Mesangial RAGE KO Transcriptomic Analysis
Mark Ziemann
2025-02-20
Source: https://github.com/markziemann/mesangial_rageko
Introduction
Looking at doing comparison of control and RAGE KO Mouse mesangial cells RNA-seq and miRNA-seq.
Methods
RAGE KO data sequenced at Baker. 61 nt length.
WT data sequenced at BGI with 91 nt length.
Quality trimming with skewer 0.2.2 to ensure 3’ end base quality > 20.
GENECODE mouse transcriptome v30 was downloaded and indexed.
Kallisto 0.46.0 was used for mapping paired end reads to the transcriptome.
Count data was loaded into R, followed by DE analysis with DESeq2.
Enrichment analysis was performed with mitch, using REACTOME pathways.
OS, R and package versions are shown in the session info section at the end of this report.
suppressPackageStartupMessages({
library("reshape2")
library("DESeq2")
library("gplots")
library("mitch")
library("dplyr")
library("biomaRt")
library("kableExtra")
library("beeswarm")
})Data
tmp <- read.table("3col.tsv.gz",header=F)
x <- as.matrix(acast(tmp, V2~V1, value.var="V3", fun.aggregate = sum))
x <- as.data.frame(x)
txinfo <- data.frame(do.call(rbind,strsplit(rownames(x),"\\|")))
colnames(txinfo) <- c("tx","GeneID","altGeneID","altTxID",
"txname","genename","length","biotype")
x$GeneID <- paste(txinfo$GeneID , txinfo$genename)
# write out transcript table
x2 <- x
x2$GeneID = NULL
xrpm <- apply(x2, 2, function(x){x/sum(x,na.rm=T)}) * 1000000
colnames(xrpm) <- gsub("$","_RPM",colnames(xrpm))
colnames(x2) <- gsub("$","_counts",colnames(x2))
x2 <- cbind(xrpm,x2)
write.table(x2,file="Tx_RPM_count_table_biotype.tsv")
xx <- aggregate(. ~ GeneID, x , sum)
colnames(xx) <- gsub("mRNA_","",colnames(xx))
rownames(xx) <- xx$GeneID
xx$GeneID <- NULL
xx <- round(xx)
dim(xx)## [1] 56691 12head(xx)## rageko_ctrl_1 rageko_ctrl_2 rageko_ctrl_3
## ENSMUSG00000000001.5 Gnai3 2856 2448 2865
## ENSMUSG00000000003.16 Pbsn 0 0 0
## ENSMUSG00000000028.16 Cdc45 124 95 112
## ENSMUSG00000000031.18 H19 1 0 1
## ENSMUSG00000000037.18 Scml2 9 7 12
## ENSMUSG00000000049.12 Apoh 4 2 4
## rageko_TGF_1 rageko_TGF_2 rageko_TGF_3 wt_ctrl_1_R1
## ENSMUSG00000000001.5 Gnai3 2279 2047 2717 727
## ENSMUSG00000000003.16 Pbsn 0 0 0 0
## ENSMUSG00000000028.16 Cdc45 102 89 114 28
## ENSMUSG00000000031.18 H19 0 0 0 1452
## ENSMUSG00000000037.18 Scml2 7 6 9 0
## ENSMUSG00000000049.12 Apoh 0 1 0 4
## wt_ctrl_2_R1 wt_ctrl_3_R1 wt_TGF_1_R1 wt_TGF_2_R1
## ENSMUSG00000000001.5 Gnai3 780 621 1127 1150
## ENSMUSG00000000003.16 Pbsn 0 0 0 0
## ENSMUSG00000000028.16 Cdc45 29 31 49 52
## ENSMUSG00000000031.18 H19 1099 1065 11 6
## ENSMUSG00000000037.18 Scml2 6 1 1 3
## ENSMUSG00000000049.12 Apoh 4 5 0 0
## wt_TGF_3_R1
## ENSMUSG00000000001.5 Gnai3 1136
## ENSMUSG00000000003.16 Pbsn 0
## ENSMUSG00000000028.16 Cdc45 52
## ENSMUSG00000000031.18 H19 6
## ENSMUSG00000000037.18 Scml2 2
## ENSMUSG00000000049.12 Apoh 0write.table(x=xx,file="mRNA_count_matrix.tsv",sep="\t")Now quantify the gene biotypes. Starting with all samples.
txinfo2 <- txinfo
txinfo2$gene <- paste(txinfo2$GeneID , txinfo2$genename)
biotype <- unique(txinfo2[,c("gene","biotype")])
xxbiotype <- merge(xx,biotype,by.x=0,by.y="gene")
xxbiotype$Row.names=NULL
xxbiotype <- aggregate(. ~ biotype,xxbiotype,sum)
rownames(xxbiotype) <- xxbiotype$biotype
xxbiotype$biotype = NULL
# remove biotypes with very few reads
xxbiotype <- xxbiotype[which(rowMeans(xxbiotype)>10),]
# keep top 10 classes for chart
n=10
xxbiotype <- xxbiotype[tail(order(rowMeans(xxbiotype)),n),]
# make percent
xxbiotype2 <- apply(xxbiotype, 2, function(x){x*100/sum(x,na.rm=T)})
# create color palette:
library(RColorBrewer)
pal <- brewer.pal(n, "Paired")
par(mfrow=c(1,2))
par(mar=c(10,5,3,1))
barplot(as.matrix(xxbiotype2),col=pal,las=2)
plot.new()
legend("topleft", legend=rev(rownames(xxbiotype2)),fill=rev(pal),bg="white",cex=1)
#restore default setting
par(mar=c(5.1, 4.1, 4.1, 2.1))Now with just the samples not treated with TGFb.
