library(tidyverse)
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## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 3.5.1 ✔ tibble 3.2.1
## ✔ lubridate 1.9.4 ✔ tidyr 1.3.1
## ✔ purrr 1.0.4
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(WGCNA)
## Loading required package: dynamicTreeCut
## Loading required package: fastcluster
##
## Attaching package: 'fastcluster'
##
## The following object is masked from 'package:stats':
##
## hclust
##
##
##
## Attaching package: 'WGCNA'
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## The following object is masked from 'package:stats':
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## cor
library(conflicted)
options(stringsAsFactors = FALSE)
uni_data <- read.csv("/Users/lorandacalderonzamora/Respaldo/LORANDA/microarreglo/Conjuto de datos/Hipertensión/GSE24752/datExprunificada .csv")
dim(uni_data)
## [1] 13022 18
names(uni_data)
## [1] "X" "GSM609525" "GSM609526" "GSM609529" "GSM609530" "GSM631755"
## [7] "GSM631756" "GSM631757" "GSM631758" "GSM631759" "GSM631760" "GSM631761"
## [13] "GSM631762" "GSM631763" "GSM631764" "GSM631765" "GSM631766" "GSM631767"
rownames(uni_data) <- uni_data$X
uni_data <- uni_data[, -1]
datExpr <- as.data.frame(t(uni_data))
dim(datExpr)
## [1] 17 13022
gsg = goodSamplesGenes(datExpr, verbose = 3);
## Flagging genes and samples with too many missing values...
## ..step 1
gsg$allOK
## [1] TRUE
sampleTree = hclust(dist(datExpr), method = "average");
sizeGrWindow(12,9)
par(cex = 0.6);
par(mar = c(0,4,2,0))
plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5,
cex.axis = 1.5, cex.main = 2)
traitData <- read.csv("/Users/lorandacalderonzamora/Respaldo/LORANDA/microarreglo/Conjuto de datos/Hipertensión/GSE24752/datMeta_unificado.csv")
dim(traitData )
## [1] 17 5
names(traitData )
## [1] "geo_accession" "Disease" "Age" "Gender"
## [5] "BMI"
sampleNames <- rownames(datExpr)
head(traitData$geo_accession)
## [1] "GSM631755" "GSM631756" "GSM631757" "GSM631758" "GSM631759" "GSM631760"
all(sampleNames %in% traitData$geo_accession)
## [1] TRUE
traitRows <- match(sampleNames, traitData$geo_accession)
datTraits <- traitData[traitRows, ]
rownames(datTraits) <- datTraits$geo_accession
datTraits[] <- lapply(datTraits, function(x) {
if (is.character(x) || is.factor(x)) {
as.numeric(as.factor(x))
} else {
x
}
})
datTraits_clean <- datTraits[, sapply(datTraits, is.numeric)]
str(datTraits_clean)
## 'data.frame': 17 obs. of 5 variables:
## $ geo_accession: num 1 2 3 4 5 6 7 8 9 10 ...
## $ Disease : num 2 2 1 1 1 1 1 1 1 1 ...
## $ Age : int 47 49 54 38 47 33 47 54 76 77 ...
## $ Gender : num 2 2 2 1 2 2 2 2 1 1 ...
## $ BMI : num NA NA NA NA 27.7 22.9 28.4 23.1 25.9 23.8 ...
sampleTree2 <- hclust(dist(datExpr), method = "average")
traitColors <- numbers2colors(datTraits_clean, signed = FALSE)
plotDendroAndColors(sampleTree2, traitColors,
groupLabels = names(datTraits_clean),
main = "Sample dendrogram and trait heatmap")
save(datExpr, datTraits_clean, file = "HTA-DMdataInput.RData")
lnames = load(file = "HTA-DMdataInput.RData");
#The variable lnames contains the names of loaded variables.
lnames
## [1] "datExpr" "datTraits_clean"
# Filter the least variable genes (optional)
variance_genes <- apply(datExpr, 2, var)
datExpr_filtered <- datExpr[, variance_genes > quantile(variance_genes, 0.60)]
# Select a narrower range of powers due to few samples
powers = c(1:10)
sft = pickSoftThreshold(datExpr_filtered, powerVector = powers, verbose = 5)
## pickSoftThreshold: will use block size 5209.
## pickSoftThreshold: calculating connectivity for given powers...
## ..working on genes 1 through 5209 of 5209
## Warning: executing %dopar% sequentially: no parallel backend registered
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.9560 2.6200 0.9430 3100 3380 3890
## 2 2 0.9060 1.0800 0.8840 2230 2470 3240
## 3 3 0.8070 0.5330 0.7690 1720 1900 2800
## 4 4 0.5090 0.2410 0.4140 1380 1500 2480
## 5 5 0.0182 0.0274 -0.0807 1140 1210 2230
## 6 6 0.3310 -0.1200 0.2320 966 994 2030
## 7 7 0.6340 -0.2310 0.5690 827 825 1860
## 8 8 0.7520 -0.3270 0.6900 717 691 1710
## 9 9 0.8120 -0.3950 0.7590 628 581 1590
## 10 10 0.8490 -0.4560 0.8060 555 493 1480
sizeGrWindow(9, 5)
par(mfrow = c(1, 2))
cex1 = 0.9
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3]) * sft$fitIndices[,2],
xlab = "Soft Threshold (power)",
ylab = "Scale Free Topology Model Fit, signed R^2", type = "n",
main = "Scale independence")
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3]) * sft$fitIndices[,2],
labels = powers, cex = cex1, col = "red")
abline(h = 0.80, col = "red")
plot(sft$fitIndices[,1], sft$fitIndices[,5],
xlab = "Soft Threshold (power)",
ylab = "Mean Connectivity", type = "n",
main = "Mean connectivity")
text(sft$fitIndices[,1], sft$fitIndices[,5], labels = powers, cex = cex1, col = "red")
net = blockwiseModules(
datExpr,
power = 6,
TOMType = "unsigned",
minModuleSize = 200,
reassignThreshold = 0,
mergeCutHeight = 0.20,
numericLabels = TRUE,
pamRespectsDendro = FALSE,
saveTOMs = TRUE,
saveTOMFileBase = "TOM_unification",
verbose = 3
)
## Calculating module eigengenes block-wise from all genes
## Flagging genes and samples with too many missing values...
## ..step 1
## ....pre-clustering genes to determine blocks..
## Projective K-means:
## ..k-means clustering..
## ..merging smaller clusters...
## Block sizes:
## gBlocks
## 1 2 3
## 4963 4178 3881
## ..Working on block 1 .
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## ..saving TOM for block 1 into file TOM_unification-block.1.RData
## ....clustering..
## ....detecting modules..
## ....calculating module eigengenes..
## ....checking kME in modules..
## ..removing 32 genes from module 1 because their KME is too low.
## ..removing 27 genes from module 2 because their KME is too low.
## ..removing 23 genes from module 3 because their KME is too low.
## ..removing 11 genes from module 4 because their KME is too low.
## ..Working on block 2 .
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## ..saving TOM for block 2 into file TOM_unification-block.2.RData
## ....clustering..
## ....detecting modules..
## ....calculating module eigengenes..
## ....checking kME in modules..
## ..removing 185 genes from module 1 because their KME is too low.
## ..Working on block 3 .
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## ..saving TOM for block 3 into file TOM_unification-block.3.RData
