSM1923001
## 1 5.830 5.773 5.765
## 2 5.109 5.129 5.192
## 3 5.613 4.946 5.179
## 4 4.269 4.652 4.761
## 5 8.135 7.859 8.005
## 6 6.694 6.688 6.785
## EGCG_post_EG_GSM1923005 EGCG_post_EG_GSM1923011 EGCG_post_EG_GSM1923013
## 1 5.656 5.769 5.399
## 2 5.037 5.247 4.868
## 3 5.383 5.412 4.975
## 4 4.438 4.681 4.337
## 5 8.171 8.118 8.163
## 6 7.020 6.989 6.822
## EGCG_post_EG_GSM1923021 EGCG_post_EG_GSM1923006 EGCG_post_EG_GSM1923014
## 1 5.663 5.907 5.761
## 2 4.890 5.117 4.948
## 3 5.113 5.219 5.222
## 4 4.753 4.410 4.232
## 5 7.842 8.045 8.419
## 6 6.704 6.703 6.822
## EGCG_post_EQ_GSM192996 EGCG_post_EQ_GSM1923003 EGCG_post_EQ_GSM1923009
## 1 5.528 5.765 5.765
## 2 4.849 4.864 4.815
## 3 5.222 5.072 5.080
## 4 4.709 4.658 4.689
## 5 8.247 8.209 7.751
## 6 6.800 6.560 6.948
## EGCG_post_EQ_GSM1923016 EGCG_post_EQ_GSM1923019 EGCG_post_EQ_GSM1923023
## 1 6.007 5.873 5.724
## 2 4.981 5.054 4.996
## 3 5.563 5.067 5.358
## 4 4.377 4.080 4.436
## 5 8.223 8.119 8.235
## 6 6.551 6.927 6.725
## EGCG_post_EQ_GSM192997 hemo_GSM3440208 hemo_GSM3440209 hemo_GSM3440210
## 1 5.220 4.56238 4.81020 4.45365
## 2 4.841 2.09868 2.31653 2.04278
## 3 5.292 4.10513 4.62942 4.74245
## 4 4.429 3.06069 3.20523 2.84005
## 5 8.116 5.57012 5.27629 5.62929
## 6 6.999 5.48106 5.39062 5.51213
## hemo_GSM3440211 hemo_GSM3440212 hemo_GSM3440213 hemo_GSM3440214
## 1 4.59318 5.00831 4.81082 4.63670
## 2 2.48208 2.30071 2.27742 2.59693
## 3 4.78624 4.33010 4.17939 4.36168
## 4 3.23898 3.10777 3.21977 2.89653
## 5 5.41060 5.24918 5.50758 5.57909
## 6 5.65298 5.68062 5.57775 5.74754
## hemo_GSM3440215 hemo_GSM3440216 hemo_GSM3440217 hemo_GSM3440218
## 1 4.79158 4.23071 4.78755 4.76449
## 2 2.01602 2.12694 2.33522 2.41957
## 3 3.59048 3.95629 4.26871 4.24737
## 4 3.04496 2.89996 3.50474 3.17661
## 5 5.14901 5.55669 5.46598 5.54285
## 6 5.32404 5.46950 5.16949 5.65141
## hemo_GSM3440219 hemo_GSM3440220 hemo_GSM3440221 hemo_GSM3440222
## 1 4.81271 4.28263 4.75098 4.65848
## 2 2.14875 2.47212 2.29080 2.24461
## 3 4.55171 4.37237 4.46928 3.94993
## 4 2.83115 2.98749 3.20899 3.31792
## 5 5.44622 5.42027 5.43238 5.31140
## 6 5.49682 5.37619 5.14108 5.39534
## hemo_GSM3440223 hemo_GSM3440224 hemo_GSM3440225 hemo_GSM3440226
## 1 5.12404 4.99079 4.84154 4.46118
## 2 2.49484 2.26881 2.25023 2.42566
## 3 4.57669 4.55858 4.15320 4.44834
## 4 3.41741 3.12679 3.43749 2.74246
## 5 5.02996 5.11653 5.46749 5.57488
## 6 5.52559 5.54575 5.38569 5.76546
## hemo_GSM3440227 hemo_GSM3440228 hemo_GSM3440229 hemo_GSM3440230
## 1 4.78024 5.00344 4.94174 4.69164
## 2 2.13643 2.15766 2.80044 2.29346
## 3 4.31399 3.60776 3.61760 4.37981
## 4 3.17802 3.14240 3.50765 3.20787
## 5 5.20048 5.51172 5.02345 5.55104
## 6 5.65881 5.72042 5.47654 5.46720
## hemo_GSM3440231
## 1 4.58005
## 2 2.19948
## 3 4.92526
## 4 3.13028
## 5 5.80198
## 6 5.55052colnames(otherStudies)## [1] "GENE_SYMBOL"
## [2] "Tetanis_Means"
## [3] "Alz_Females_AD1_Mean"
## [4] "Alz_Females_control1_Mean"
## [5] "Alz_males_AD1_Mean"
## [6] "Alz_males_control1_Mean"
## [7] "Alz_FC_fem_ctrl_AD"
## [8] "Alz_FC_male_ctrl_AD"
## [9] "FC_MI_males"
## [10] "HealthyMI_Male_Means"
## [11] "MI_Male_Means"
## [12] "FC_t1"
## [13] "FC_t3"
## [14] "FC_t7"
## [15] "FC_t21"
## [16] "FC_nt1"
## [17] "FC_nt3"
## [18] "FC_nt7"
## [19] "FC_nt21"
## [20] "FCB_1"
## [21] "FCB_3"
## [22] "FCB_7"
## [23] "FCB_21"
## [24] "T0_Mean"
## [25] "T1_Mean"
## [26] "T3_Mean"
## [27] "T7_Mean"
## [28] "T21_Mean"
## [29] "NT0_Mean"
## [30] "NT1_Mean"
## [31] "NT3_Mean"
## [32] "NT7_Mean"
## [33] "NT21_Mean"
## [34] "FC_egcg_quer"
## [35] "FC_egcg"
## [36] "DE_EGCG"
## [37] "DE_Quercentin"
## [38] "Pre_Means"
## [39] "Post_EGCG_Means"
## [40] "Post_EGCG_Quercentin_Means"
## [41] "hemo_G1M_Mean"
## [42] "hemo_G2M_Mean"
## [43] "hemo_G3M_Mean"
## [44] "hemo_G1F_Mean"
## [45] "hemo_G2F_Mean"
## [46] "hemo_G3F_Mean"
## [47] "hemo_healthyFemale_Mean"
## [48] "hemo_healthyMale_Mean"
## [49] "hemo_Female_Mean"
## [50] "hemo_Male_Mean"
## [51] "hemo_FC_1m"
## [52] "hemo_FC_2m"
## [53] "hemo_FC_3m"
## [54] "hemo_FC_1F"
## [55] "hemo_FC_2F"
## [56] "hemo_FC_3F"
## [57] "hemo_FC_malesOverall"
## [58] "hemo_FC_femalesOverall"
## [59] "tetanis_GSM1443061"
## [60] "tetanis_GSM1443062"
## [61] "tetanis_GSM1443063"
## [62] "tetanis_GSM1443064"
## [63] "tetanis_GSM1443065"
## [64] "tetanis_GSM1443066"
## [65] "Alz_GSM2973262"
## [66] "Alz_GSM2973263"
## [67] "Alz_GSM2973264"
## [68] "Alz_GSM2973265"
## [69] "Alz_GSM2973266"
## [70] "Alz_GSM2973267"
## [71] "Alz_GSM2973268"
## [72] "Alz_GSM2973269"
## [73] "Alz_GSM2973270"
## [74] "Alz_GSM2973271"
## [75] "Alz_GSM2973272"
## [76] "Alz_GSM2973273"
## [77] "Alz_GSM2973274"
## [78] "Alz_GSM2973275"
## [79] "Alz_GSM2973276"
## [80] "Alz_GSM2973277"
## [81] "Alz_GSM2973278"
## [82] "Alz_GSM2973279"
## [83] "Alz_GSM2973280"
## [84] "Alz_GSM2973281"
## [85] "Alz_GSM2973282"
## [86] "Alz_GSM2973283"
## [87] "Alz_GSM2973284"
## [88] "Alz_GSM2973285"
## [89] "Alz_GSM2973286"
## [90] "Alz_GSM2973287"