txinfo2 <- txinfo
txinfo2$gene <- paste(txinfo2$GeneID , txinfo2$genename)
biotype <- unique(txinfo2[,c("gene","biotype")])
xxbiotype <- merge(xx,biotype,by.x=0,by.y="gene")
xxbiotype$Row.names=NULL
xxbiotype <- aggregate(. ~ biotype,xxbiotype,sum)
rownames(xxbiotype) <- xxbiotype$biotype
xxbiotype$biotype = NULL
# remove TGFb samples
xxbiotype <- xxbiotype[,grep("TGF",colnames(xxbiotype),invert=TRUE)]
# remove biotypes with very few reads
xxbiotype <- xxbiotype[which(rowMeans(xxbiotype)>10),]
# keep top 10 classes for chart
n=10
xxbiotype <- xxbiotype[tail(order(rowMeans(xxbiotype)),n),]
# make percent
xxbiotype2 <- apply(xxbiotype, 2, function(x){x*100/sum(x,na.rm=T)})
# create color palette:
library(RColorBrewer)
pal <- brewer.pal(n, "Paired")
par(mfrow=c(1,2))
par(mar=c(10,5,3,1))
barplot(as.matrix(xxbiotype2),col=pal,las=2)
plot.new()
legend("topleft", legend=rev(rownames(xxbiotype2)),fill=rev(pal),bg="white",cex=1)
#restore default setting
par(mar=c(5.1, 4.1, 4.1, 2.1))Samplesheet
#colnames(xx) <- sapply(strsplit(colnames(xx),"_"),"[[",1)
mysamples <- colnames(xx)
ko <- as.numeric(grepl("ko",mysamples))
tgf <- as.numeric(grepl("TGF",mysamples))
ss <- data.frame(mysamples,ko,tgf)
rownames(ss) <- mysamples
ss## mysamples ko tgf
## rageko_ctrl_1 rageko_ctrl_1 1 0
## rageko_ctrl_2 rageko_ctrl_2 1 0
## rageko_ctrl_3 rageko_ctrl_3 1 0
## rageko_TGF_1 rageko_TGF_1 1 1
## rageko_TGF_2 rageko_TGF_2 1 1
## rageko_TGF_3 rageko_TGF_3 1 1
## wt_ctrl_1_R1 wt_ctrl_1_R1 0 0
## wt_ctrl_2_R1 wt_ctrl_2_R1 0 0
## wt_ctrl_3_R1 wt_ctrl_3_R1 0 0
## wt_TGF_1_R1 wt_TGF_1_R1 0 1
## wt_TGF_2_R1 wt_TGF_2_R1 0 1
## wt_TGF_3_R1 wt_TGF_3_R1 0 1QC
TODO: rRNA carryover.
par(mar=c(5,8,3,1))
barplot(colSums(xx),horiz=TRUE,las=1,xlab="num reads",col=ss$cols)
grid()
MDS plot
And correlation heat map.
par(mar=c(5,5,3,3))
mds <- cmdscale(dist(t(xx)))
plot(mds, xlab="Coordinate 1", ylab="Coordinate 2",
type = "p",bty="n", cex=4 )
text(mds, labels=rownames(mds) ,col="black")
heatmap.2(cor(xx),trace="n",main="Pearson correlation heatmap",margin=c(8,8),cexRow=0.7,cexCol=0.7)
Differential expression
Compare wt control to RAGE KO control.
maplot <- function(de,contrast_name) {
de <- de[which(!is.na(de$padj)),]
sig <-subset(de, padj < 0.05 )
up <-rownames(subset(de, padj < 0.05 & log2FoldChange > 0))
dn <-rownames(subset(de, padj < 0.05 & log2FoldChange < 0))
GENESUP <- length(up)
GENESDN <- length(dn)
DET=nrow(de)
SUBHEADER = paste(GENESUP, "up, ", GENESDN, "down", DET, "detected")
ns <-subset(de, padj > 0.05 )
plot(log2(de$baseMean),de$log2FoldChange,
xlab="log2 basemean", ylab="log2 foldchange",
pch=19, cex=0.5, col="dark gray",
main=contrast_name, cex.main=1)
points(log2(sig$baseMean),sig$log2FoldChange,
pch=19, cex=0.5, col="red")
mtext(SUBHEADER,cex = 1)
}
make_volcano <- function(de,name) {
de <- de[which(!is.na(de$padj)),]
de$pvalue[which(de$pvalue==0)] <- 1e-320
sig <- subset(de,padj<0.05)
N_SIG=nrow(sig)
N_UP=nrow(subset(sig,log2FoldChange>0))
N_DN=nrow(subset(sig,log2FoldChange<0))
DET=nrow(de)
HEADER=paste(N_SIG,"@5%FDR,", N_UP, "up", N_DN, "dn", DET, "detected")
plot(de$log2FoldChange,-log10(de$pval),cex=0.5,pch=19,col="darkgray",
main=name, xlab="log2 FC", ylab="-log10 pval")
mtext(HEADER)
grid()
points(sig$log2FoldChange,-log10(sig$pval),cex=0.5,pch=19,col="red")
}ss1 <- subset(ss,tgf==0)
xx1 <- xx[,which(colnames(xx) %in% rownames(ss1) )]
dim(xx1)## [1] 56691 6xx1 <- xx1[which(rowMeans(xx1)>10),]
dim(xx1)## [1] 16920 6dds <- DESeqDataSetFromMatrix(countData = xx1 , colData = ss1 , design = ~ ko )## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() functionres <- DESeq(dds)## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testingz <- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>% kbl(caption = "Top gene expression differences") %>%
kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| ENSMUSG00000001020.9 S100a4 | 4192.9386 | 5.170496 | 0.1377328 | 37.54005 | 0 | 0 |
| ENSMUSG00000020044.14 Timp3 | 10285.4824 | 2.798266 | 0.0714929 | 39.14049 | 0 | 0 |
| ENSMUSG00000020256.15 Aldh1l2 | 3821.4378 | 5.927939 | 0.1206065 | 49.15108 | 0 | 0 |
| ENSMUSG00000022037.16 Clu | 4747.7435 | -7.309490 | 0.1278150 | -57.18804 | 0 | 0 |
| ENSMUSG00000023036.15 Pcdhgc4 | 1683.2516 | -5.431429 | 0.1290685 | -42.08175 | 0 | 0 |
| ENSMUSG00000027204.14 Fbn1 | 4626.3922 | 4.515813 | 0.0992572 | 45.49608 | 0 | 0 |
| ENSMUSG00000029661.17 Col1a2 | 55636.8192 | 11.118047 | 0.1666730 | 66.70573 | 0 | 0 |
| ENSMUSG00000029810.16 Tmem176b | 2962.7398 | -3.721489 | 0.0945140 | -39.37500 | 0 | 0 |
| ENSMUSG00000035202.9 Lars2 | 440443.9343 | 7.995812 | 0.1385554 | 57.70843 | 0 | 0 |
| ENSMUSG00000037071.4 Scd1 | 6218.4972 | 3.718488 | 0.0894171 | 41.58586 | 0 | 0 |
| ENSMUSG00000040152.9 Thbs1 | 13191.7357 | 4.102414 | 0.0771886 | 53.14789 | 0 | 0 |
| ENSMUSG00000069833.14 Ahnak | 36337.4655 | 3.850237 | 0.0825342 | 46.65023 | 0 | 0 |
| ENSMUSG00000089774.3 Slc5a3 | 3102.6441 | 4.271342 | 0.1133767 | 37.67390 | 0 | 0 |
| ENSMUSG00000101249.2 Gm29216 | 134092.2407 | -4.575209 | 0.0892471 | -51.26454 | 0 | 0 |
| ENSMUSG00000119584.1 Rn18s-rs5 | 1624546.6620 | 8.192274 | 0.1498508 | 54.66955 | 0 | 0 |
| ENSMUSG00000006205.14 Htra1 | 2118.8069 | 4.111353 | 0.1106220 | 37.16579 | 0 | 0 |
| ENSMUSG00000002266.18 Zim1 | 4852.0107 | -3.413030 | 0.0930200 | -36.69137 | 0 | 0 |
| ENSMUSG00000006519.12 Cyba | 1888.1110 | -3.138444 | 0.0904406 | -34.70173 | 0 | 0 |
| ENSMUSG00000023904.11 Hcfc1r1 | 3021.9117 | -2.955816 | 0.0856391 | -34.51480 | 0 | 0 |
| ENSMUSG00000031980.11 Agt | 922.7918 | -4.844777 | 0.1423726 | -34.02887 | 0 | 0 |
d1up <- rownames(subset(dge,padj <= 0.05 & log2FoldChange > 0))
d1dn <- rownames(subset(dge,padj <= 0.05 & log2FoldChange < 0))
txinfo$GeneID <- sapply(strsplit(txinfo$GeneID,"\\."),"[[",1)
g <- sapply(strsplit(rownames(dge),"\\."),"[[",1)
dge$biotype <- sapply(g, function(x) {
paste(unique(txinfo[txinfo$GeneID==x,"biotype"]),collapse=",") }
)
write.table(dge,file="mRNA_DE_ctrl_vs_rageko.tsv",quote=FALSE,sep="\t")
maplot(dge,"Cont1: Effect of RAGE KO")
make_volcano(dge,"Cont1: Effect of RAGE KO")
#agerdat <- assay(vsd)[grep("Ager",rownames(assay(vsd))),]
#par(mar=c(5,8,3,1))
#barplot(agerdat,horiz=TRUE,las=1,xlab="Normalised Ager expression",xlim=c(0,10))Make a heatmap of the top 30 genes.