## ....clustering..
## ....detecting modules..
## ....calculating module eigengenes..
## ....checking kME in modules..
## ..removing 92 genes from module 1 because their KME is too low.
## ..merging modules that are too close..
## mergeCloseModules: Merging modules whose distance is less than 0.2
## Calculating new MEs...
sizeGrWindow(12, 9)
mergedColors = labels2colors(net$colors)
for (i in 1:length(net$dendrograms)) {
plotDendroAndColors(
net$dendrograms[[i]],
mergedColors[net$blockGenes[[i]]],
"Module colors",
dendroLabels = FALSE,
hang = 0.03,
addGuide = TRUE, guideHang = 0.05
)
}
table(net$colors) # Gene counts per module
##
## 0 1 2 3 4
## 370 7782 2163 1754 953
MEs = net$MEs # # Module Eigengene
moduleTraitCor = cor(MEs, datTraits_clean, use = "pairwise.complete.obs")
moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nrow(datExpr))
print(moduleTraitCor)
## geo_accession Disease Age Gender BMI
## ME2 0.15785652 -0.39945711 0.04469491 -0.03625056 -0.01780674
## ME4 -0.37025105 -0.73720634 -0.31795501 0.04308868 -0.06742734
## ME1 0.78446936 0.29268963 0.53111550 -0.18535989 0.11634170
## ME3 0.75521695 0.71808742 0.58793457 -0.18256024 0.07576975
## ME0 -0.09904741 -0.03022755 -0.39356341 0.14880918 0.06809534
print(moduleTraitPvalue)
## geo_accession Disease Age Gender BMI
## ME2 0.5451145809 0.1121696309 0.86475125 0.8901419 0.9459197
## ME4 0.1434970488 0.0007337838 0.21361224 0.8695720 0.7970814
## ME1 0.0001927002 0.2542619477 0.02825012 0.4763072 0.6565607
## ME3 0.0004563371 0.0011684026 0.01305886 0.4831097 0.7725615
## ME0 0.7052755669 0.9083154065 0.11806203 0.5686703 0.7951111
# Extract the correlations and p-values for the trait "Disease"
cor_Disease = moduleTraitCor[, "Disease"]
pval_Disease = moduleTraitPvalue[, "Disease"]
best_module = which.max(abs(cor_Disease))
print(paste("Most significant module:", names(cor_Disease)[best_module]))
## [1] "Most significant module: ME4"
print(paste("Correlation:", cor_Disease[best_module]))
## [1] "Correlation: -0.737206342634251"
print(paste("P-value:", pval_Disease[best_module]))
## [1] "P-value: 0.000733783760714797"
module4_genes = names(datExpr)[net$colors == 4]
head(module4_genes)
## [1] "ENSG00000000419" "ENSG00000004534" "ENSG00000004961" "ENSG00000005421"
## [5] "ENSG00000005471" "ENSG00000007171"
str(module4_genes)
## chr [1:953] "ENSG00000000419" "ENSG00000004534" "ENSG00000004961" ...
write.csv(module4_genes, "Module_Eigengene_ME4_unification.csv", row.names = FALSE)
# PPI network analysis
library(STRINGdb)
string_db <- STRINGdb$new(version = "11.5", species = 9606,
score_threshold = 400, input_directory = "")
# Mapping Module 16 genes and visualizing Protein-Protein Interaction Network
module4_genes <- gsub("\\..*", "", module4_genes)
df_genes <- data.frame(ENSEMBL = module4_genes)
mapped_genes <- string_db$map(df_genes, "ENSEMBL", removeUnmappedRows = TRUE)
## Warning: we couldn't map to STRING 11% of your identifiers
print(head(mapped_genes))
## ENSEMBL STRING_id
## 1 ENSG00000000419 9606.ENSP00000360644
## 2 ENSG00000004534 9606.ENSP00000266022
## 3 ENSG00000004961 9606.ENSP00000326579
## 4 ENSG00000005421 9606.ENSP00000222381
## 5 ENSG00000005471 9606.ENSP00000265723
## 6 ENSG00000007171 9606.ENSP00000327251
unmapped_genes <- base::setdiff(df_genes$ENSEMBL, mapped_genes$ENSEMBL)
print(unmapped_genes)
## [1] "ENSG00000060303" "ENSG00000133136" "ENSG00000171570" "ENSG00000179073"
## [5] "ENSG00000185834" "ENSG00000196205" "ENSG00000199787" "ENSG00000200170"
## [9] "ENSG00000200769" "ENSG00000204054" "ENSG00000211666" "ENSG00000213178"
## [13] "ENSG00000213693" "ENSG00000213908" "ENSG00000214019" "ENSG00000215908"
## [17] "ENSG00000216754" "ENSG00000218690" "ENSG00000225670" "ENSG00000225849"
## [21] "ENSG00000226781" "ENSG00000228286" "ENSG00000229132" "ENSG00000231225"
## [25] "ENSG00000231325" "ENSG00000232036" "ENSG00000232150" "ENSG00000232541"
## [29] "ENSG00000232569" "ENSG00000232702" "ENSG00000232957" "ENSG00000233247"
## [33] "ENSG00000233259" "ENSG00000233314" "ENSG00000233401" "ENSG00000233718"
## [37] "ENSG00000234241" "ENSG00000235259" "ENSG00000236349" "ENSG00000238018"
## [41] "ENSG00000239791" "ENSG00000241293" "ENSG00000242600" "ENSG00000244723"
## [45] "ENSG00000248161" "ENSG00000249264" "ENSG00000249859" "ENSG00000250474"
## [49] "ENSG00000254389" "ENSG00000254413" "ENSG00000256206" "ENSG00000259137"
## [53] "ENSG00000261771" "ENSG00000262860" "ENSG00000272670" "ENSG00000273032"
## [57] "ENSG00000273175" "ENSG00000273457" "ENSG00000273859" "ENSG00000274442"
## [61] "ENSG00000274853" "ENSG00000275199" "ENSG00000275272" "ENSG00000276230"
## [65] "ENSG00000276463" "ENSG00000276495" "ENSG00000276996" "ENSG00000277042"
## [69] "ENSG00000277568" "ENSG00000278032" "ENSG00000278855" "ENSG00000278943"
## [73] "ENSG00000281078" "ENSG00000281244" "ENSG00000283812" "ENSG00000283883"
## [77] "ENSG00000284468" "ENSG00000284752" "ENSG00000284816" "ENSG00000284832"
## [81] "ENSG00000284915" "ENSG00000285007" "ENSG00000285417" "ENSG00000285982"
## [85] "ENSG00000286190" "ENSG00000286905" "ENSG00000288283" "ENSG00000288325"
## [89] "ENSG00000288427" "ENSG00000288431" "ENSG00000288445" "ENSG00000288984"
## [93] "ENSG00000290986" "ENSG00000291480" "ENSG00000291527" "ENSG00000291544"
## [97] "ENSG00000291629" "ENSG00000291761" "ENSG00000291975" "ENSG00000292035"
## [101] "ENSG00000292096" "ENSG00000292099" "ENSG00000292332" "ENSG00000292334"
## [105] "ENSG00000292373" "ENSG00000293434"
string_db$plot_network(mapped_genes$STRING_id)
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
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## Loading required package: BiocGenerics
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## Loading required package: Biobase
## Welcome to Bioconductor
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# Functional enrichment analysis
enrichment_results_GO <- string_db$get_enrichment(
string_ids = mapped_genes$STRING_id,
category = "Process", # GO "Process" or "Pathway" by KEGG
methodMT = "fdr",
iea = FALSE
)