## [91] "Alz_GSM2973288"
## [92] "Alz_GSM2973289"
## [93] "Alz_GSM2973290"
## [94] "Alz_GSM2973291"
## [95] "Alz_GSM2973292"
## [96] "Alz_GSM2973293"
## [97] "Alz_GSM2973294"
## [98] "Alz_GSM2973295"
## [99] "Alz_GSM2973296"
## [100] "Alz_GSM2973297"
## [101] "Alz_GSM2973298"
## [102] "Alz_GSM2973299"
## [103] "Alz_GSM2973300"
## [104] "Alz_GSM2973301"
## [105] "Alz_GSM2973302"
## [106] "Alz_GSM2973303"
## [107] "Alz_GSM2973304"
## [108] "Alz_GSM2973305"
## [109] "Alz_GSM2973306"
## [110] "Alz_GSM2973307"
## [111] "Alz_GSM2973308"
## [112] "Alz_GSM2973309"
## [113] "Alz_GSM2973310"
## [114] "Alz_GSM2973311"
## [115] "Alz_GSM2973312"
## [116] "Alz_GSM2973313"
## [117] "Alz_GSM2973314"
## [118] "Alz_GSM2973315"
## [119] "Alz_GSM2973316"
## [120] "Alz_GSM2973317"
## [121] "Alz_GSM2973318"
## [122] "Alz_GSM2973319"
## [123] "Alz_GSM2973320"
## [124] "Alz_GSM2973321"
## [125] "Alz_GSM2973322"
## [126] "Alz_GSM2973323"
## [127] "Alz_GSM2973324"
## [128] "Alz_GSM2973325"
## [129] "Alz_GSM2973326"
## [130] "Alz_GSM2973327"
## [131] "Alz_GSM2973328"
## [132] "Alz_GSM2973329"
## [133] "Alz_GSM2973330"
## [134] "Alz_GSM2973331"
## [135] "Alz_GSM2973332"
## [136] "Alz_GSM2973333"
## [137] "Alz_GSM2973334"
## [138] "Alz_GSM2973335"
## [139] "Alz_GSM2973336"
## [140] "Alz_GSM2973337"
## [141] "Alz_GSM2973338"
## [142] "Alz_GSM2973339"
## [143] "healthy_MI_Males_GSM4205364"
## [144] "healthy_MI_Males_GSM4205363"
## [145] "healthy_MI_Males_GSM4205362"
## [146] "healthy_MI_Males_GSM4205361"
## [147] "healthy_MI_Males_GSM4205360"
## [148] "healthy_MI_Males_GSM4205359"
## [149] "MI_Males_GSM4205358"
## [150] "MI_Males_GSM4205357"
## [151] "MI_Males_GSM4205356"
## [152] "MI_Males_GSM4205355"
## [153] "MI_Males_GSM4205354"
## [154] "MI_Males_GSM4205353"
## [155] "flu_GSM3409106_29_day_0"
## [156] "flu_GSM3409107_29_day_1"
## [157] "flu_GSM3409108_29_day_3"
## [158] "flu_GSM3409004_29_day_7"
## [159] "flu_GSM3409105_29_day_21_screening"
## [160] "flu_GSM3409006_30._day_0"
## [161] "flu_GSM3409007_30_day_1"
## [162] "flu_GSM3409008_30_day_3"
## [163] "flu_GSM3409009_30_day_7"
## [164] "flu_GSM3409005_30_day_21_screening"
## [165] "flu_GSM3409013_05_.day_0"
## [166] "flu_GSM3409014_05_day_1"
## [167] "flu_GSM3409015_05_day_3"
## [168] "flu_GSM3409016_05_day_7"
## [169] "flu_GSM3409012_05_day_21_screening"
## [170] "flu_GSM3409161_33_day_0_no"
## [171] "flu_GSM3409162_33_day_1_no"
## [172] "flu_GSM3409163_33_day_3_no"
## [173] "flu_GSM3409111_33._day_7_no"
## [174] "flu_GSM3409160_33_day_21_screening_no"
## [175] "flu_GSM3409124_36_day_0_no"
## [176] "flu_GSM3409125_36_day_1_no"
## [177] "flu_GSM3409126_36_day_3_no"
## [178] "flu_GSM3409127_36_day_7_no"
## [179] "flu_GSM3409123_36_day_21_screening_no"
## [180] "flu_GSM3409135_38_day_0_no"
## [181] "flu_GSM3409136_38_day_1_no"
## [182] "flu_GSM3409137_38_day_3_no"
## [183] "flu_GSM3409138_38_day_7_no"
## [184] "flu_GSM3409134_38_day_21_screening_no"
## [185] "EGCG_pre_GSM1923000"
## [186] "EGCG_pre_GSM1923004"
## [187] "EGCG_pre_GSM1923010"
## [188] "EGCG_pre_GSM1923012"
## [189] "EGCG_pre_GSM1923007"
## [190] "EGCG_pre_GSM1923020"
## [191] "EGCG_pre_GSM192998"
## [192] "EGCG_pre_GSM1922995"
## [193] "EGCG_pre_GSM1923002"
## [194] "EGCG_pre_GSM1923008"
## [195] "EGCG_pre_GSM1923015"
## [196] "EGCG_pre_GSM1923018"
## [197] "EGCG_pre_GSM1923022"
## [198] "EGCG_pre_GSM1923017"
## [199] "EGCG_post_EG_GSM1923001"
## [200] "EGCG_post_EG_GSM1923005"
## [201] "EGCG_post_EG_GSM1923011"
## [202] "EGCG_post_EG_GSM1923013"
## [203] "EGCG_post_EG_GSM1923021"
## [204] "EGCG_post_EG_GSM1923006"
## [205] "EGCG_post_EG_GSM1923014"
## [206] "EGCG_post_EQ_GSM192996"
## [207] "EGCG_post_EQ_GSM1923003"
## [208] "EGCG_post_EQ_GSM1923009"
## [209] "EGCG_post_EQ_GSM1923016"
## [210] "EGCG_post_EQ_GSM1923019"
## [211] "EGCG_post_EQ_GSM1923023"
## [212] "EGCG_post_EQ_GSM192997"
## [213] "hemo_GSM3440208"
## [214] "hemo_GSM3440209"
## [215] "hemo_GSM3440210"
## [216] "hemo_GSM3440211"
## [217] "hemo_GSM3440212"
## [218] "hemo_GSM3440213"
## [219] "hemo_GSM3440214"
## [220] "hemo_GSM3440215"
## [221] "hemo_GSM3440216"
## [222] "hemo_GSM3440217"
## [223] "hemo_GSM3440218"
## [224] "hemo_GSM3440219"
## [225] "hemo_GSM3440220"
## [226] "hemo_GSM3440221"
## [227] "hemo_GSM3440222"
## [228] "hemo_GSM3440223"
## [229] "hemo_GSM3440224"
## [230] "hemo_GSM3440225"
## [231] "hemo_GSM3440226"
## [232] "hemo_GSM3440227"
## [233] "hemo_GSM3440228"
## [234] "hemo_GSM3440229"
## [235] "hemo_GSM3440230"
## [236] "hemo_GSM3440231"otherDF <- otherStudies[(otherStudies$GENE_SYMBOL %in% overAndDuplicatedList) | (otherStudies$GENE_SYMBOL %in% underAndDuplicatedList),]
otherDF## GENE_SYMBOL Tetanis_Means Alz_Females_AD1_Mean Alz_Females_control1_Mean