rpm1 <- apply(xx1, 2, function(x){x/sum(x,na.rm=T)}) * 1000000
agerdat <- rpm1[grep("Ager",rownames(rpm1)),]
par(mar=c(5,8,3,1))
barplot(agerdat,horiz=TRUE,las=1,xlab="Normalised Ager expression",xlim=c(0,16))
colfunc <- colorRampPalette(c("blue", "white", "red"))
rpm2 <- rpm1[which(rownames(rpm1) %in% rownames(head(dge,30))),]
heatmap.2(as.matrix(rpm2),margin=c(8, 22),cexRow=0.85,trace="none",
cexCol=0.9,col=colfunc(20),scale="row")
rownames(rpm2) <- sapply(strsplit(rownames(rpm2)," "),"[[",2)
heatmap.2(as.matrix(rpm2),margin=c(8, 22),cexRow=0.85,trace="none",
cexCol=0.9,col=colfunc(20),scale="row")
Pathway analysis
First need ortholog table.
Downloaded separately from the ensembl biomart website because the R package code is timing out.
orth <- read.table("../../ref/mart_export.txt",sep="\t",header=TRUE)
orth <- orth[which(orth$Human.gene.name != ""),]
orth <- orth[,c("Gene.stable.ID","Human.gene.name")]
orth <- unique(orth)
rownames(dge) <- sapply(strsplit(rownames(dge),"\\."),"[[",1)Run mitch.
See the other report called “mrna_analysis_mitch.html” for the detailed analysis.
#download.file("https://reactome.org/download/current/ReactomePathways.gmt.zip", destfile="ReactomePathways.gmt.zip")
#unzip("ReactomePathways.gmt.zip")
# downloaded 19th August 2022
genesets <- gmt_import("ReactomePathways.gmt")
y <- mitch_import(dge, DEtype="deseq2",geneTable=orth)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 16920## Note: no. genes in output = 12290## Note: estimated proportion of input genes in output = 0.726head(y)## x
## A4GALT 0.5563104
## AAAS -9.3505565
## AACS 17.4368054
## AAGAB 0.6211840
## AAK1 10.8699941
## AAMDC -5.4631631res <- mitch_calc(y, genesets, priority="effect",cores=16)## Note: Enrichments with large effect sizes may not be
## statistically significant.if (! file.exists("mrna_analysis_mitch.html")) {
mitch_report(res, "mrna_analysis_mitch.html")
}
head(res$enrichment_result,20) %>%
kbl(row.names=FALSE,caption = "Top pathways") %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA |
|---|---|---|---|---|
| tRNA processing in the mitochondrion | 18 | 0.0000002 | -0.7037158 | 0.0000080 |
| Cholesterol biosynthesis | 26 | 0.0000000 | 0.6836708 | 0.0000001 |
| rRNA processing in the mitochondrion | 21 | 0.0000008 | -0.6220439 | 0.0000246 |
| MET activates PTK2 signaling | 12 | 0.0005856 | 0.5732340 | 0.0078538 |
| Laminin interactions | 18 | 0.0000350 | 0.5634054 | 0.0006941 |
| ALK mutants bind TKIs | 10 | 0.0020817 | 0.5621987 | 0.0207870 |
| Apoptosis induced DNA fragmentation | 10 | 0.0048767 | 0.5141368 | 0.0352983 |
| Membrane binding and targetting of GAG proteins | 14 | 0.0015061 | -0.4899106 | 0.0163521 |
| Synthesis And Processing Of GAG, GAGPOL Polyproteins | 14 | 0.0015061 | -0.4899106 | 0.0163521 |
| Peptide chain elongation | 67 | 0.0000000 | -0.4878764 | 0.0000000 |
| Formation of a pool of free 40S subunits | 79 | 0.0000000 | -0.4854318 | 0.0000000 |
| Syndecan interactions | 19 | 0.0002648 | 0.4834119 | 0.0039379 |
| Eukaryotic Translation Termination | 71 | 0.0000000 | -0.4745138 | 0.0000000 |
| Mitochondrial translation initiation | 88 | 0.0000000 | -0.4723555 | 0.0000000 |
| Viral mRNA Translation | 67 | 0.0000000 | -0.4715602 | 0.0000000 |
| Formation of the ternary complex, and subsequently, the 43S complex | 47 | 0.0000000 | -0.4711264 | 0.0000009 |
| Mitochondrial translation termination | 88 | 0.0000000 | -0.4674085 | 0.0000000 |
| Regulation of cholesterol biosynthesis by SREBP (SREBF) | 54 | 0.0000000 | 0.4628101 | 0.0000002 |
| Telomere C-strand synthesis initiation | 13 | 0.0043234 | -0.4571463 | 0.0330386 |
| Mitochondrial translation elongation | 88 | 0.0000000 | -0.4564732 | 0.0000000 |
write.table(res$enrichment_result,file="mitch_pathways.tsv",sep="\t")MiR-214
We have a list of mir-214 targets.