## Warning in string_db$get_enrichment(string_ids = mapped_genes$STRING_id, :
## methodMT parameter is depecated. Only FDR correction is available.
## Warning in string_db$get_enrichment(string_ids = mapped_genes$STRING_id, : iea
## parameter is deprecated.
head(enrichment_results_GO)
## category term number_of_genes number_of_genes_in_background
## 34 Process GO:0044237 442 7513
## 35 Process GO:0008152 475 8298
## 36 Process GO:0071704 451 7755
## 37 Process GO:0009987 739 15024
## 38 Process GO:0044238 423 7332
## 39 Process GO:0006807 390 6852
## ncbiTaxonId
## 34 9606
## 35 9606
## 36 9606
## 37 9606
## 38 9606
## 39 9606
## inputGenes
## 34 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## 35 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## 36 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## 37 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## 38 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## 39 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06.ENSP00000357320,9606.ENSP00000357838,9606.ENSP00000357880,9606.ENSP00000357998,9606.ENSP00000358478,9606.ENSP00000358554,9606.ENSP00000358635,9606.ENSP00000358737,9606.ENSP00000359160,9606.ENSP00000359285,9606.ENSP00000359345,9606.ENSP00000359531,9606.ENSP00000359581,9606.ENSP00000359606,9606.ENSP00000359612,9606.ENSP00000359688,9606.ENSP00000359740,9606.ENSP00000360141,9606.ENSP00000360268,9606.ENSP00000360644,9606.ENSP00000361219,9606.ENSP00000361562,9606.ENSP00000361845,9606.ENSP00000362166,9606.ENSP00000362334,9606.ENSP00000362807,9606.ENSP00000363017,9606.ENSP00000363193,9606.ENSP00000363286,9606.ENSP00000364204,9606.ENSP00000364249,9606.ENSP00000366557,9606.ENSP00000366746,9606.ENSP00000366902,9606.ENSP00000366934,9606.ENSP00000366974,9606.ENSP00000367028,9606.ENSP00000367406,9606.ENSP00000367407,9606.ENSP00000367623,9606.ENSP00000367697,9606.ENSP00000368356,9606.ENSP00000368458,9606.ENSP00000368605,9606.ENSP00000368767,9606.ENSP00000368881,9606.ENSP00000368884,9606.ENSP00000369131,9606.ENSP00000369777,9606.ENSP00000369899,9606.ENSP00000370078,9606.ENSP00000370625,9606.ENSP00000371000,9606.ENSP00000371212,9606.ENSP00000371805,9606.ENSP00000372088,9606.ENSP00000372804,9606.ENSP00000374037,9606.ENSP00000374069,9606.ENSP00000374354,9606.ENSP00000376204,9606.ENSP00000376258,9606.ENSP00000376276,9606.ENSP00000376456,9606.ENSP00000376609,9606.ENSP00000377115,9606.ENSP00000377262,9606.ENSP00000377936,9606.ENSP00000378028,9606.ENSP00000378974,9606.ENSP00000379042,9606.ENSP00000379174,9606.ENSP00000379182,9606.ENSP00000379372,9606.ENSP00000379701,9606.ENSP00000379847,9606.ENSP00000380252,9606.ENSP00000380402,9606.ENSP00000380878,9606.ENSP00000381266,9606.ENSP00000383044,9606.ENSP00000383364,9606.ENSP00000383920,9606.ENSP00000383949,9606.ENSP00000384823,9606.ENSP00000385096,9606.ENSP00000385385,9606.ENSP00000385410,9606.ENSP00000387170,9606.ENSP00000387219,9606.ENSP00000387356,9606.ENSP00000387365,9606.ENSP00000387654,9606.ENSP00000391211,9606.ENSP00000392270,9606.ENSP00000393139,9606.ENSP00000398632,9606.ENSP00000400591,9606.ENSP00000400806,9606.ENSP00000401802,9606.ENSP00000403397,9606.ENSP00000404092,9606.ENSP00000406549,9606.ENSP00000409346,9606.ENSP00000410964,9606.ENSP00000411825,9606.ENSP00000414558,9606.ENSP00000415151,9606.ENSP00000416250,9606.ENSP00000416534,9606.ENSP00000418669,9606.ENSP00000418695,9606.ENSP00000419045,9606.ENSP00000419195,9606.ENSP00000419325,9606.ENSP00000420333,9606.ENSP00000420484,9606.ENSP00000424328,9606.ENSP00000424381,9606.ENSP00000426421,9606.ENSP00000428340,9606.ENSP00000428646,9606.ENSP00000430548,9606.ENSP00000432083,9606.ENSP00000432770,9606.ENSP00000433919,9606.ENSP00000434995,9606.ENSP00000438349,9606.ENSP00000438788,9606.ENSP00000438993,9606.ENSP00000440222,9606.ENSP00000440402,9606.ENSP00000440485,9606.ENSP00000441140,9606.ENSP00000441953,9606.ENSP00000444029,9606.ENSP00000447650,9606.ENSP00000449381,9606.ENSP00000451235,9606.ENSP00000451974,9606.ENSP00000462355,9606.ENSP00000462963,9606.ENSP00000468785,9606.ENSP00000470560,9606.ENSP00000477613,9606.ENSP00000478721,9606.ENSP00000481029,9606.ENSP00000481626,9606.ENSP00000482075,9606.ENSP00000483491,9606.ENSP00000484288,9606.ENSP00000485022