## 457 AMPH 0.45592993 8.337 9.070
## 10436 SPP1 0.43295941 10.536 10.022
## 12706 ZNF627 0.08859392 8.030 8.250
## Alz_males_AD1_Mean Alz_males_control1_Mean Alz_FC_fem_ctrl_AD
## 457 8.560 9.102 0.919
## 10436 10.579 9.890 1.051
## 12706 8.084 8.269 0.973
## Alz_FC_male_ctrl_AD FC_MI_males HealthyMI_Male_Means MI_Male_Means
## 457 0.940 1.0373255 3.494528 3.624963
## 10436 1.070 1.0222928 2.723883 2.784606
## 12706 0.978 0.9860705 5.587856 5.510019
## FC_t1 FC_t3 FC_t7 FC_t21 FC_nt1 FC_nt3 FC_nt7
## 457 1.1142532 0.9341522 1.0168919 1.0290093 0.9425273 1.0144486 0.9949760
## 10436 1.0243268 1.0673015 0.9024450 1.0449174 0.9172220 0.9693064 1.0762040
## 12706 0.9611538 1.0602481 0.9825869 0.9662747 1.0291837 1.0152687 0.9229262
## FC_nt21 FCB_1 FCB_3 FCB_7 FCB_21 T0_Mean T1_Mean
## 457 1.0325945 0.8123532 0.8240906 0.8199503 0.8466762 3.350786 3.733625
## 10436 0.9772526 0.8209137 0.7957169 0.8563537 0.8368739 2.753967 2.820962
## 12706 1.0415777 0.8726749 0.8859995 0.8177122 0.8517107 4.894780 4.704636
## T3_Mean T7_Mean T21_Mean NT0_Mean NT1_Mean NT3_Mean NT7_Mean NT21_Mean
## 457 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352 2.747478 2.837031
## 10436 3.010817 2.717097 2.839142 2.464801 2.260769 2.191378 2.358370 2.304723
## 12706 4.988082 4.901224 4.735929 4.150427 4.271552 4.336773 4.002521 4.168937
## FC_egcg_quer FC_egcg DE_EGCG DE_Quercentin Pre_Means Post_EGCG_Means
## 457 0.973 1.011 -0.048 0.122 4.484 4.531
## 10436 1.030 0.964 0.184 -0.153 5.139 4.955
## 12706 0.987 1.007 -0.048 0.093 6.920 6.968
## Post_EGCG_Quercentin_Means hemo_G1M_Mean hemo_G2M_Mean hemo_G3M_Mean
## 457 4.361 3.658333 3.750322 3.578494
## 10436 5.292 3.721615 3.442055 3.504246
## 12706 6.827 4.406948 4.338910 4.230894
## hemo_G1F_Mean hemo_G2F_Mean hemo_G3F_Mean hemo_healthyFemale_Mean
## 457 3.638660 3.736075 3.65605 3.766800
## 10436 3.629805 3.838200 3.68552 3.409640
## 12706 4.577210 4.264085 4.55656 4.273485
## hemo_healthyMale_Mean hemo_Female_Mean hemo_Male_Mean hemo_FC_1m
## 457 3.633565 3.681104 3.655930 1.0068163
## 10436 3.214490 3.724306 3.551993 1.1577622
## 12706 4.590043 4.447830 4.318300 0.9601104
## hemo_FC_2m hemo_FC_3m hemo_FC_1F hemo_FC_2F hemo_FC_3F
## 457 1.0321330 0.9848438 0.9659817 0.9918432 0.9705984
## 10436 1.0707935 1.0901406 1.0645713 1.1256907 1.0809118
## 12706 0.9452875 0.9217549 1.0710720 0.9978004 1.0662398
## hemo_FC_malesOverall hemo_FC_femalesOverall tetanis_GSM1443061
## 457 1.0061551 0.9772497 0.26303441
## 10436 1.1049943 1.0922872 0.51601515
## 12706 0.9407974 1.0407969 0.04264434
## tetanis_GSM1443062 tetanis_GSM1443063 tetanis_GSM1443064
## 457 0.29865832 0.43295941 0.4646683
## 10436 0.62293035 0.37851162 0.1763228
## 12706 0.05658353 0.08406426 0.0976108
## tetanis_GSM1443065 tetanis_GSM1443066 Alz_GSM2973262 Alz_GSM2973263
## 457 0.6415460 0.5945485 7.351 8.523
## 10436 0.5058909 0.3561438 9.594 11.423
## 12706 0.0976108 0.1505597 8.243 7.866
## Alz_GSM2973264 Alz_GSM2973265 Alz_GSM2973266 Alz_GSM2973267
## 457 7.833 7.911 9.426 7.727
## 10436 11.940 10.491 11.691 8.645
## 12706 8.315 8.064 8.010 7.954
## Alz_GSM2973268 Alz_GSM2973269 Alz_GSM2973270 Alz_GSM2973271
## 457 8.635 8.223 7.551 8.910
## 10436 11.469 8.285 8.372 9.105
## 12706 8.087 8.112 8.005 8.252
## Alz_GSM2973272 Alz_GSM2973273 Alz_GSM2973274 Alz_GSM2973275
## 457 7.848 9.858 7.712 7.834
## 10436 10.175 8.293 8.807 9.835
## 12706 7.989 8.201 8.234 7.735
## Alz_GSM2973276 Alz_GSM2973277 Alz_GSM2973278 Alz_GSM2973279
## 457 8.278 8.791 7.684 9.398
## 10436 9.892 8.289 10.310 8.978
## 12706 7.608 8.133 8.203 8.403
## Alz_GSM2973280 Alz_GSM2973281 Alz_GSM2973282 Alz_GSM2973283
## 457 8.061 8.344 8.145 8.886
## 10436 10.914 9.714 11.574 9.847
## 12706 7.745 7.917 8.153 8.555
## Alz_GSM2973284 Alz_GSM2973285 Alz_GSM2973286 Alz_GSM2973287
## 457 9.393 9.601 8.516 8.890
## 10436 9.646 9.184 11.294 11.348
## 12706 8.370 8.806 7.939 8.105
## Alz_GSM2973288 Alz_GSM2973289 Alz_GSM2973290 Alz_GSM2973291
## 457 9.889 9.000 9.562 9.402
## 10436 9.471 11.045 10.503 9.962
## 12706 8.227 8.094 8.038 8.182
## Alz_GSM2973292 Alz_GSM2973293 Alz_GSM2973294 Alz_GSM2973295
## 457 7.837 7.635 9.044 10.102
## 10436 10.659 10.752 10.874 11.448
## 12706 8.596 8.189 8.215 8.222
## Alz_GSM2973296 Alz_GSM2973297 Alz_GSM2973298 Alz_GSM2973299
## 457 7.902 7.204 8.396 7.971
## 10436 10.353 8.784 11.280 10.472
## 12706 8.148 8.156 8.363 8.106
## Alz_GSM2973300 Alz_GSM2973301 Alz_GSM2973302 Alz_GSM2973303
## 457 7.389 9.239 7.641 8.355
## 10436 12.232 10.298 9.885 12.194
## 12706 7.845 8.163 8.054 8.349
## Alz_GSM2973304 Alz_GSM2973305 Alz_GSM2973306 Alz_GSM2973307
## 457 7.418 9.645 8.384 7.741
## 10436 9.963 11.011 9.110 11.210
## 12706 7.962 7.909 8.170 7.943
## Alz_GSM2973308 Alz_GSM2973309 Alz_GSM2973310 Alz_GSM2973311
## 457 9.709 8.019 7.413 8.836
## 10436 9.975 10.668 9.259 10.471
## 12706 7.956 8.146 7.692 7.867
## Alz_GSM2973312 Alz_GSM2973313 Alz_GSM2973314 Alz_GSM2973315
## 457 8.926 9.511 8.586 8.859
## 10436 9.114 8.829 10.731 10.914
## 12706 8.266 8.171 8.015 8.017
## Alz_GSM2973316 Alz_GSM2973317 Alz_GSM2973318 Alz_GSM2973319
## 457 9.801 9.225 9.466 8.526
## 10436 9.952 9.739 11.288 10.814
## 12706 8.312 8.414 7.875 7.556
## Alz_GSM2973320 Alz_GSM2973321 Alz_GSM2973322 