mir214_targ <- readLines("miR214_targets.txt")
mir214_targ <- list(mir214_targ)
names(mir214_targ) <- "mir214_targ"
res2 <- mitch_calc(y, mir214_targ, priority="effect",cores=16)## Note: Enrichments with large effect sizes may not be
## statistically significant.res2$enrichment_result## set setSize pANOVA s.dist p.adjustANOVA
## 1 mir214_targ 3522 6.87026e-34 0.139368 6.87026e-34if (! file.exists("mrna_analysis_mitch_mir214.html")) {
mitch_report(res2, "mrna_analysis_mitch_mir214.html")
}
par(mfrow=c(2,1))
MIN=min(res2$ranked_profile[,1])
MAX=max(res2$ranked_profile[,1])
beeswarm(res2$detailed_sets$mir214_targ,pch=19,
lty="blank",cex=0.45,horiz=TRUE,ylim=c(MIN,MAX),
main="miR-214 targets",
xlab="position in rank (Ctrl vs RAGE KO)"
)
abline(v=0,lwd=2,lty=2,col="red")
abline(v=MIN,lwd=2,lty=2,col="black")
abline(v=MAX,lwd=2,lty=2,col="black")
grid()
par(mfrow=c(1,1))
It appears that they are upregulated in this contrast.
Reactome analysis of miR-214 targets
Here we are going to try running a 1 sample t-test.
Extract the miR214 targets from the mitch rank.
For each Reactome, get the set that intersects with miR-214 targets.
Run 1-sample t-test to determine enrichment.
Collect and format results.
Present chart and enriched genes for the top 10 pathways
head(res2$ranked_profile)## x
## A4GALT 526
## AAAS -5347
## AACS 6082
## AAGAB 572
## AAK1 5492
## AAMDC -4203MIN=min(as.vector(res2$ranked_profile))
MAX=max(as.vector(res2$ranked_profile))
str(res2$detailed_sets)## List of 1
## $ mir214_targ: Named num [1:3522] 526 6082 572 5492 194 ...
## ..- attr(*, "names")= chr [1:3522] "A4GALT" "AACS" "AAGAB" "AAK1" ...head(res2$detailed_sets[[1]])## A4GALT AACS AAGAB AAK1 AAR2 ABCA1
## 526 6082 572 5492 194 -5926tail(res2$detailed_sets[[1]])## ZSCAN29 ZSWIM4 ZSWIM7 ZWILCH ZYG11B ZZEF1
## -2295 -3450 -1109 2951 4762 5688hist(res2$detailed_sets[[1]],xlab="gene rank")
hist(res2$detailed_sets[[1]],xlab="gene rank",breaks=100)
y <- res2$detailed_sets[[1]]
names(genesets[lapply(genesets,length) >500])## [1] "Adaptive Immune System"
## [2] "Axon guidance"
## [3] "Cell Cycle"
## [4] "Cell Cycle, Mitotic"
## [5] "Cellular responses to stimuli"
## [6] "Cellular responses to stress"
## [7] "Cytokine Signaling in Immune system"
## [8] "Developmental Biology"
## [9] "Disease"
## [10] "GPCR downstream signalling"
## [11] "Gene expression (Transcription)"
## [12] "Generic Transcription Pathway"
## [13] "Hemostasis"
## [14] "Immune System"
## [15] "Infectious disease"
## [16] "Innate Immune System"
## [17] "Membrane Trafficking"
## [18] "Metabolism"
## [19] "Metabolism of RNA"
## [20] "Metabolism of lipids"
## [21] "Metabolism of proteins"
## [22] "Nervous system development"
## [23] "Post-translational protein modification"
## [24] "RNA Polymerase II Transcription"
## [25] "Sensory Perception"
## [26] "Signal Transduction"
## [27] "Signaling by GPCR"
## [28] "Signaling by Receptor Tyrosine Kinases"
## [29] "Signaling by Rho GTPases"
## [30] "Signaling by Rho GTPases, Miro GTPases and RHOBTB3"
## [31] "Transport of small molecules"
## [32] "Vesicle-mediated transport"# 1 sample t-test self contained test
# z = profile
# i = geneset index
# gsl = gene set library
# n = min number fo genes overlap=5
t1 <- function(y,i,gsl,n=5) {
gs <- gsl[[i]]
gsname <- names(gsl)[i]
z <- y[names(y) %in% gs]
len=length(z)
if (len >= n ) {
tres=t.test(z)
pval=tres$p.value
zmean=mean(z)
zmedian=median(z)
zcil=tres$conf.int[1]
zciu=tres$conf.int[2]
res = list(gsname=gsname,"p-value"=pval,"mean"=zmean,"median"=zmedian,
"lower conf interval"=zcil,"upper conf interval"=zciu,numgenes=len)
return(res)
}
}
# test it
t1(y,143,genesets)## $gsname
## [1] "Anti-inflammatory response favouring Leishmania parasite infection"
##
## $`p-value`
## [1] 0.03426701
##
## $mean
## [1] 1790.6
##
## $median
## [1] 2580
##
## $`lower conf interval`
## [1] 147.4795
##
## $`upper conf interval`
## [1] 3433.721
##
## $numgenes
## [1] 20# run it for all
res <- lapply(1:length(genesets), function(i) {
unlist(t1(y,i,gsl=genesets,n=5))
})
# format the results
out <- t(do.call(cbind,res))
rownames(out) <- out[,1]
out <- out[,2:ncol(out)]
out <- as.matrix(out)
out2 <- apply(out,2,as.numeric)
rownames(out2) <- rownames(out)
out <- as.data.frame(out2)
out$padj <- p.adjust(out$`p-value`)
out <- out[order(out$`p-value`),]
out %>% kbl(caption = "All reactome pathways") %>%
kable_paper("hover", full_width = F)| p-value | mean | median | lower conf interval | upper conf interval | numgenes | padj | |
|---|---|---|---|---|---|---|---|
| Signal Transduction | 0.0000000 | 1434.685303 | 2135.50 | 1152.664119 | 1716.706488 | 626 | 0.0000000 |
| Post-translational protein modification | 0.0000000 | 1297.844262 | 2105.50 | 930.780252 | 1664.908272 | 366 | 0.0000000 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 0.0000000 | 1805.338235 | 2904.00 | 1302.860661 | 2307.815810 | 204 | 0.0000000 |