## preferredNames
## 34 CRY1,RANBP9,RFC2,HDAC7,DERL2,KIF22,PRLH,C12orf5,OXCT1,DLD,TGFBR3,MAPK12,SNAPC1,PIGH,CSTF1,IDH3G,USB1,PSMD7,NME4,EIF3E,SLC5A5,PON1,NOD1,SFXN3,C1QBP,NFKB1,CTSC,KITLG,ART4,CNOT2,KRR1,GAPDH,TPI1,CMAS,SRSF9,NEK4,GGCX,ODC1,ORC2,TMEM59,AKR7A2,ACYP1,RIF1,INSIG2,THOC2,ATG14,EIF3K,DHX40,CUL9,EPO,EIF2S3,NOL11,NDFIP1,FUS,THAP1,PTCD3,COQ3,UTP3,EIF2S1,CYP27A1,REV1,NUPL2,RSL24D1,RTCA,GALC,MAN2A1,SNW1,POMT2,CDK2AP1,EIF3J,RBM25,ATP5B,PIK3C3,WIPI1,MTFR1,PKMYT1,CFAP20,RPL8,CCNE1,PLD2,METTL16,UFD1L,LIG1,BIRC3,CHMP2B,LTK,MAP4K3,MCM6,AGPS,ARID4B,PIKFYVE,THRA,PSMD3,STAT3,DNMT3A,PAPSS1,PCNP,PECR,VDAC1,PIP5K1B,FBXO3,SQLE,RBM6,PELI2,HDC,HEXA,MAP1LC3B,COPS3,G6PC3,GALNT1,NPC1,PFKL,DNMT3L,RCN3,PSMA5,CERS2,RQCD1,SLC25A38,ALDH1L1,CRH,TERF1,FLT1,MED21,UXS1,GTF2E1,AKR1B1,NUP205,SLC26A2,HMGCR,DUSP2,UBE2Q1,PSME3,LUC7L,NEU3,HDAC11,MTMR14,NPM1,NOS3,SPTSSA,NEMF,SNRPD1,PGAP3,SRRM2,POLR2G,LSM3,TRMT61B,ACHE,PDS5A,ZCCHC4,CBR4,CD2BP2,SOCS5,MRPL39,GPR37,DESI2,MRPL13,GLB1,MCM7,HLTF,UBE3C,PSMD1,DPYSL2,POLD4,PPP1R8,LTBP4,SSH3,AOC3,KCTD2,GRHPR,PHKB,KHDRBS1,PER1,CRAT,SWAP70,CCDC101,SFTPC,FKBP10,COX5A,CES2,HINFP,PRKRA,PRMT5,TRIT1,SLC25A22,STK11,PPP2R2A,KARS,CYP11B2,PSEN1,HCCS,NOS2,CSF1,RLIM,FBXO21,SP1,PDGFB,NDUFB1,IP6K2,MORF4L1,NPLOC4,CALCA,IDH2,PURA,TRMT11,SEL1L,ZBTB16,MRPL35,CDK10,ZC3H15,NDUFA4,CIR1,TAF1A,HUWE1,ACACB,JAK1,DHRS2,RPL36AL,RPL22,DDX21,HNRNPA2B1,PGAP1,CGI-74,WARS,UVRAG,UPF2,PIK3R4,PEX2,PTPRS,COPS5,RAD23B,RHOT1,TRIM33,TTC37,EDC4,MARCH5,NAE1,PHF2,CPZ,TAF11,SLC26A1,MVB12B,NRG2,NAA35,ILF2,CTR9,APOBEC3C,MTR,TOMM20,TSNAX,IARS2,PIK3C2B,DNM3,MPC2,SGK1,UFC1,APOA1BP,SYT11,DAP3,OAT,AMD1,TTF2,BCAS2,SYNCRIP,ATP5F1,TRMT13,CHRNA4,RPL5,GTF2B,HS2ST1,ZNHIT6,BCL10,RPF1,ZNF451,GNAS,NFIA,ALDH18A1,SCP2,DPM1,EPS15,SURF1,GTF3C4,CTSA,ZMPSTE24,MEAF6,PSMB2,PEF1,RAB14,RPA2,MED12,POLE3,PINK1,PLA2G5,PDSS1,CRNKL1,STAM,ZBTB48,NOL9,HIST1H4B,TCOF1,TAF2,NMT2,HSPA14,ATP6AP2,PLCH2,UQCRQ,PRKD3,PCNA,ECHDC3,ACOT9,ASPH,KIN,RPS6KA3,SIN3B,ZNF768,RRAGA,PDE4A,IDH3B,POLR2B,IDI1,CRYZL1,RNF6,RBM47,FBXL18,CD9,RAD51,RNMT,SACM1L,VPS9D1,PTPRN2,EXOSC8,ALPP,ASH1L,RNF34,SRSF2,DYNLL1,B3GALT1,GRK5,LIPT1,SRPK2,PPP2R2B,RNF14,MAPK8,ERO1L,POLM,RAE1,GTF2A2,HNF4G,ZNF143,NFE2L2,MPST,PPP3CC,WDR4,USP25,PLA2G2A,ASXL2,NHP2L1,FBXO11,KCTD17,PDIA6,NOLC1,GIGYF2,NFU1,ACAN,PWP1,PCYOX1,PSMC2,STRAP,PIK3R5,CDC7,CALCOCO2,CD44,SNRPE,APTX,GK,PSMC6,ZDHHC17,SMC6,CHMP3,TAF1,CISH,ERLIN1,PDCD6IP,ABHD4,CBFB,EIF2B1,DDX46,NDUFA5,SEPHS2,PSMD6,GCH1,CAMKV,SUCLG2,SSBP1,ARMC8,OARD1,MRPS30,ASTE1,ANGPT1,FBXO41,COX6C,GRIA1,PTDSS1,HSPA8,EYA4,CLNS1A,CLP1,ECHDC1,ADM,MDH1,TRMT112,CUL7,ZCCHC8,ARF1,LUC7L2,DDX11,PSMD9,NOL8,ORC4,NAT1,NUP153,GPRASP1,RT14,MAPKAPK5,ENSP00000451235,XRCC3,ETFA,HIST2H4B,TEFM,MBD1,EMG1,H6PD,BIRC2,RYK,PTMS,PLP1,PSMC3,C18orf25,PTGES3,PPIP5K2,OXA1L,LIG4,ENSP00000485022
## 35 CRY1,RANBP9,CD4,RFC2,HDAC7,DERL2,KIF22,PRLH,C12orf5,OXCT1,DLD,TGFBR3,MAPK12,SNAPC1,PIGH,CSTF1,IDH3G,USB1,PSMD7,NME4,EIF3E,SLC5A5,PON1,NOD1,SFXN3,C1QBP,NFKB1,CTSC,KITLG,ART4,CNOT2,KRR1,GAPDH,TPI1,CMAS,SRSF9,NEK4,SNX17,GGCX,ODC1,ORC2,TMEM59,AKR7A2,ACYP1,PYROXD1,RIF1,INSIG2,THOC2,NECAB3,ATG14,EIF3K,DHX40,CUL9,EPO,EIF2S3,NOL11,NDFIP1,FUS,THAP1,PTCD3,COQ3,UTP3,EIF2S1,MBD2,ADAMTS8,CYP27A1,REV1,NUPL2,RSL24D1,RTCA,GALC,RSBN1,MAN2A1,SNW1,POMT2,CDK2AP1,EIF3J,RBM25,ATP5B,PIK3C3,WIPI1,MTFR1,PKMYT1,CFAP20,RPL8,CCNE1,PLD2,METTL16,UFD1L,LIG1,BIRC3,LCN1,CHMP2B,LTK,MAP4K3,MCM6,AGPS,ARID4B,PIKFYVE,GZMM,THRA,PSMD3,STAT3,UFSP2,DNMT3A,PAPSS1,PCNP,PECR,VDAC1,PIP5K1B,FBXO3,ABCB4,SQLE,RBM6,PELI2,HDC,HEXA,MAP1LC3B,COPS3,DPEP3,G6PC3,GALNT1,NPC1,PFKL,DNMT3L,RCN3,PSMA5,CERS2,RQCD1,SLC25A38,ALDH1L1,CRH,TERF1,CAPN5,FLT1,MED21,UXS1,GTF2E1,AKR1B1,NUP205,SLC26A2,HMGCR,DUSP2,UBE2Q1,PSME3,LUC7L,NEU3,HDAC11,MTMR14,NPM1,NOS3,SPTSSA,NEMF,SNRPD1,PGAP3,SRRM2,POLR2G,FADD,LSM3,TRMT61B,ACHE,PDS5A,ZCCHC4,CBR4,CD2BP2,SOCS5,MRPL39,GPR37,DESI2,MRPL13,GLB1,MCM7,MMP14,HLTF,UBE3C,PSMD1,DPYSL2,POLD4,PPP1R8,LTBP4,SSH3,AOC3,KCTD2,GRHPR,PHKB,KHDRBS1,PER1,CRAT,SWAP70,CCDC101,SFTPC,PITPNA,FKBP10,COX5A,CES2,HINFP,PRKRA,PRMT5,TRIT1,SLC25A22,STK11,PPP2R2A,KARS,CYP11B2,PSEN1,HCCS,NOS2,CSF1,RLIM,PAWR,IL25,FBXO21,SP1,PDGFB,NDUFB1,IP6K2,MORF4L1,NPLOC4,CALCA,IDH2,PURA,TRMT11,SEL1L,ZBTB16,MRPL35,TASP1,CDK10,ZC3H15,DPP8,NDUFA4,CIR1,TAF1A,HUWE1,ACACB,JAK1,DHRS2,RPL36AL,RPL22,DDX21,HNRNPA2B1,PGAP1,CGI-74,WARS,MMP23B,UVRAG,UPF2,PIK3R4,PEX2,PTPRS,COPS5,RAD23B,TMCC2,RHOT1,TRIM33,TTC37,EDC4,MARCH5,NAE1,PHF2,AMZ2,DPP4,CPZ,TAF11,SLC26A1,MVB12B,NRG2,NAA35,ILF2,CTR9,APOBEC3C,MTR,TOMM20,TSNAX,IARS2,PIK3C2B,DNM3,MPC2,SGK1,UFC1,APOA1BP,SYT11,DAP3,OAT,AMD1,SEC63,TTF2,BCAS2,SYNCRIP,ATP5F1,TRMT13,CHRNA4,RPL5,GTF2B,HS2ST1,ZNHIT6,BCL10,RPF1,ZNF451,FPGT,GNAS,NFIA,ALDH18A1,SCP2,DPM1,EPS15,SURF1,GTF3C4,CTSA,ZMPSTE24,MEAF6,PSMB2,PEF1,RAB14,RPA2,MED12,POLE3,TXN,PINK1,PLA2G5,PDSS1,CRNKL1,STAM,ZBTB48,NOL9,HIST1H4B,TCOF1,TAF2,NMT2,HSPA14,ATP6AP2,PLCH2,UQCRQ,PRKD3,PCNA,ECHDC3,ACOT9,ASPH,KIN,RPS6KA3,SIN3B,ZNF768,RRAGA,PDE4A,IDH3B,POLR2B,IDI1,CRYZL1,RNF6,RBM47,FBXL18,CD9,RAD51,RNMT,SACM1L,VPS9D1,PTPRN2,EXOSC8,ALPP,ASH1L,RNF34,SRSF2,DYNLL1,B3GALT1,GRK5,LIPT1,SRPK2,PPP2R2B,RNF14,MAPK8,ERO1L,POLM,RAE1,GTF2A2,HNF4G,ZNF143,NFE2L2,MPST,PPP3CC,WDR4,USP25,PLA2G2A,ASXL2,NHP2L1,FBXO11,KCTD17,PDIA6,NOLC1,GIGYF2,ATHL1,NFU1,ACAN,PWP1,PCYOX1,PSMC2,STRAP,PIK3R5,CDC7,CALCOCO2,CD44,SNRPE,APTX,GK,PSMC6,ZDHHC17,SMC6,CHMP3,TRPV4,TAF1,CISH,ERLIN1,PDCD6IP,ABHD4,CBFB,EIF2B1,DDX46,NDUFA5,SEPHS2,PSMD6,GCH1,CAMKV,SUCLG2,SSBP1,ARMC8,OARD1,MRPS30,LMF2,ASTE1,ANGPT1,FBXO41,COX6C,GRIA1,PTDSS1,HSPA8,EYA4,CLNS1A,CLP1,ECHDC1,ADM,MDH1,TRMT112,CUL7,ZCCHC8,ARF1,LUC7L2,DDX11,PSMD9,NOL8,ORC4,NAT1,NUP153,GPRASP1,RT14,MAPKAPK5,ENSP00000451235,XRCC3,ETFA,TRPV1,VR1,HIST2H4B,TEFM,MBD1,EMG1,H6PD,BIRC2,RYK,PTMS,PLP1,PSMC3,C18orf25,PTGES3,PPIP5K2,OXA1L,LIG4,ENSP00000485022,NXF2
## 36 CRY1,RANBP9,CD4,RFC2,HDAC7,DERL2,KIF22,PRLH,C12orf5,OXCT1,DLD,TGFBR3,MAPK12,SNAPC1,PIGH,CSTF1,IDH3G,USB1,PSMD7,NME4,EIF3E,SLC5A5,PON1,NOD1,C1QBP,NFKB1,CTSC,KITLG,ART4,CNOT2,KRR1,GAPDH,TPI1,CMAS,SRSF9,NEK4,SNX17,GGCX,ODC1,ORC2,TMEM59,AKR7A2,RIF1,INSIG2,THOC2,NECAB3,EIF3K,DHX40,CUL9,EPO,EIF2S3,NOL11,NDFIP1,FUS,THAP1,PTCD3,COQ3,UTP3,EIF2S1,MBD2,ADAMTS8,CYP27A1,REV1,NUPL2,RSL24D1,RTCA,GALC,MAN2A1,SNW1,POMT2,CDK2AP1,EIF3J,RBM25,ATP5B,PIK3C3,WIPI1,PKMYT1,CFAP20,RPL8,CCNE1,PLD2,METTL16,UFD1L,LIG1,BIRC3,LCN1,LTK,MAP4K3,MCM6,AGPS,ARID4B,PIKFYVE,GZMM,THRA,PSMD3,STAT3,UFSP2,DNMT3A,PAPSS1,PCNP,PECR,VDAC1,PIP5K1B,FBXO3,ABCB4,SQLE,RBM6,PELI2,HDC,HEXA,COPS3,DPEP3,G6PC3,GALNT1,NPC1,PFKL,DNMT3L,RCN3,PSMA5,CERS2,RQCD1,SLC25A38,ALDH1L1,CRH,TERF1,CAPN5,FLT1,MED21,UXS1,GTF2E1,AKR1B1,NUP205,SLC26A2,HMGCR,DUSP2,UBE2Q1,PSME3,LUC7L,NEU3,HDAC11,MTMR14,NPM1,NOS3,SPTSSA,NEMF,SNRPD1,PGAP3,SRRM2,POLR2G,FADD,LSM3,TRMT61B,ACHE,PDS5A,ZCCHC4,CBR4,CD2BP2,SOCS5,MRPL39,GPR37,DESI2,MRPL13,GLB1,MCM7,MMP14,HLTF,UBE3C,PSMD1,DPYSL2,POLD4,PPP1R8,LTBP4,SSH3,AOC3,KCTD2,GRHPR,PHKB,KHDRBS1,PER1,CRAT,SWAP70,CCDC101,SFTPC,PITPNA,FKBP10,CES2,HINFP,PRKRA,PRMT5,TRIT1,STK11,PPP2R2A,KARS,CYP11B2,PSEN1,HCCS,NOS2,CSF1,RLIM,PAWR,IL25,FBXO21,SP1,PDGFB,IP6K2,MORF4L1,NPLOC4,CALCA,IDH2,PURA,TRMT11,SEL1L,ZBTB16,MRPL35,TASP1,CDK10,ZC3H15,DPP8,CIR1,TAF1A,HUWE1,ACACB,JAK1,DHRS2,RPL36AL,RPL22,DDX21,HNRNPA2B1,PGAP1,CGI-74,WARS,MMP23B,UVRAG,UPF2,PIK3R4,PEX2,PTPRS,COPS5,