Alz_GSM2973323
## 457 9.303 9.368 9.241 9.571
## 10436 10.701 10.888 10.701 9.388
## 12706 8.241 8.293 8.191 8.294
## Alz_GSM2973324 Alz_GSM2973325 Alz_GSM2973326 Alz_GSM2973327
## 457 9.613 9.050 8.136 9.620
## 10436 9.393 10.714 10.114 10.159
## 12706 8.488 8.373 8.148 8.098
## Alz_GSM2973328 Alz_GSM2973329 Alz_GSM2973330 Alz_GSM2973331
## 457 9.182 9.863 9.468 9.846
## 10436 10.516 9.136 11.167 9.382
## 12706 8.168 8.486 8.379 8.321
## Alz_GSM2973332 Alz_GSM2973333 Alz_GSM2973334 Alz_GSM2973335
## 457 9.462 9.155 9.525 8.603
## 10436 10.380 12.186 12.411 12.126
## 12706 8.206 7.996 8.302 8.069
## Alz_GSM2973336 Alz_GSM2973337 Alz_GSM2973338 Alz_GSM2973339
## 457 8.210 7.350 9.865 8.755
## 10436 11.369 10.136 10.437 10.511
## 12706 8.140 8.169 8.305 7.999
## healthy_MI_Males_GSM4205364 healthy_MI_Males_GSM4205363
## 457 3.412627 3.475266
## 10436 2.685236 2.724470
## 12706 5.592901 5.514610
## healthy_MI_Males_GSM4205362 healthy_MI_Males_GSM4205361
## 457 3.600933 3.487505
## 10436 2.718469 2.692620
## 12706 5.573070 5.709375
## healthy_MI_Males_GSM4205360 healthy_MI_Males_GSM4205359
## 457 3.466251 3.524585
## 10436 2.724916 2.797590
## 12706 5.605968 5.531211
## MI_Males_GSM4205358 MI_Males_GSM4205357 MI_Males_GSM4205356
## 457 3.546433 3.580199 3.632625
## 10436 2.740118 2.824891 2.848807
## 12706 5.513211 5.348236 5.661221
## MI_Males_GSM4205355 MI_Males_GSM4205354 MI_Males_GSM4205353
## 457 3.621817 3.643875 3.724826
## 10436 2.761843 2.783520 2.748459
## 12706 5.546281 5.513648 5.477519
## flu_GSM3409106_29_day_0 flu_GSM3409107_29_day_1 flu_GSM3409108_29_day_3
## 457 3.185025 3.763626 3.299779
## 10436 2.742751 2.800032 3.582503
## 12706 4.868354 4.660128 4.705391
## flu_GSM3409004_29_day_7 flu_GSM3409105_29_day_21_screening
## 457 3.560371 3.226569
## 10436 2.738583 2.773408
## 12706 5.001571 4.865538
## flu_GSM3409006_30._day_0 flu_GSM3409007_30_day_1 flu_GSM3409008_30_day_3
## 457 3.497350 3.631924 3.597716
## 10436 2.581613 2.777213 2.628174
## 12706 4.942641 4.574103 4.878183
## flu_GSM3409009_30_day_7 flu_GSM3409005_30_day_21_screening
## 457 3.296959 3.826730
## 10436 2.676103 2.642041
## 12706 4.981108 4.691217
## flu_GSM3409013_05_.day_0 flu_GSM3409014_05_day_1 flu_GSM3409015_05_day_3
## 457 3.369984 3.805324 3.565827
## 10436 2.937537 2.885642 2.821775
## 12706 4.873345 4.879678 5.380672
## flu_GSM3409016_05_day_7 flu_GSM3409012_05_day_21_screening
## 457 3.782736 3.895429
## 10436 2.736606 3.101977
## 12706 4.720993 4.651032
## flu_GSM3409161_33_day_0_no flu_GSM3409162_33_day_1_no
## 457 2.686933 2.923901
## 10436 2.618819 2.214539
## 12706 4.049369 4.564882
## flu_GSM3409163_33_day_3_no flu_GSM3409111_33._day_7_no
## 457 2.438495 2.585848
## 10436 2.183103 2.588914
## 12706 4.632300 3.842338
## flu_GSM3409160_33_day_21_screening_no flu_GSM3409124_36_day_0_no
## 457 2.687149 3.228487
## 10436 2.206506 2.460708
## 12706 4.589850 4.083583
## flu_GSM3409125_36_day_1_no flu_GSM3409126_36_day_3_no
## 457 2.904799 2.994339
## 10436 2.350458 2.266848
## 12706 4.013606 4.379273
## flu_GSM3409127_36_day_7_no flu_GSM3409123_36_day_21_screening_no
## 457 2.739510 2.928245
## 10436 2.353179 2.206796
## 12706 3.792321 3.793917
## flu_GSM3409135_38_day_0_no flu_GSM3409136_38_day_1_no
## 457 2.748590 2.337366
## 10436 2.314875 2.217312
## 12706 4.318329 4.236167
## flu_GSM3409137_38_day_3_no flu_GSM3409138_38_day_7_no
## 457 2.851221 2.917078
## 10436 2.124184 2.133017
## 12706 3.998746 4.372904
## flu_GSM3409134_38_day_21_screening_no EGCG_pre_GSM1923000
## 457 2.895698 4.450
## 10436 2.500868 4.374
## 12706 4.123043 6.713
## EGCG_pre_GSM1923004 EGCG_pre_GSM1923010 EGCG_pre_GSM1923012
## 457 4.742 4.571 4.395
## 10436 5.399 5.618 5.415
## 12706 6.539 7.106 6.879
## EGCG_pre_GSM1923007 EGCG_pre_GSM1923020 EGCG_pre_GSM192998
## 457 4.453 4.158 4.434
## 10436 4.694 4.612 5.095
## 12706 7.333 7.170 7.524
## EGCG_pre_GSM1922995 EGCG_pre_GSM1923002 EGCG_pre_GSM1923008
## 457 4.330 4.363 4.636
## 10436 5.082 5.139 5.681
## 12706 7.033 6.972 6.601
## EGCG_pre_GSM1923015 EGCG_pre_GSM1923018 EGCG_pre_GSM1923022
## 457 4.807 4.411 4.498
## 10436 5.669 5.470 4.621
## 12706 6.783 6.666 7.008
## EGCG_pre_GSM1923017 EGCG_post_EG_GSM1923001 EGCG_post_EG_GSM1923005
## 457 4.521 4.877 4.416
## 10436 5.072 4.496 5.153
## 12706 6.559 6.746 7.077
## EGCG_post_EG_GSM1923011 EGCG_post_EG_GSM1923013 EGCG_post_EG_GSM1923021
## 457 4.497 4.465 4.819
## 10436 5.145 5.736 4.841
## 12706 6.979 7.185 6.988
## EGCG_post_EG_GSM1923006 EGCG_post_EG_GSM1923014 EGCG_post_EQ_GSM192996
## 457 4.465 4.179 4.098
## 10436 4.459 4.855 4.805
## 12706 6.968 6.834 7.038
## EGCG_post_EQ_GSM1923003 EGCG_post_EQ_GSM1923009 EGCG_post_EQ_GSM1923016
## 457 4.494 4.465 4.520
## 10436 5.011 5.531 5.575
## 12706 6.453 6.885 6.902
## EGCG_post_EQ_GSM1923019 EGCG_post_EQ_GSM1923023 EGCG_post_EQ_GSM192997
## 457 4.054 4.432 4.465
## 10436 5.763 4.526 5.832
## 12706 6.478 6.981 7.052
## hemo_GSM3440208 hemo_GSM3440209 hemo_GSM3440210 hemo_GSM3440211