| Signaling by Rho GTPases | 0.0000000 | 1735.719388 | 2777.00 | 1218.915786 | 2252.522990 | 196 | 0.0000004 |
| Metabolism | 0.0000000 | 1062.229935 | 1515.00 | 735.443464 | 1389.016406 | 461 | 0.0000005 |
| Metabolism of proteins | 0.0000000 | 1099.817352 | 1845.25 | 760.997828 | 1438.636875 | 438 | 0.0000005 |
| Disease | 0.0000000 | 1009.993781 | 1254.00 | 659.002109 | 1360.985453 | 402 | 0.0000327 |
| Metabolism of lipids | 0.0000001 | 1496.677249 | 2451.00 | 974.845025 | 2018.509472 | 189 | 0.0000628 |
| Hemostasis | 0.0000002 | 1762.119718 | 3011.50 | 1131.461110 | 2392.778327 | 142 | 0.0001725 |
| Post-translational protein phosphorylation | 0.0000004 | 3920.590909 | 5015.00 | 2787.733904 | 5053.447914 | 22 | 0.0004774 |
| Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | 0.0000005 | 3682.583333 | 4799.50 | 2583.906583 | 4781.260084 | 24 | 0.0005053 |
| RHO GTPase cycle | 0.0000019 | 1605.845588 | 2479.50 | 968.715751 | 2242.975426 | 136 | 0.0020742 |
| Immune System | 0.0000023 | 865.087760 | 1078.00 | 509.851525 | 1220.323995 | 433 | 0.0025878 |
| RHOA GTPase cycle | 0.0000041 | 2580.152174 | 3678.50 | 1589.030997 | 3571.273351 | 46 | 0.0045121 |
| Vesicle-mediated transport | 0.0000061 | 1208.164975 | 1664.00 | 695.537535 | 1720.792414 | 197 | 0.0067981 |
| G alpha (12/13) signalling events | 0.0000100 | 3472.000000 | 4896.00 | 2195.761730 | 4748.238270 | 24 | 0.0110150 |
| Metabolism of steroids | 0.0000103 | 2737.277778 | 3653.00 | 1657.575866 | 3816.979689 | 36 | 0.0113625 |
| Synthesis of PIPs at the early endosome membrane | 0.0000111 | 4014.500000 | 4129.00 | 3154.223503 | 4874.776496 | 8 | 0.0122884 |
| Membrane Trafficking | 0.0000128 | 1169.976804 | 1594.00 | 654.916460 | 1685.037148 | 194 | 0.0140567 |
| Diseases of signal transduction by growth factor receptors and second messengers | 0.0000128 | 1458.411111 | 2599.00 | 821.880549 | 2094.941673 | 135 | 0.0141259 |
| RHO GTPases Activate Formins | 0.0000146 | 2563.868421 | 3614.00 | 1522.656050 | 3605.080792 | 38 | 0.0160397 |
| RHO GTPase Effectors | 0.0000184 | 1769.634146 | 2393.00 | 996.370049 | 2542.898243 | 82 | 0.0202084 |
| Resolution of Sister Chromatid Cohesion | 0.0000340 | 2709.875000 | 3617.00 | 1567.791972 | 3851.958028 | 32 | 0.0373665 |
| Sphingolipid metabolism | 0.0000456 | 2700.769231 | 3448.00 | 1570.705843 | 3830.832618 | 26 | 0.0500145 |
| Signaling by GPCR | 0.0000514 | 1514.030612 | 1830.00 | 805.004165 | 2223.057059 | 98 | 0.0563419 |
| PI Metabolism | 0.0000624 | 2565.793103 | 3047.00 | 1448.308889 | 3683.277318 | 29 | 0.0683471 |
| NRAGE signals death through JNK | 0.0000764 | 3470.578947 | 5098.00 | 2038.068470 | 4903.089425 | 19 | 0.0836336 |
| Glucagon-like Peptide-1 (GLP1) regulates insulin secretion | 0.0001056 | 4044.090909 | 4422.00 | 2583.534035 | 5504.647783 | 11 | 0.1154165 |
| Intra-Golgi and retrograde Golgi-to-ER traffic | 0.0001107 | 1629.816901 | 2218.00 | 836.535703 | 2423.098100 | 71 | 0.1208773 |
| Laminin interactions | 0.0001125 | 5063.666667 | 5165.00 | 3870.372479 | 6256.960855 | 6 | 0.1227584 |
| GPCR downstream signalling | 0.0001469 | 1507.197802 | 2062.00 | 752.026614 | 2262.368991 | 91 | 0.1601696 |
| SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion | 0.0001579 | 5237.600000 | 5484.00 | 4187.078656 | 6288.121345 | 5 | 0.1719302 |
| Regulation of insulin secretion | 0.0001726 | 3064.727273 | 4167.00 | 1665.384634 | 4464.069911 | 22 | 0.1877879 |
| Synthesis of PIPs at the plasma membrane | 0.0001904 | 2681.136364 | 3155.00 | 1445.756071 | 3916.516657 | 22 | 0.2070125 |
| EML4 and NUDC in mitotic spindle formation | 0.0001965 | 2551.966667 | 3606.00 | 1326.852783 | 3777.080550 | 30 | 0.2134122 |
| Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal | 0.0002036 | 2626.310345 | 3677.00 | 1366.046664 | 3886.574026 | 29 | 0.2209414 |
| Amplification of signal from the kinetochores | 0.0002036 | 2626.310345 | 3677.00 | 1366.046664 | 3886.574026 | 29 | 0.2209414 |
| O-linked glycosylation of mucins | 0.0002232 | 3162.000000 | 2995.00 | 1907.086239 | 4416.913761 | 11 | 0.2417653 |
| COPI-dependent Golgi-to-ER retrograde traffic | 0.0002436 | 2888.238095 | 3200.00 | 1535.525176 | 4240.951014 | 21 | 0.2636000 |
| Infectious disease | 0.0002692 | 961.142857 | 1045.00 | 450.129643 | 1472.156072 | 203 | 0.2910324 |
| Regulation of cholesterol biosynthesis by SREBP (SREBF) | 0.0003100 | 3419.441176 | 4676.00 | 1835.741928 | 5003.140425 | 17 | 0.3347908 |
| Extracellular matrix organization | 0.0003317 | 2071.421053 | 3264.00 | 986.452428 | 3156.389677 | 57 | 0.3578716 |
| Integration of energy metabolism | 0.0003588 | 2553.718750 | 4163.00 | 1253.719138 | 3853.718362 | 32 | 0.3868328 |