RAD23B,TMCC2,RHOT1,TRIM33,TTC37,EDC4,MARCH5,NAE1,PHF2,AMZ2,DPP4,CPZ,TAF11,SLC26A1,MVB12B,NRG2,NAA35,ILF2,CTR9,APOBEC3C,MTR,TOMM20,TSNAX,IARS2,PIK3C2B,DNM3,MPC2,SGK1,UFC1,APOA1BP,DAP3,OAT,AMD1,TTF2,BCAS2,SYNCRIP,ATP5F1,TRMT13,CHRNA4,RPL5,GTF2B,HS2ST1,ZNHIT6,BCL10,RPF1,ZNF451,FPGT,GNAS,NFIA,ALDH18A1,SCP2,DPM1,EPS15,GTF3C4,CTSA,ZMPSTE24,MEAF6,PSMB2,PEF1,RAB14,RPA2,MED12,POLE3,TXN,PINK1,PLA2G5,PDSS1,CRNKL1,STAM,ZBTB48,NOL9,HIST1H4B,TCOF1,TAF2,NMT2,HSPA14,ATP6AP2,PLCH2,PRKD3,PCNA,ECHDC3,ACOT9,ASPH,KIN,RPS6KA3,SIN3B,ZNF768,RRAGA,PDE4A,IDH3B,POLR2B,IDI1,CRYZL1,RNF6,RBM47,FBXL18,CD9,RAD51,RNMT,SACM1L,VPS9D1,PTPRN2,EXOSC8,ASH1L,RNF34,SRSF2,B3GALT1,GRK5,LIPT1,SRPK2,PPP2R2B,RNF14,MAPK8,ERO1L,POLM,RAE1,GTF2A2,HNF4G,ZNF143,NFE2L2,MPST,PPP3CC,WDR4,USP25,PLA2G2A,ASXL2,NHP2L1,FBXO11,KCTD17,PDIA6,NOLC1,GIGYF2,ATHL1,NFU1,ACAN,PWP1,PCYOX1,PSMC2,STRAP,PIK3R5,CDC7,CD44,SNRPE,APTX,GK,PSMC6,ZDHHC17,SMC6,TAF1,CISH,ERLIN1,PDCD6IP,ABHD4,CBFB,EIF2B1,DDX46,SEPHS2,PSMD6,GCH1,CAMKV,SUCLG2,SSBP1,ARMC8,OARD1,MRPS30,LMF2,ASTE1,ANGPT1,FBXO41,GRIA1,PTDSS1,HSPA8,EYA4,CLNS1A,CLP1,ECHDC1,ADM,MDH1,TRMT112,CUL7,ZCCHC8,ARF1,LUC7L2,DDX11,PSMD9,NOL8,ORC4,NUP153,GPRASP1,RT14,MAPKAPK5,ENSP00000451235,XRCC3,ETFA,TRPV1,VR1,HIST2H4B,TEFM,MBD1,EMG1,H6PD,BIRC2,RYK,PTMS,PLP1,PSMC3,C18orf25,PTGES3,PPIP5K2,OXA1L,LIG4,ENSP00000485022,NXF2
## 37 CRY1,RANBP9,CD4,AKAP11,RFC2,HDAC7,DERL2,KIF22,PRLH,C12orf5,OSTM1,OXCT1,SPG21,DLD,TGFBR3,MAPK12,SNAPC1,PIGH,CSTF1,IDH3G,NXT2,GLRA2,ATP12A,MLNR,C16orf70,USB1,PSMD7,NME4,EIF3E,RETN,CDC37,SLC5A5,ERF,PON1,GTPBP10,BET1,HOXA2,NOD1,C5,TNFSF8,SFXN3,C1QBP,RANGRF,NFKB1,CTSC,KITLG,MYF5,GLI1,ART4,CNOT2,KRR1,GAPDH,TPI1,GOLT1B,CMAS,SRSF9,MDFI,EXOC2,TMEM30A,HRG,NEK4,DAZAP1,SLC30A3,SNX17,GGCX,ODC1,CEBPZ,ORC2,TMEM59,AKR7A2,ZFAND5,ACYP1,PYROXD1,RIF1,RAB22A,INSIG2,THOC2,NECAB3,SLURP1,ATG14,EIF3K,TUBA4A,AAMP,SMO,DHX40,SNX4,CUL9,KRT6B,EPO,EIF2S3,LRP3,NOL11,NDFIP1,FUS,THAP1,ACTR10,WDR7,PTCD3,COQ3,UTP3,EIF2S1,MBD2,SLC38A2,HRH4,ADAMTS8,CYP27A1,REV1,KDELR2,NUPL2,CCL21,PRKRIR,RSL24D1,RTCA,RAB21,GALC,RSBN1,MAN2A1,SNW1,POMT2,AP5M1,CDK2AP1,EIF3J,TRIP4,RBM25,ATP5B,PIK3C3,WIPI1,MTFR1,PKMYT1,CFAP20,RPL8,CCNE1,CELSR1,CSE1L,ITGAE,PLD2,METTL16,UFD1L,ARFGAP3,LIG1,BIRC3,CHMP2B,LTK,MAP4K3,MCAM,MCM6,AGPS,ARID4B,FAM13A,PIKFYVE,GZMM,THRA,PSMD3,STAT3,DNMT3A,ANXA3,PAPSS1,PCNP,PECR,VDAC1,PIP5K1B,FBXO3,ABCB4,SMARCA2,FSCN3,SQLE,RBM6,PELI2,RTN1,HDC,HEXA,MAP1LC3B,DEF8,GAS8,NCOR1,COPS3,G6PC3,GALNT1,NPC1,PFKL,DNMT3L,RCN3,PSMA5,CERS2,JTB,RQCD1,SLC25A38,ALDH1L1,CENPC,AP1AR,HTR2C,CRH,TERF1,CDKN2B,CAPN5,GPM6A,CYSLTR2,FLT1,MED21,ZIC1,UXS1,GTF2E1,AKR1B1,NUP205,SLC26A2,VBP1,GNAQ,HMGCR,DUSP2,SLAMF8,OGFR,NPTN,AGRP,CSTB,UBE2Q1,CABP5,PSME3,CHRNE,LUC7L,SSTR5,NEU3,CABP2,HDAC11,MTMR14,NPM1,T,SOX17,NOS3,SPTSSA,NEMF,WAPAL,SLC9A5,GPR182,MAPRE2,SNRPD1,PGAP3,KRT16,SRRM2,POLR2G,FADD,SCARA3,MFF,LSM3,NHLH1,INSL5,TRMT61B,TMED10,ACHE,PDS5A,ZCCHC4,CBR4,STARD5,CTNNA1,CD2BP2,ROBO4,RFXANK,SOCS5,CNNM3,MRPL39,SLCO1A2,GPR37,DESI2,MRPL13,SEMA4C,ETV5,GLB1,MCM7,GCC2,MMP14,LEMD3,KRT17,HLTF,UBE3C,CD164,PSMD1,DPYSL2,POLD4,GPR162,PPP1R8,LTBP4,SSH3,AOC3,KCTD2,GRHPR,PHKB,KHDRBS1,PER1,CCZ1B,CRAT,SWAP70,CCDC101,SFTPC,PITPNA,FKBP10,COX5A,CES2,KIAA0196,HINFP,PRKRA,RAP2B,PRMT5,GPR4,SIGLEC8,SH2B1,TRIT1,SLC25A22,NDUFAF3,PLEC,BAIAP3,STK11,PPP2R2A,AP3S1,KARS,PLAG1,CYP11B2,FRAS1,PSEN1,HCCS,PRR7,VIPR1,NOS2,CSF1,WRB,RLIM,PAWR,IL25,OR7A17,FBXO21,SP1,COPB2,PDGFB,NDUFB1,IP6K2,MORF4L1,GAST,NPLOC4,CALCA,IDH2,SLIT3,ATP6V0A2,CCR4,PURA,TUBA8,TRMT11,GPR144,SEL1L,ARHGEF1,NIPA2,ZBTB16,MTDH,MRPL35,CDK10,ZC3H15,DPP8,NDUFA4,CIR1,MIOS,TAF1A,HUWE1,ACACB,RANBP3,NECAP1,SLPI,JAK1,FOXN3,YIF1B,FOXN2,DHRS2,CRTC1,FBLN5,SAMM50,RPL36AL,RPL22,DDX21,NRDE2,HNRNPA2B1,PGAP1,CGI-74,HTT,WARS,TBCD,ZNF536,MMP23B,UVRAG,UPF2,PTGER3,PIK3R4,PEX2,RASSF1,DOK3,COL9A1,PTPRS,SLC29A2,TOR4A,PLN,COPS5,ANKLE2,RAD23B,TPM1,RHOT1,TRIM33,TTC37,STIP1,EDC4,MARCH5,NAE1,KCNQ2,KIRREL,PHF2,DPP4,CPZ,MACF1,DFNB31,TAF11,SLC26A1,MVB12B,CNTNAP2,NRG2,NAA35,ILF2,CTR9,FCRL2,CACNA1S,APOBEC3C,SOX15,MTR,TOMM20,TSNAX,LEFTY2,IARS2,SLC30A1,PIK3C2B,SYNE1,KATNA1,DNM3,MPC2,SGK1,UFC1,SLAMF7,COPA,CASQ1,APOA1BP,SYT11,DAP3,YY1AP1,CFAP46,OAT,AMD1,SEMA6C,SEC63,NHLRC2,PEX11B,RRAGD,TTF2,BCAS2,SYNCRIP,ATP5F1,ATP6AP1,TRMT13,CHRNA4,TMED5,MTF2,RPL5,SLC17A9,OGFRL1,GTF2B,SOX3,HS2ST1,ZNHIT6,BCL10,RPF1,ZNF451,GNAS,NFIA,ALDH18A1,SCP2,DPM1,EPS15,SURF1,GHITM,GTF3C4,CTSA,TBC1D13,ZMPSTE24,WISP2,JPH2,MEAF6,PSMB2,SAR1A,NCDN,MAFB,PEF1,RAB14,RPA2,MED12,POLE3,TMEM50A,GDF5,TXN,PINK1,PLA2G5,PDSS1,PLP2,VSX1,CRNKL1,STAM,TBC1D4,ZBTB48,NOL9,HIST1H4B,TCOF1,SLC22A6,TAF2,NMT2,HSPA14,ATP6AP2,PLCH2,UQCRQ,IL1RAPL1,PRKD3,PCNA,ECHDC3,TNFRSF4,FEZ2,ACOT9,ASPH,TOM1L2,KIN,RPS6KA3,SPEF1,DNAJA1,SIN3B,SOHLH2,IFNA6,FAM50B,ZNF768,RRAGA,PDE4A,SERPINB1,IDH3B,RUFY3,POLR2B,EXOC1,IDI1,CRYZL1,RNF6,HMG20A,CATSPER2,RBM47,C1QTNF3,LGI2,SACS,FBXL18,CD9,RAD51,RNMT,SACM1L,VPS9D1,PTPRN2,EXOSC8,ALPP,MAG,ASH1L,RNF34,SRSF2,DYNLL1,INF2,B3GALT1,GRK5,MKS1,CBX1,LIPT1,MON2,SRPK2,GAPVD1,PPP2R2B,RNF14,ZNF207,EML3,KIF20A,MAPK8,ERO1L,POLM,RAE1,BCAS1,GTF2A2,HNF4G,ZNF143,HRH1,NFE2L2,MPST,EIF4ENIF1,PPP3CC,WDR4,DIAPH1,SEPT7,RPGRIP1,USP25,DEPDC5,PLA2G2A,ASXL2,NHP2L1,FBLN2,FBXO11,XPO1,CACNA1I,KCTD17,PDIA6,NOLC1,PSG2,ARHGAP35,GIGYF2,NFU1,ACAN,PWP1,PCYOX1,PSMC2,STRAP,SLC13A2,AKIRIN1,PIK3R5,CDC7,CORO1C,LPAR3,CLDN9,ATP9B,CALCOCO2,CD44,BEST1,DNAI2,SNRPE,APTX,GK,PSMC6,ZDHHC17,SMC6,CHMP3,TRPV4,TAF1,SLC9A3R2,KIF5A,CISH,TSPYL4,ERLIN1,BCL7B,PDCD6IP,ABHD4,CBFB,EIF2B1,DDX46,NDUFA5,SEPHS2,PSMD6,GCH1,CAMKV,SUCLG2,SSBP1,RAB9A,ARMC8,OARD1,TMEM33,MRPS30,ROPN1B,ASTE1,TNFAIP8,CEP192,WDR1,CETN3,ANGPT1,SEC24B,FBXO41,COX6C,GRIA1,PGRMC2,PTDSS1,BAI1,HSPA8,EYA4,BBIP1,CLNS1A,CLP1,ECHDC1,ADM,HTR2A,BCORL1,MDH1,TRMT112,CUL7,ZCCHC8,DMXL1,ARF1,LUC7L2,ANKRD49,DDX11,PSMD9,NOL8,ORC4,MFSD5,NAT1,NUP153,GPRASP1,RT14,KRT4,MAPKAPK5,SLC38A1,C14orf79,VTI1B,RGS6,ENSP00000451235,XRCC3,ITGA7,ETFA,SLC38A7,CEMP1,TRPV1,VR1,VEZF1,HIST2H4B,TEFM,MBD1,PRICKLE3,EMG1,SEPW1,H6PD,BIRC2,RYK,PTMS,TRAPPC3,DNAI1,PLP1,PSMC3,C18orf25,TBC1D2,PTGES3,PPIP5K2,OXA1L,LIG4,ENSP00000485022,NXF2
## 38 CRY1,RANBP9,RFC2,HDAC7,DERL2,KIF22,PRLH,DLD,TGFBR3,MAPK12,SNAPC1,PIGH,CSTF1,IDH3G,USB1,PSMD7,NME4,EIF3E,PON1,NOD1,C1QBP,NFKB1,CTSC,KITLG,ART4,CNOT2,KRR1,GAPDH,TPI1,SRSF9,NEK4,SNX17,GGCX,ODC1,ORC2,TMEM59,AKR7A2,RIF1,INSIG2,THOC2,NECAB3,EIF3K,DHX40,CUL9,EPO,EIF2S3,NOL11,NDFIP1,FUS,THAP1,PTCD3,COQ3,UTP3,EIF2S1,ADAMTS8,CYP27A1,REV1,NUPL2,RSL24D1,RTCA,GALC,MAN2A1,SNW1,POMT2,EIF3J,RBM25,ATP5B,PIK3C3,WIPI1,PKMYT1,CFAP20,RPL8,CCNE1,PLD2,METTL16,UFD1L,LIG1,BIRC3,LCN1,LTK,MAP4K3,MCM6,AGPS,ARID4B,PIKFYVE,GZMM,THRA,PSMD3,STAT3,UFSP2,DNMT3A,PAPSS1,PCNP,PECR,PIP5K1B,FBXO3,ABCB4,SQLE,RBM6,PELI2,HDC,HEXA,COPS3,DPEP3,G6PC3,GALNT1,NPC1,PFKL,DNMT3L,RCN3,PSMA5,CERS2,RQCD1,CRH,TERF1,CAPN5,FLT1,MED21,UXS1,GTF2E1,AKR1B1,NUP205,SLC26A2,HMGCR,DUSP2,UBE2Q1,PSME3,LUC7L,NEU3,HDAC11,MTMR14,NPM1,NOS3,SPTSSA,NEMF,SNRPD1,PGAP3,SRRM2,POLR2G,FADD,LSM3,TRMT61B,ACHE,PDS5A,ZCCHC4,CBR4,CD2BP2,SOCS5,MRPL39,DESI2,MRPL13,GLB1,MCM7,MMP14,HLTF,UBE3C,PSMD1,DPYSL2,POLD4,PPP1R8,LTBP4,SSH3,KCTD2,PHKB,KHDRBS1,PER1,CRAT,SWAP70,CCDC101,SFTPC,PITPNA,FKBP10,CES2,HINFP,PRKRA,PRMT5,TRIT1,STK11,PPP2R2A,KARS,CYP11B2,PSEN1,HCCS,NOS2,CSF1,RLIM,FBXO21,SP1,PDGFB,IP6K2,MORF4L1,NPLOC4,CALCA,IDH2,PURA,TRMT11,SEL1L,ZBTB16,MRPL35,TASP1,CDK10,ZC3H15,DPP8,CIR1,TAF1A,HUWE1,ACACB,JAK1,DHRS2,RPL36AL,RPL22,DDX21,HNRNPA2B1,PGAP1,CGI-74,WARS,MMP23B,UVRAG,UPF2,PIK3R4,PEX2,PTPRS,COPS5,RAD23B,TMCC2,RHOT1,TRIM33,TTC37,EDC4,MARCH5,NAE1,PHF2,AMZ2,DPP4,CPZ,TAF11,SLC26A1,MVB12B,NRG2,NAA35,ILF2,CTR9,APOBEC3C,MTR,TOMM20,TSNAX,IARS2,PIK3C2B,MPC2,SGK1,UFC1,APOA1BP,DAP3,OAT,AMD1,TTF2,BCAS2,SYNCRIP,ATP5F1,TRMT13,CHRNA4,RPL5,GTF2B,HS2ST1,ZNHIT6,BCL10,RPF1,ZNF451,FPGT,GNAS,ALDH18A1,SCP2,DPM1,GTF3C4,CTSA,ZMPSTE24,MEAF6,PSMB2,PEF1,RAB14,RPA2,MED12,POLE3,PINK1,PLA2G5,PDSS1,CRNKL1,STAM,ZBTB48,NOL9,HIST1H4B,TCOF1,TAF2,NMT2,HSPA14,ATP6AP2,PLCH2,PRKD3,PCNA,ECHDC3,ACOT9,ASPH,KIN,RPS6KA3,SIN3B,ZNF768,RRAGA,PDE4A,IDH3B,POLR2B,IDI1,RNF6,RBM47,FBXL18,RAD51,RNMT,SACM1L,VPS9D1,PTPRN2,EXOSC8,ASH1L,RNF34,SRSF2,B3GALT1,GRK5,LIPT1,SRPK2,PPP2R2B,RNF14,MAPK8,ERO1L,POLM,RAE1,GTF2A2,HNF4G,ZNF143,NFE2L2,MPST,PPP3CC,WDR4,USP25,PLA2G2A,ASXL2,NHP2L1,FBXO11,KCTD17,PDIA6,NOLC1,GIGYF2,ATHL1,NFU1,ACAN,PWP1,PCYOX1,PSMC2,STRAP,PIK3R5,CDC7,SNRPE,APTX,GK,PSMC6,ZDHHC17,SMC6,TAF1,CISH,ERLIN1,PDCD6IP,ABHD4,CBFB,EIF2B1,DDX46,SEPHS2,PSMD6,CAMKV,SUCLG2,ARMC8,OARD1,MRPS30,LMF2,ASTE1,ANGPT1,FBXO41,PTDSS1,HSPA8,EYA4,CLNS1A,CLP1,ECHDC1,ADM,MDH1,TRMT112,CUL7,ZCCHC8,ARF1,LUC7L2,DDX11,PSMD9,NOL8,ORC4,NUP153,RT14,MAPKAPK5,ENSP00000451235,XRCC3,ETFA,TRPV1,VR1,HIST2H4B,TEFM,MBD1,EMG1,H6PD,BIRC2,RYK,PLP1,PSMC3,C18orf25,PTGES3,PPIP5K2,OXA1L,LIG4,ENSP00000485022
## 39 CRY1,RANBP9,RFC2,HDAC7,DERL2,KIF22,DLD,TGFBR3,MAPK12,SNAPC1,PIGH,CSTF1,USB1,PSMD7,NME4,EIF3E,SLC5A5,PON1,NOD1,C1QBP,NFKB1,CTSC,KITLG,ART4,CNOT2,KRR1,GAPDH,TPI1,CMAS,SRSF9,NEK4,GGCX,ODC1,ORC2,TMEM59,AKR7A2,RIF1,THOC2,NECAB3,EIF3K,DHX40,CUL9,EPO,EIF2S3,NOL11,NDFIP1,FUS,THAP1,PTCD3,UTP3,EIF2S1,ADAMTS8,REV1,NUPL2,RSL24D1,RTCA,GALC,MAN2A1,SNW1,POMT2,EIF3J,RBM25,ATP5B,PIK3C3,WIPI1,PKMYT1,CFAP20,RPL8,CCNE1,METTL16,UFD1L,LIG1,BIRC3,LCN1,LTK,MAP4K3,MCM6,ARID4B,GZMM,THRA,PSMD3,STAT3,UFSP2,DNMT3A,PAPSS1,PCNP,FBXO3,RBM6,PELI2,HDC,HEXA,COPS3,DPEP3,GALNT1,NPC1,PFKL,DNMT3L,RCN3,PSMA5,CERS2,RQCD1,SLC25A38,ALDH1L1,TERF1,CAPN5,FLT1,MED21,UXS1,GTF2E1,AKR1B1,NUP205,SLC26A2,HMGCR,DUSP2,UBE2Q1,PSME3,LUC7L,NEU3,HDAC11,MTMR14,NPM1,NOS3,SPTSSA,NEMF,SNRPD1,PGAP3,SRRM2,POLR2G,FADD,LSM3,TRMT61B,ACHE,PDS5A,ZCCHC4,CBR4,CD2BP2,SOCS5,MRPL39,GPR37,DESI2,MRPL13,GLB1,MCM7,MMP14,HLTF,UBE3C,PSMD1,DPYSL2,POLD4,PPP1R8,LTBP4,SSH3,AOC3,KCTD2,GRHPR,PHKB,KHDRBS1,PER1,CRAT,SWAP70,CCDC101,SFTPC,FKBP10,HINFP,PRKRA,PRMT5,TRIT1,STK11,PPP2R2A,KARS,PSEN1,HCCS,NOS2,CSF1,RLIM,FBXO21,SP1,PDGFB,MORF4L1,NPLOC4,CALCA,IDH2,PURA,TRMT11,SEL1L,ZBTB16,MRPL35,TASP1,CDK10,ZC3H15,DPP8,CIR1,TAF1A,HUWE1,ACACB,JAK1,RPL36AL,RPL22,DDX21,HNRNPA2B1,PGAP1,CGI-74,WARS,MMP23B,UVRAG,UPF2,PIK3R4,PEX2,PTPRS,COPS5,RAD23B,TMCC2,RHOT1,TRIM33,TTC37,EDC4,MARCH5,NAE1,PHF2,AMZ2,DPP4,CPZ,TAF11,SLC26A1,MVB12B,NRG2,NAA35,ILF2,CTR9,APOBEC3C,MTR,TOMM20,TSNAX,IARS2,MPC2,SGK1,UFC1,APOA1BP,DAP3,OAT,AMD1,SEC63,TTF2,BCAS2,SYNCRIP,ATP5F1,TRMT13,CHRNA4,RPL5,GTF2B,HS2ST1,ZNHIT6,BCL10,RPF1,ZNF451,GNAS,ALDH18A1,DPM1,GTF3C4,CTSA,ZMPSTE24,MEAF6,PSMB2,PEF1,RPA2,MED12,POLE3,PINK1,PLA2G5,CRNKL1,STAM,ZBTB48,NOL9,HIST1H4B,TCOF1,TAF2,NMT2,HSPA14,ATP6AP2,PRKD3,PCNA,ACOT9,ASPH,KIN,RPS6KA3,SIN3B,ZNF768,RRAGA,PDE4A,POLR2B,RNF6,RBM47,FBXL18,RAD51,RNMT,VPS9D1,PTPRN2,EXOSC8,ASH1L,RNF34,SRSF2,B3GALT1,GRK5,LIPT1,SRPK2,PPP2R2B,RNF14,MAPK8,ERO1L,POLM,RAE1,GTF2A2,HNF4G,ZNF143,NFE2L2,MPST,PPP3CC,WDR4,USP25,PLA2G2A,ASXL2,NHP2L1,FBXO11,KCTD17,PDIA6,NOLC1,GIGYF2,NFU1,ACAN,PWP1,PCYOX1,PSMC2,STRAP,CDC7,CD44,SNRPE,APTX,PSMC6,ZDHHC17,SMC6,TAF1,CISH,ERLIN1,PDCD6IP,ABHD4,CBFB,EIF2B1,DDX46,SEPHS2,PSMD6,GCH1,CAMKV,SUCLG2,ARMC8,OARD1,MRPS30,LMF2,ASTE1,ANGPT1,FBXO41,PTDSS1,HSPA8,EYA4,CLNS1A,CLP1,TRMT112,CUL7,ZCCHC8,LUC7L2,DDX11,PSMD9,NOL8,ORC4,NUP153,RT14,MAPKAPK5,ENSP00000451235,XRCC3,HIST2H4B,TEFM,MBD1,EMG1,BIRC2,RYK,PSMC3,C18orf25,PTGES3,OXA1L,LIG4,ENSP00000485022
## p_value fdr description
## 34 2.04e-15 2.62e-11 Cellular metabolic process
## 35 5.94e-15 3.56e-11 Metabolic process
## 36 5.53e-15 3.56e-11 Organic substance metabolic process
## 37 9.51e-14 3.06e-10 Cellular process
## 38 5.27e-13 1.35e-09 Primary metabolic process
## 39 9.62e-11 2.06e-07 Nitrogen compound metabolic process
write.csv(enrichment_results_GO, "enrichment_results_GO_module4.csv", row.names = FALSE)