## 457 3.44224 3.98188 3.62239 3.66955
## 10436 3.73802 3.53148 3.04535 3.06117
## 12706 3.99445 4.34297 4.20735 4.44159
## hemo_GSM3440212 hemo_GSM3440213 hemo_GSM3440214 hemo_GSM3440215
## 457 3.58570 3.66521 3.65605 3.57693
## 10436 3.48090 3.47155 3.68552 3.78541
## 12706 4.24116 4.37803 4.55656 4.33348
## hemo_GSM3440216 hemo_GSM3440217 hemo_GSM3440218 hemo_GSM3440219
## 457 3.39117 3.66448 3.97782 3.73208
## 10436 3.59330 4.14078 3.86078 3.10126
## 12706 4.33044 4.51631 4.51842 4.32528
## hemo_GSM3440220 hemo_GSM3440221 hemo_GSM3440222 hemo_GSM3440223
## 457 3.53226 3.55228 3.82612 3.80767
## 10436 4.33112 3.76982 3.25909 3.53562
## 12706 4.45365 4.22023 4.60776 4.01186
## hemo_GSM3440224 hemo_GSM3440225 hemo_GSM3440226 hemo_GSM3440227
## 457 3.45120 3.79758 3.38209 3.47638
## 10436 4.00052 3.40575 3.30258 3.16488
## 12706 4.54666 4.35085 4.82860 4.36876
## hemo_GSM3440228 hemo_GSM3440229 hemo_GSM3440230 hemo_GSM3440231
## 457 3.86309 3.70777 3.82583 3.81270
## 10436 3.43230 3.84018 2.97910 2.95820
## 12706 4.64929 3.87705 4.66992 4.51352There are 3 genes that are in the list of over and under expressed genes in our covid-19 dataframe of genes that are more than 3 fold up regulated or less than 60% down regulated as well as having more than one CNV. Those genes are shown above to be AMPH, SPP1, and ZNF627. Lets look at what these gene values are in each of these other studies. There are original samples and fold change values in a fat dataframe for these six studies of blood samples. The zinc finger gene that starts with a ZN above as one of the genes in common among all 7 diseases or infections and diseases is a specific type of gene. These genes are able to cut DNA at specific regions and are able to modify sequences being transcribed from DNA into RNA due to their chemical makeup of two cisteine and two histidine residues that bind zic atoms and interact with these specific DNA sequences (Essentials of Genetics, 9E, Klutz et. al p. 526). They are used for gene targeting in removing or duplicating genes for gene therapy to remove genes and in combination with integrases as of 2016 have shown an effectiveness to cut out defective sequences, recombining homologous sequences into the genome to replace defective sequences. Still in progress as of 2016, but has shown progress in inserting the HIV resistance CCR5 gene mutation into a person suffering leukemia and also infected with HIV to keep the person, Timothy Brown 2007, from having HIV, thus curing him. The cells reproduced the mutation and overpowered the dominant or wild type CCR5 gene that normally is overpowered by HIV.
Interestingly enough, if you don’t know a lot about vaccines and delivering treatment through a vector like deactivated AAV or adeno-associated virus fluids derived from the common cold or retroviral vectors like the lentivirus derived from heat killed or deactivated HIV and other viruses. Fun fact: retroviral vectors are made when the replicating and disease-causing part of the virus gene is replaced after being removed, with cloned human genes. The altered RNA is placed into the virus and this recombinant viral vector holding the therapeutic human gene is used to deliver treatment to a human via a shot or infection. Breaking it down, the virus particles carry RNA copies of the therapeutic gene, and when they arrive in the cell, they cannot replicate their own virus. However, the therapeutic RNA is reverse transcribed into the genome of the host cell’s chromosome. The theory is that if this inserted vector of gene therapeutic is properly expressed it produces a normal gene product that outweighs the mutated version the diseased individual is producing and theoretically cure the person. Scary truth with these vectors to deliver treatment: they are not without faults. Adenovirus doesn’t attach to the human genome in replication and many of those types of therapeutics have to be delivered in billions or millions of gene replications to treat host. But retrovirals can only work in dividing cells but most tissue in the human body have only a small amount of dividing cells at any time, an adverse immune response could be developed thats fatal, it can also mutate an essential gene that isn’t the target and effect other human body responses or activate otherwise suppressed genes as the retroviral interacts with chromatin associated proteins the can navigate transcriptionally active genes. Also, as already noted, the human genes are normally much longer in kb length than a retroviral or AAV can hold as a vector of transmission of gene therapeutics. Another scary fun fact: if the inactivated vector were to recombine with another unaltered viral genome already present in the host cell, then a fully infectious virus could be created.
There is more information in ‘Special Topic: Gene Therapy’ a subsection of an intro to genetics course in the back of the book, Essentials of Genetics, 9E, by Klug et. al. 2016 pp 519-530.
The AAV can only hold genes 5kb long and the retroviral vectors about 10kb long. And of note are the Zinc Finger genes that start with ZN.
dataBlood7studies <- merge(otherDF,overexpressedAndDuplicated2,
by.x='GENE_SYMBOL',by.y='ORF')
dataBlood7studies2 <- merge(otherDF,suppressedAndDuplicated2,
by.x='GENE_SYMBOL', by.y='ORF')
studies7_DF <- rbind(dataBlood7studies,dataBlood7studies2)fc <- grep('FC',colnames(studies7_DF))
mean <- grep('[Mm]ean',colnames(studies7_DF))
studies7_DF2 <- studies7_DF[,c(1,237,238,mean,fc)]
head(studies7_DF2)## GENE_SYMBOL SEQUENCE
## 1 AMPH CCAGAGATATGGATTGTTGTACCAAGAAATAGAGGCTGACAAAGACGAGGCTTCTGGTGG
## 2 AMPH GCAGACAGACCAGAGTATGATCTGCAACTTGGCTGAATCTGAACAGGCTCCACCCACAGA
## 3 AMPH ACCAAGGTCTACATGATGGAATTCAAAAGGCTTCTGGTGGTTCATTTAATGGATTCACAC
## 4 SPP1 GCTTAATGAAGACATTAAAAGAACTTTACAACAAATACCCAGATGCTGTGGCCACATGGC
## 5 SPP1 CTAAAAGCTTCAGGGTTATGTCTATGTTCATTCTATAGAAGAAATGCAAACTATCACTGT
## 6 ZNF627 CTGGGCAACACGAGACGGGGCCTTACTCTGCTGCCTAGGCTGGAGTACAGTGGCACAATC
## numberOfGenes Tetanis_Means Alz_Females_AD1_Mean Alz_Females_control1_Mean
## 1 3 0.45592993 8.337 9.070
## 2 3 0.45592993 8.337 9.070
## 3 3 0.45592993 8.337 9.070
## 4 2 0.43295941 10.536 10.022
## 5 2 0.43295941 10.536 10.022
## 6 2 0.08859392 8.030 8.250
## Alz_males_AD1_Mean Alz_males_control1_Mean HealthyMI_Male_Means MI_Male_Means
## 1 8.560 9.102 3.494528 3.624963
## 2 8.560 9.102 3.494528 3.624963
## 3 8.560 9.102 3.494528 3.624963
## 4 10.579 9.890 2.723883 2.784606
## 5 10.579 9.890 2.723883 2.784606
## 6 8.084 8.269 5.587856 5.510019
## T0_Mean T1_Mean T3_Mean T7_Mean T21_Mean NT0_Mean NT1_Mean NT3_Mean
## 1 3.350786 3.733625 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352
## 2 3.350786 3.733625 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352
## 3 3.350786 3.733625 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352
## 4 2.753967 2.820962 3.010817 2.717097 2.839142 2.464801 2.260769 2.191378
## 5 2.753967 2.820962 3.010817 2.717097 2.839142 2.464801 2.260769 2.191378
## 6 4.894780 4.704636 4.988082 4.901224 4.735929 4.150427 4.271552 4.336773
## NT7_Mean NT21_Mean Pre_Means Post_EGCG_Means Post_EGCG_Quercentin_Means
## 1 2.747478 2.837031 4.484 4.531 4.361
## 2 2.747478 2.837031 4.484 4.531 4.361
## 3 2.747478 2.837031 4.484 4.531 4.361
## 4 2.358370 2.304723 5.139 4.955 5.292
## 5 2.358370 2.304723 5.139 4.955 5.292
## 6 4.002521 4.168937 6.920 6.968 6.827
## hemo_G1M_Mean hemo_G2M_Mean hemo_G3M_Mean hemo_G1F_Mean hemo_G2F_Mean
## 1 3.658333 3.750322 3.578494 3.638660 3.736075
## 2 3.658333 3.750322 3.578494 3.638660 3.736075
## 3 3.658333 3.750322 3.578494 3.638660 3.736075
## 4 3.721615 3.442055 3.504246 3.629805 3.838200
## 5 3.721615 3.442055 3.504246 3.629805 3.838200
## 6 4.406948 4.338910 4.230894 4.577210 4.264085
## hemo_G3F_Mean hemo_healthyFemale_Mean hemo_healthyMale_Mean hemo_Female_Mean
## 1 3.65605 3.766800 3.633565 3.681104
## 2 3.65605 3.766800 3.633565 3.681104
## 3 3.65605 3.766800 3.633565 3.681104
## 4 3.68552 3.409640 3.214490 3.724306
## 5 3.68552 3.409640 3.214490 3.724306
## 6 4.55656 4.273485 4.590043 4.447830
## hemo_Male_Mean healthyMean mildMean severeMean Alz_FC_fem_ctrl_AD
## 1 3.655930 2.434463 5.174168 8.275405 0.919
## 2 3.655930 2.434463 5.174168 8.275405 0.919
## 3 3.655930 2.434463 5.174168 8.275405 0.919
## 4 3.551993 2.532664 3.117238 9.198678 1.051
## 5 3.551993 2.532664 3.117238 9.198678 1.051
## 6 4.318300 9.670570 6.171725 3.805882 0.973
## Alz_FC_male_ctrl_AD FC_MI_males FC_t1 FC_t3 FC_t7 FC_t21
## 1 0.940 1.0373255 1.1142532 0.9341522 1.0168919 1.0290093
## 2 0.940 1.0373255 1.1142532 0.9341522 1.0168919 1.0290093
## 3 0.940 1.0373255 1.1142532 0.9341522 1.0168919 1.0290093
## 4 1.070 1.0222928 1.0243268 1.0673015 0.9024450 1.0449174
## 5 1.070 1.0222928 1.0243268 1.0673015 0.9024450 1.0449174
## 6 0.978 0.9860705 0.9611538 1.0602481 0.9825869 0.9662747
## FC_nt1 FC_nt3 FC_nt7 FC_nt21 FCB_1 FCB_3 FCB_7
## 1 0.9425273 1.0144486 0.9949760 1.0325945 0.8123532 0.8240906 0.8199503
## 2 0.9425273 1.0144486 0.9949760 1.0325945 0.8123532 0.8240906 0.8199503
## 3 0.9425273 1.0144486 0.9949760 1.0325945 0.8123532 0.8240906 0.8199503
## 4 0.9172220 0.9693064 1.0762040 0.9772526 0.8209137 0.7957169 0.8563537
## 5 0.9172220 0.9693064 1.0762040 0.9772526 0.8209137 0.7957169 0.8563537
## 6 1.0291837 1.0152687 0.9229262 1.0415777 0.8726749 0.8859995 0.8177122
## FCB_21 FC_egcg_quer FC_egcg hemo_FC_1m hemo_FC_2m hemo_FC_3m hemo_FC_1F
## 1 0.8466762 0.973 1.011 1.0068163 1.0321330 0.9848438 0.9659817
## 2 0.8466762 0.973 1.011 1.0068163 1.0321330 0.9848438 0.9659817
## 3 0.8466762 0.973 1.011 1.0068163 1.0321330 0.9848438 0.9659817
## 4 0.8368739 1.030 0.964 1.1577622 1.0707935 1.0901406 1.0645713
## 5 0.8368739 1.030 0.964 1.1577622 1.0707935 1.0901406 1.0645713
## 6 0.8517107 0.987 1.007 0.9601104 0.9452875 0.9217549 1.0710720
## hemo_FC_2F hemo_FC_3F hemo_FC_malesOverall hemo_FC_femalesOverall
## 1 0.9918432 0.9705984 1.0061551 0.9772497
## 2 0.9918432 0.9705984 1.0061551 0.9772497
## 3 0.9918432 0.9705984 1.0061551 0.9772497
## 4 1.1256907 1.0809118 1.1049943 1.0922872
## 5 1.1256907 1.0809118 1.1049943 1.0922872
## 6 0.9978004 1.0662398 0.9407974 1.0407969
## FC_mildOverHealthy FC_severeOverHealthy
## 1 2.1253836 3.399273
## 2 2.1253836 3.399273
## 3 2.1253836 3.399273
## 4 1.2308138 3.632017
## 5 1.2308138 3.632017
## 6 0.6381966 0.393553colnames(studies7_DF2)## [1] "GENE_SYMBOL" "SEQUENCE"
## [3] "numberOfGenes" "Tetanis_Means"