| CDC42 GTPase cycle | 0.0003686 | 1887.555556 | 2636.00 | 892.673267 | 2882.437844 | 54 | 0.3970165 |
| Cell Cycle, Mitotic | 0.0003853 | 1065.286232 | 1590.00 | 486.575249 | 1643.997214 | 138 | 0.4146279 |
| Asparagine N-linked glycosylation | 0.0003875 | 1394.960227 | 2054.00 | 643.987131 | 2145.933324 | 88 | 0.4165460 |
| Factors involved in megakaryocyte development and platelet production | 0.0004634 | 2120.700000 | 3038.50 | 998.595546 | 3242.804453 | 40 | 0.4977156 |
| Mitotic Prometaphase | 0.0005761 | 1674.963636 | 2626.00 | 757.184950 | 2592.742323 | 55 | 0.6181126 |
| Signaling by TGFB family members | 0.0006011 | 2034.382979 | 3176.00 | 923.113400 | 3145.652557 | 47 | 0.6443555 |
| Metabolism of carbohydrates | 0.0007404 | 1347.753165 | 1849.50 | 583.979620 | 2111.526709 | 79 | 0.7929858 |
| RHOC GTPase cycle | 0.0007451 | 2491.800000 | 3855.00 | 1139.839905 | 3843.760095 | 30 | 0.7972585 |
| Golgi-to-ER retrograde transport | 0.0008275 | 2170.756757 | 2773.00 | 964.316589 | 3377.196924 | 37 | 0.8846426 |
| Inhibition of DNA recombination at telomere | 0.0008383 | -4252.200000 | -4388.00 | -5561.739818 | -2942.660182 | 5 | 0.8953187 |
| Insulin receptor signalling cascade | 0.0008795 | 2975.055556 | 3756.50 | 1415.357057 | 4534.754054 | 18 | 0.9384355 |
| Cell Cycle | 0.0009364 | 930.746951 | 1274.50 | 385.484597 | 1476.009305 | 164 | 0.9982310 |
| Deubiquitination | 0.0009401 | 1559.014925 | 2599.00 | 660.390341 | 2457.639510 | 67 | 1.0000000 |
| Cell surface interactions at the vascular wall | 0.0009728 | 2499.612903 | 3672.00 | 1103.386952 | 3895.838855 | 31 | 1.0000000 |
| PI3K events in ERBB2 signaling | 0.0010483 | -4078.000000 | -4261.00 | -5409.290807 | -2746.709193 | 5 | 1.0000000 |
| Nervous system development | 0.0010695 | 1084.551471 | 1474.50 | 443.112335 | 1725.990606 | 136 | 1.0000000 |
| Glycosphingolipid metabolism | 0.0011206 | 3202.666667 | 2999.00 | 1710.744662 | 4694.588671 | 9 | 1.0000000 |
| IGF1R signaling cascade | 0.0011229 | 2876.722222 | 3756.50 | 1325.124663 | 4428.319781 | 18 | 1.0000000 |
| IRS-related events triggered by IGF1R | 0.0011229 | 2876.722222 | 3756.50 | 1325.124663 | 4428.319781 | 18 | 1.0000000 |
| Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) | 0.0011229 | 2876.722222 | 3756.50 | 1325.124663 | 4428.319781 | 18 | 1.0000000 |
| Signaling by MET | 0.0014582 | 2265.125000 | 3277.50 | 968.652615 | 3561.597385 | 24 | 1.0000000 |
| Activation of gene expression by SREBF (SREBP) | 0.0014928 | 3259.900000 | 4676.00 | 1483.452897 | 5036.347103 | 15 | 1.0000000 |
| Cytokine Signaling in Immune system | 0.0015122 | 867.184659 | 1046.00 | 336.196608 | 1398.172710 | 176 | 1.0000000 |
| Glycosaminoglycan metabolism | 0.0015135 | 1905.081081 | 2894.00 | 779.887071 | 3030.275091 | 37 | 1.0000000 |
| RHOB GTPase cycle | 0.0015821 | 2426.555556 | 3647.00 | 1012.521149 | 3840.589962 | 27 | 1.0000000 |
| SARS-CoV-2 Infection | 0.0017142 | 1318.753731 | 1078.00 | 513.409473 | 2124.097990 | 67 | 1.0000000 |
| Adaptive Immune System | 0.0017617 | 914.944118 | 1381.50 | 346.662577 | 1483.225659 | 170 | 1.0000000 |
| Axon guidance | 0.0017899 | 1050.834586 | 1504.00 | 398.781226 | 1702.887947 | 133 | 1.0000000 |
| SARS-CoV Infections | 0.0019404 | 1130.857955 | 949.00 | 427.647279 | 1834.068630 | 88 | 1.0000000 |
| IRS-mediated signalling | 0.0019507 | 2997.312500 | 3756.50 | 1291.420704 | 4703.204296 | 16 | 1.0000000 |
| Elastic fibre formation | 0.0021026 | 4282.900000 | 5793.00 | 2010.049246 | 6555.750754 | 10 | 1.0000000 |
| ESR-mediated signaling | 0.0022144 | 1699.235294 | 3281.00 | 641.337972 | 2757.132617 | 51 | 1.0000000 |
| HCMV Early Events | 0.0024586 | 2314.423077 | 2640.00 | 898.879626 | 3729.966528 | 26 | 1.0000000 |
| G alpha (s) signalling events | 0.0024749 | 3142.000000 | 4365.00 | 1326.974695 | 4957.025305 | 14 | 1.0000000 |
| Mitotic Spindle Checkpoint | 0.0025715 | 2127.666667 | 3535.00 | 802.568077 | 3452.765256 | 33 | 1.0000000 |
| Transport to the Golgi and subsequent modification | 0.0026428 | 1584.435185 | 2578.00 | 577.241619 | 2591.628751 | 54 | 1.0000000 |
| RAC1 GTPase cycle | 0.0026589 | 1585.457627 | 2448.00 | 574.691967 | 2596.223288 | 59 | 1.0000000 |
| Diseases associated with glycosaminoglycan metabolism | 0.0028371 | 3079.181818 | 4185.00 | 1331.784163 | 4826.579473 | 11 | 1.0000000 |
| RHOG GTPase cycle | 0.0028738 | 2731.217391 | 3936.00 | 1042.091689 | 4420.343094 | 23 | 1.0000000 |
| PPARA activates gene expression | 0.0028853 | 2016.569444 | 3454.00 | 738.965453 | 3294.173436 | 36 | 1.0000000 |
| Regulation of lipid metabolism by PPARalpha | 0.0028853 | 2016.569444 | 3454.00 | 738.965453 | 3294.173436 | 36 | 1.0000000 |
| Signaling by Receptor Tyrosine Kinases | 0.0028974 | 907.311688 | 860.50 | 315.184720 | 1499.438657 | 154 | 1.0000000 |
| Signaling by Nuclear Receptors | 0.0029202 | 1388.268116 | 2322.00 | 491.038514 | 2285.497718 | 69 | 1.0000000 |
| Amino acid transport across the plasma membrane | 0.0029931 | 3411.714286 | 4557.50 | 1386.919132 | 5436.509439 | 14 | 1.0000000 |
| Signaling by ALK fusions and activated point mutants | 0.0034713 | 2868.000000 | 4737.00 | 1075.801070 | 4660.198930 | 19 | 1.0000000 |
| Signaling by ALK in cancer | 0.0034713 | 2868.000000 | 4737.00 | 1075.801070 | 4660.198930 | 19 | 1.0000000 |
| CRMPs in Sema3A signaling | 0.0035887 | 4620.833333 | 5396.50 | 2318.254505 | 6923.412161 | 6 | 1.0000000 |
| Separation of Sister Chromatids | 0.0037029 | 1780.238095 | 2974.00 | 612.351455 | 2948.124736 | 42 | 1.0000000 |
| TGF-beta receptor signaling activates SMADs | 0.0037158 | 2705.318182 | 3595.50 | 981.215698 | 4429.420666 | 22 | 1.0000000 |
| Platelet activation, signaling and aggregation | 0.0039506 | 1471.049180 | 2270.00 | 489.536068 | 2452.562293 | 61 | 1.0000000 |
| FLT3 signaling in disease | 0.0039780 | 3030.916667 | 3859.50 | 1191.618571 | 4870.214762 | 12 | 1.0000000 |
| Mitochondrial translation termination | 0.0041988 | -2484.812500 | -3206.50 | -4055.847102 | -913.777898 | 16 | 1.0000000 |
| M Phase | 0.0044956 | 1084.559783 | 1516.50 | 345.147718 | 1823.971847 | 92 | 1.0000000 |
| Signaling by TGF-beta Receptor Complex | 0.0047184 | 1840.250000 | 3090.00 | 598.442500 | 3082.057500 | 40 | 1.0000000 |
| PI3K Cascade | 0.0049622 | 3069.142857 | 4333.50 | 1105.381436 | 5032.904279 | 14 | 1.0000000 |
| Integrin cell surface interactions | 0.0050004 | 3237.562500 | 4375.50 | 1137.533307 | 5337.591693 | 16 | 1.0000000 |
| Signaling by BMP | 0.0052008 | 3300.166667 | 4030.50 | 1209.470187 | 5390.863147 | 12 | 1.0000000 |
| MET promotes cell motility | 0.0057630 | 3273.100000 | 3854.00 | 1215.422246 | 5330.777754 | 10 | 1.0000000 |
| Signaling by Interleukins | 0.0058345 | 935.350427 | 816.00 | 275.819476 | 1594.881378 | 117 | 1.0000000 |
| Sphingolipid de novo biosynthesis | 0.0061384 | 2435.058824 | 4063.00 | 798.580700 | 4071.536947 | 17 | 1.0000000 |
| NGF-stimulated transcription | 0.0061494 | 2122.916667 | 2806.50 | 740.259976 | 3505.573358 | 12 | 1.0000000 |
| Transport of small molecules | 0.0062449 | 873.187898 | 1054.00 | 251.026915 | 1495.348881 | 157 | 1.0000000 |
| Collagen formation | 0.0062743 | 3073.187500 | 4320.00 | 1010.219696 | 5136.155304 | 16 | 1.0000000 |
| Kinesins | 0.0064523 | 3316.909091 | 3677.00 | 1161.432950 | 5472.385232 | 11 | 1.0000000 |
| Syndecan interactions | 0.0070529 | 4441.625000 | 5508.50 | 1650.096902 | 7233.153098 | 8 | 1.0000000 |
| Chondroitin sulfate/dermatan sulfate metabolism | 0.0071938 | 2590.785714 | 3331.50 | 832.588377 | 4348.983052 | 14 | 1.0000000 |
| Signaling by Insulin receptor | 0.0074543 | 2100.384615 | 3080.00 | 614.806719 | 3585.962512 | 26 | 1.0000000 |
| Signaling by FGFR1 in disease | 0.0077512 | 2180.133333 | 3428.00 | 674.319319 | 3685.947347 | 15 | 1.0000000 |
| NCAM signaling for neurite out-growth | 0.0078415 | 1993.000000 | 2062.00 | 592.972029 | 3393.027971 | 19 | 1.0000000 |
| Downstream signal transduction | 0.0080215 | 2555.000000 | 3016.00 | 800.672123 | 4309.327877 | 13 | 1.0000000 |
| HCMV Infection | 0.0081203 | 1750.424242 | 1849.50 | 487.300951 | 3013.547534 | 33 | 1.0000000 |
| Interleukin-4 and Interleukin-13 signaling | 0.0086093 | 2139.590909 | 2239.50 | 604.059105 | 3675.122713 | 22 | 1.0000000 |
| Mitochondrial translation initiation | 0.0092694 | -2299.466667 | -3120.00 | -3935.177568 | -663.755766 | 15 | 1.0000000 |
| Glucagon signaling in metabolic regulation | 0.0094769 | 3571.333333 | 4365.00 | 1324.952705 | 5817.713961 | 6 | 1.0000000 |
| Gamma carboxylation, hypusine formation and arylsulfatase activation | 0.0096550 | 3602.166667 | 3624.50 | 1325.821461 | 5878.511872 | 6 | 1.0000000 |
| Signaling by WNT | 0.0103266 | 1201.797101 | 2599.00 | 292.739216 | 2110.854987 | 69 | 1.0000000 |
| Mitotic Anaphase | 0.0104314 | 1352.642857 | 2424.00 | 330.533783 | 2374.751931 | 56 | 1.0000000 |
| Mitotic Metaphase and Anaphase | 0.0104314 | 1352.642857 | 2424.00 | 330.533783 | 2374.751931 | 56 | 1.0000000 |
| GPCR ligand binding | 0.0105441 | 1701.640000 | 1598.00 | 435.633469 | 2967.646531 | 25 | 1.0000000 |
| SARS-CoV-2 activates/modulates innate and adaptive immune responses | 0.0107831 | 1518.500000 | 1451.00 | 374.653584 | 2662.346416 | 35 | 1.0000000 |
| Signaling by FLT3 fusion proteins | 0.0108523 | 2923.000000 | 3672.00 | 880.689724 | 4965.310277 | 9 | 1.0000000 |
| O-linked glycosylation | 0.0111656 | 1745.863636 | 2177.50 | 440.890701 | 3050.836571 | 22 | 1.0000000 |
| Death Receptor Signalling | 0.0118437 | 1449.800000 | 1504.00 | 337.084387 | 2562.515612 | 45 | 1.0000000 |