## [5] "Alz_Females_AD1_Mean" "Alz_Females_control1_Mean"
## [7] "Alz_males_AD1_Mean" "Alz_males_control1_Mean"
## [9] "HealthyMI_Male_Means" "MI_Male_Means"
## [11] "T0_Mean" "T1_Mean"
## [13] "T3_Mean" "T7_Mean"
## [15] "T21_Mean" "NT0_Mean"
## [17] "NT1_Mean" "NT3_Mean"
## [19] "NT7_Mean" "NT21_Mean"
## [21] "Pre_Means" "Post_EGCG_Means"
## [23] "Post_EGCG_Quercentin_Means" "hemo_G1M_Mean"
## [25] "hemo_G2M_Mean" "hemo_G3M_Mean"
## [27] "hemo_G1F_Mean" "hemo_G2F_Mean"
## [29] "hemo_G3F_Mean" "hemo_healthyFemale_Mean"
## [31] "hemo_healthyMale_Mean" "hemo_Female_Mean"
## [33] "hemo_Male_Mean" "healthyMean"
## [35] "mildMean" "severeMean"
## [37] "Alz_FC_fem_ctrl_AD" "Alz_FC_male_ctrl_AD"
## [39] "FC_MI_males" "FC_t1"
## [41] "FC_t3" "FC_t7"
## [43] "FC_t21" "FC_nt1"
## [45] "FC_nt3" "FC_nt7"
## [47] "FC_nt21" "FCB_1"
## [49] "FCB_3" "FCB_7"
## [51] "FCB_21" "FC_egcg_quer"
## [53] "FC_egcg" "hemo_FC_1m"
## [55] "hemo_FC_2m" "hemo_FC_3m"
## [57] "hemo_FC_1F" "hemo_FC_2F"
## [59] "hemo_FC_3F" "hemo_FC_malesOverall"
## [61] "hemo_FC_femalesOverall" "FC_mildOverHealthy"
## [63] "FC_severeOverHealthy"studies7_DF2## GENE_SYMBOL SEQUENCE
## 1 AMPH CCAGAGATATGGATTGTTGTACCAAGAAATAGAGGCTGACAAAGACGAGGCTTCTGGTGG
## 2 AMPH GCAGACAGACCAGAGTATGATCTGCAACTTGGCTGAATCTGAACAGGCTCCACCCACAGA
## 3 AMPH ACCAAGGTCTACATGATGGAATTCAAAAGGCTTCTGGTGGTTCATTTAATGGATTCACAC
## 4 SPP1 GCTTAATGAAGACATTAAAAGAACTTTACAACAAATACCCAGATGCTGTGGCCACATGGC
## 5 SPP1 CTAAAAGCTTCAGGGTTATGTCTATGTTCATTCTATAGAAGAAATGCAAACTATCACTGT
## 6 ZNF627 CTGGGCAACACGAGACGGGGCCTTACTCTGCTGCCTAGGCTGGAGTACAGTGGCACAATC
## 7 ZNF627 AGATGGGCCCGGGAGAGGAGGGCAGGGCCTGCGCCTCCCTACGGAGCCTTTGTTTCTGGC
## numberOfGenes Tetanis_Means Alz_Females_AD1_Mean Alz_Females_control1_Mean
## 1 3 0.45592993 8.337 9.070
## 2 3 0.45592993 8.337 9.070
## 3 3 0.45592993 8.337 9.070
## 4 2 0.43295941 10.536 10.022
## 5 2 0.43295941 10.536 10.022
## 6 2 0.08859392 8.030 8.250
## 7 2 0.08859392 8.030 8.250
## Alz_males_AD1_Mean Alz_males_control1_Mean HealthyMI_Male_Means MI_Male_Means
## 1 8.560 9.102 3.494528 3.624963
## 2 8.560 9.102 3.494528 3.624963
## 3 8.560 9.102 3.494528 3.624963
## 4 10.579 9.890 2.723883 2.784606
## 5 10.579 9.890 2.723883 2.784606
## 6 8.084 8.269 5.587856 5.510019
## 7 8.084 8.269 5.587856 5.510019
## T0_Mean T1_Mean T3_Mean T7_Mean T21_Mean NT0_Mean NT1_Mean NT3_Mean
## 1 3.350786 3.733625 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352
## 2 3.350786 3.733625 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352
## 3 3.350786 3.733625 3.487774 3.546689 3.649576 2.888003 2.722022 2.761352
## 4 2.753967 2.820962 3.010817 2.717097 2.839142 2.464801 2.260769 2.191378
## 5 2.753967 2.820962 3.010817 2.717097 2.839142 2.464801 2.260769 2.191378
## 6 4.894780 4.704636 4.988082 4.901224 4.735929 4.150427 4.271552 4.336773
## 7 4.894780 4.704636 4.988082 4.901224 4.735929 4.150427 4.271552 4.336773
## NT7_Mean NT21_Mean Pre_Means Post_EGCG_Means Post_EGCG_Quercentin_Means
## 1 2.747478 2.837031 4.484 4.531 4.361
## 2 2.747478 2.837031 4.484 4.531 4.361
## 3 2.747478 2.837031 4.484 4.531 4.361
## 4 2.358370 2.304723 5.139 4.955 5.292
## 5 2.358370 2.304723 5.139 4.955 5.292
## 6 4.002521 4.168937 6.920 6.968 6.827
## 7 4.002521 4.168937 6.920 6.968 6.827
## hemo_G1M_Mean hemo_G2M_Mean hemo_G3M_Mean hemo_G1F_Mean hemo_G2F_Mean
## 1 3.658333 3.750322 3.578494 3.638660 3.736075
## 2 3.658333 3.750322 3.578494 3.638660 3.736075
## 3 3.658333 3.750322 3.578494 3.638660 3.736075
## 4 3.721615 3.442055 3.504246 3.629805 3.838200
## 5 3.721615 3.442055 3.504246 3.629805 3.838200
## 6 4.406948 4.338910 4.230894 4.577210 4.264085
## 7 4.406948 4.338910 4.230894 4.577210 4.264085
## hemo_G3F_Mean hemo_healthyFemale_Mean hemo_healthyMale_Mean hemo_Female_Mean
## 1 3.65605 3.766800 3.633565 3.681104
## 2 3.65605 3.766800 3.633565 3.681104
## 3 3.65605 3.766800 3.633565 3.681104
## 4 3.68552 3.409640 3.214490 3.724306
## 5 3.68552 3.409640 3.214490 3.724306
## 6 4.55656 4.273485 4.590043 4.447830
## 7 4.55656 4.273485 4.590043 4.447830
## hemo_Male_Mean healthyMean mildMean severeMean Alz_FC_fem_ctrl_AD
## 1 3.655930 2.434463 5.174168 8.275405 0.919
## 2 3.655930 2.434463 5.174168 8.275405 0.919
## 3 3.655930 2.434463 5.174168 8.275405 0.919
## 4 3.551993 2.532664 3.117238 9.198678 1.051
## 5 3.551993 2.532664 3.117238 9.198678 1.051
## 6 4.318300 9.670570 6.171725 3.805882 0.973
## 7 4.318300 9.670570 6.171725 3.805882 0.973
## Alz_FC_male_ctrl_AD FC_MI_males FC_t1 FC_t3 FC_t7 FC_t21
## 1 0.940 1.0373255 1.1142532 0.9341522 1.0168919 1.0290093
## 2 0.940 1.0373255 1.1142532 0.9341522 1.0168919 1.0290093
## 3 0.940 1.0373255 1.1142532 0.9341522 1.0168919 1.0290093
## 4 1.070 1.0222928 1.0243268 1.0673015 0.9024450 1.0449174
## 5 1.070 1.0222928 1.0243268 1.0673015 0.9024450 1.0449174
## 6 0.978 0.9860705 0.9611538 1.0602481 0.9825869 0.9662747
## 7 0.978 0.9860705 0.9611538 1.0602481 0.9825869 0.9662747
## FC_nt1 FC_nt3 FC_nt7 FC_nt21 FCB_1 FCB_3 FCB_7
## 1 0.9425273 1.0144486 0.9949760 1.0325945 0.8123532 0.8240906 0.8199503
## 2 0.9425273 1.0144486 0.9949760 1.0325945 0.8123532 0.8240906 0.8199503
## 3 0.9425273 1.0144486 0.9949760 1.0325945 0.8123532 0.8240906 0.8199503
## 4 0.9172220 0.9693064 1.0762040 0.9772526 0.8209137 0.7957169 0.8563537
## 5 0.9172220 0.9693064 1.0762040 0.9772526 0.8209137 0.7957169 0.8563537
## 6 1.0291837 1.0152687 0.9229262 1.0415777 0.8726749 0.8859995 0.8177122
## 7 1.0291837 1.0152687 0.9229262 1.0415777 0.8726749 0.8859995 0.8177122
## FCB_21 FC_egcg_quer FC_egcg hemo_FC_1m hemo_FC_2m hemo_FC_3m hemo_FC_1F
## 1 0.8466762 0.973 1.011 1.0068163 1.0321330 0.9848438 0.9659817
## 2 0.8466762 0.973 1.011 1.0068163 1.0321330 0.9848438 0.9659817
## 3 0.8466762 0.973 1.011 1.0068163 1.0321330 0.9848438 0.9659817
## 4 0.8368739 1.030 0.964 1.1577622 1.0707935 1.0901406 1.0645713
## 5 0.8368739 1.030 0.964 1.1577622 1.0707935 1.0901406 1.0645713
## 6 0.8517107 0.987 1.007 0.9601104 0.9452875 0.9217549 1.0710720
## 7 0.8517107 0.987 1.007 0.9601104 0.9452875 0.9217549 1.0710720
## hemo_FC_2F hemo_FC_3F hemo_FC_malesOverall hemo_FC_femalesOverall
## 1 0.9918432 0.9705984 1.0061551 0.9772497
## 2 0.9918432 0.9705984 1.0061551 0.9772497
## 3 0.9918432 0.9705984 1.0061551 0.9772497
## 4 1.1256907 1.0809118 1.1049943 1.0922872
## 5 1.1256907 1.0809118 1.1049943 1.0922872
## 6 0.9978004 1.0662398 0.9407974 1.0407969
## 7 0.9978004 1.0662398 0.9407974 1.0407969
## FC_mildOverHealthy FC_severeOverHealthy
## 1 2.1253836 3.399273
## 2 2.1253836 3.399273
## 3 2.1253836 3.399273
## 4 1.2308138 3.632017
## 5 1.2308138 3.632017
## 6 0.6381966 0.393553
## 7 0.6381966 0.393553In the above tables the study mean or average values are given per gene, when we extracted the mean values it was of the gene not sequence, but we attached the sequence information for CNV data from our covid19 data. All values other than the number of genes is the same for each gene, not sequence. The columns with ‘FC’ in them toward the later columns in this dataframe are for fold change compared to healthy. The hemochromatosis groups were in 3 groups divided by age and female or males hence the ending in f or m. The FC_t1 through FCB_21 are columns for flu vaccinated blood that was either treated or not treated with antibiotics over 1 day, 3 days, 7 days, 21 days or fold change both for 1 day, 3 days, 7 days, 21 days where both means fold change of the treated to not treated for 1 day. The tetanis vaccinated only have samples of tetanis vaccinated, not healthy blood. None of the other fold change values from the six other studies gets as high as 3 fold or as low as 60% down regulation. But it was interesting to compare.
In reading about some genes involved in tumor growth that Trisomy-21 people are associated with, lets look up how the covid-19 samples of original data in the GeneNames dataframe show the DSCR1 and VEGF genes. Down Syndrome Critical region 1 or DSCR1 is a gene that encodes a protein that suppresses the VEGF gene that is a vascular endothelial growth factor. You can go to genecards.org to read more about these genes.
trisomy21 <- grep('DSCR1',GeneNames$ORF)
trisomy21b <- grep('VEGF',GeneNames$ORF)
Trisomy21 <- GeneNames[c(trisomy21,trisomy21b),]
Trisomy21## ORF healthy_1 healthy_2 healthy_3 healthy_4 healthy_5 mild_1
## 46787 DSCR10 4.284106 2.383626 2.466728 2.565290 2.627493 2.422889
## 54439 DSCR10 2.703713 2.332730 2.466728 2.333917 2.335227 2.332686
## 10202 VEGFD 2.703713 3.582696 4.274793 3.357919 3.575944 4.264393
## 15982 VEGFC 7.368491 5.772253 5.550074 5.452434 5.939206 7.904537
## 19474 VEGFB 9.391573 10.106543 11.273678 11.694358 10.822802 9.466585
## 20321 VEGFA 12.208064 13.794988 13.306095 13.545909 14.548692 13.145064
## mild_2 mild_3 mild_4 mild_5 severe_1 severe_2 severe_3
## 46787 2.434184 2.332103 2.698987 2.360941 2.814921 2.745772 2.620153
## 54439 2.332743 2.335587 2.339235 2.360941 2.814921 2.745772 2.620153
## 10202 3.687151 3.515328 3.351295 3.882377 2.814921 2.745772 2.620153
## 15982 7.982902 7.330977 8.042081 6.771441 8.761332 9.322675 10.024815
## 19474 9.426872 9.691578 9.406987 9.797964 8.209225 8.315594 7.879903
## 20321 12.905175 13.150264 12.302969 12.572036 12.236580 12.146345 12.318765
## severe_4 severe_5 healthyMean mildMean severeMean FC_mildOverHealthy
## 46787 2.747991 2.887757 2.865449 2.449821 2.763319 0.8549519
## 54439 2.747991 2.333044 2.434463 2.340238 2.652376 0.9612955
## 10202 2.747991 3.483412 3.499013 3.740109 2.882450 1.0689041
## 15982 9.174083 7.630152 6.016492 7.606388 8.982611 1.2642563
## 19474 8.554661 9.838326 10.657791 9.557997 8.559542 0.8968085
## 20321 12.365036 12.771201 13.480750 12.815102 12.367585 0.9506223
## FC_severeOverHealthy
## 46787 0.9643581
## 54439 1.0895118
## 10202 0.8237894
## 15982 1.4929982
## 19474 0.8031253
## 20321 0.9174256If we scroll to the far right to look at the fold change values, every copy number variant of the gene or type of gene searched shows few changes in fold change values for the DSCR1 gene, but the VEGFD, VEGFC, and VEGFB genes show fold change values of more than 15% in down or up regulation. The VEGFD and VEGFB genes are under expressed 18-20% while the VEGFC gene is overexpressed 49% more in severe cases. That is interesting that this gene is overexpressed in severe cases of covid19 by almost 50%. It could be a reason that people with severe covid19 have to be hospitalized. This gene is involved in the lymphatic system and that system is important in draining fluid from tissues that is known as edema. People with an overexpression of the VEGFC gene have lymphedema in their bodies from my understanding of the genecards.org gene description of this gene.
It would be interesting to note and compare with the pfizer, moderna, and Johnson&Johnson vaccines after treatment in covid19 patients how these specific genes’ fold change values are and if there is a correlation between the trisomy-21 genes and this virus, covid-19.