| Intracellular signaling by second messengers | 0.0121230 | 928.235294 | 1120.00 | 207.432788 | 1649.037800 | 102 | 1.0000000 |
| Diseases of glycosylation | 0.0122582 | 1395.833333 | 1887.00 | 324.904008 | 2466.762659 | 33 | 1.0000000 |
| Drug ADME | 0.0122917 | 3104.000000 | 3342.00 | 879.099207 | 5328.900793 | 9 | 1.0000000 |
| Plasma lipoprotein clearance | 0.0125466 | 3785.300000 | 5425.00 | 1030.724416 | 6539.875584 | 10 | 1.0000000 |
| Miro GTPase Cycle | 0.0127107 | 3448.285714 | 4214.00 | 1042.651122 | 5853.920307 | 7 | 1.0000000 |
| Disassembly of the destruction complex and recruitment of AXIN to the membrane | 0.0128945 | 3023.833333 | 4246.50 | 778.033356 | 5269.633311 | 12 | 1.0000000 |
| FGFR1 mutant receptor activation | 0.0131264 | 2413.416667 | 3499.50 | 614.922385 | 4211.910948 | 12 | 1.0000000 |
| Gene expression (Transcription) | 0.0137007 | 504.329755 | 570.00 | 104.022713 | 904.636796 | 326 | 1.0000000 |
| PI3K/AKT Signaling in Cancer | 0.0139715 | 1764.588235 | 3080.00 | 381.670929 | 3147.505542 | 34 | 1.0000000 |
| Class I MHC mediated antigen processing & presentation | 0.0146013 | 1039.752809 | 1738.50 | 210.368566 | 1869.137052 | 89 | 1.0000000 |
| Regulation of actin dynamics for phagocytic cup formation | 0.0146179 | 2092.200000 | 2106.50 | 462.003385 | 3722.396615 | 20 | 1.0000000 |
| Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. | 0.0152564 | -1788.300000 | -2390.50 | -3192.086019 | -384.513981 | 20 | 1.0000000 |
| PIP3 activates AKT signaling | 0.0156702 | 986.873563 | 1372.00 | 191.148846 | 1782.598280 | 87 | 1.0000000 |
| Molecules associated with elastic fibres | 0.0161274 | 3813.000000 | 4738.50 | 951.673516 | 6674.326485 | 8 | 1.0000000 |
| Inositol phosphate metabolism | 0.0167687 | 1744.275000 | 2574.25 | 352.033113 | 3136.516887 | 20 | 1.0000000 |
| Transport of inorganic cations/anions and amino acids/oligopeptides | 0.0167857 | 1789.096774 | 4016.00 | 346.437296 | 3231.756253 | 31 | 1.0000000 |
| Estrogen-dependent gene expression | 0.0173948 | 1915.461538 | 3356.50 | 366.657417 | 3464.265660 | 26 | 1.0000000 |
| Signaling by PDGFR in disease | 0.0175436 | 3074.875000 | 4164.00 | 722.549158 | 5427.200842 | 8 | 1.0000000 |
| Non-integrin membrane-ECM interactions | 0.0176939 | 3499.727273 | 4847.00 | 749.332163 | 6250.122382 | 11 | 1.0000000 |
| Cell Cycle Checkpoints | 0.0177519 | 1181.559322 | 1592.00 | 212.350523 | 2150.768122 | 59 | 1.0000000 |
| Mitochondrial translation | 0.0181638 | -1967.944444 | -2858.00 | -3556.593349 | -379.295540 | 18 | 1.0000000 |
| SUMOylation | 0.0181992 | 1186.898148 | 2126.50 | 210.043563 | 2163.752733 | 54 | 1.0000000 |
| MAPK1/MAPK3 signaling | 0.0183286 | 975.660000 | 1178.00 | 169.788507 | 1781.531493 | 75 | 1.0000000 |
| RAC3 GTPase cycle | 0.0185056 | 1620.103448 | 2415.00 | 293.215869 | 2946.991027 | 29 | 1.0000000 |
| Cytochrome P450 - arranged by substrate type | 0.0186154 | 2469.375000 | 2189.00 | 554.129087 | 4384.620913 | 8 | 1.0000000 |
| Ovarian tumor domain proteases | 0.0186400 | 2765.571429 | 4937.50 | 542.273540 | 4988.869318 | 14 | 1.0000000 |
| Signaling by Hedgehog | 0.0188049 | 1734.607143 | 3164.00 | 310.817580 | 3158.396705 | 28 | 1.0000000 |
| SLC-mediated transmembrane transport | 0.0190803 | 1247.087719 | 1990.00 | 212.131014 | 2282.044425 | 57 | 1.0000000 |
| SLC transporter disorders | 0.0191628 | 1539.979167 | 1609.25 | 275.427653 | 2804.530680 | 24 | 1.0000000 |
| FRS-mediated FGFR1 signaling | 0.0191710 | 2852.777778 | 3672.00 | 603.007879 | 5102.547677 | 9 | 1.0000000 |
| RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known | 0.0191950 | -2086.400000 | -2415.00 | -3777.872766 | -394.927234 | 15 | 1.0000000 |
| SUMO E3 ligases SUMOylate target proteins | 0.0193095 | 1205.528846 | 2126.50 | 203.808432 | 2207.249260 | 52 | 1.0000000 |
| ADORA2B mediated anti-inflammatory cytokines production | 0.0202670 | 2640.545454 | 2877.00 | 505.780191 | 4775.310718 | 11 | 1.0000000 |
| SHC1 events in ERBB2 signaling | 0.0212520 | -2543.000000 | -3431.00 | -4609.133126 | -476.866874 | 10 | 1.0000000 |
| Cell death signalling via NRAGE, NRIF and NADE | 0.0215728 | 1781.689655 | 2448.00 | 282.171116 | 3281.208194 | 29 | 1.0000000 |
| Synthesis of very long-chain fatty acyl-CoAs | 0.0225500 | 3569.500000 | 4368.00 | 751.251756 | 6387.748244 | 6 | 1.0000000 |
| RHOT2 GTPase cycle | 0.0228989 | 3672.166667 | 4425.00 | 760.486999 | 6583.846335 | 6 | 1.0000000 |
| A tetrasaccharide linker sequence is required for GAG synthesis | 0.0231721 | 3301.857143 | 4185.00 | 633.209305 | 5970.504981 | 7 | 1.0000000 |
| Developmental Biology | 0.0232092 | 604.926540 | 705.00 | 83.433873 | 1126.419208 | 211 | 1.0000000 |
| Transmission across Chemical Synapses | 0.0241457 | 991.131147 | 921.00 | 134.136454 | 1848.125841 | 61 | 1.0000000 |
| Pyruvate metabolism and Citric Acid (TCA) cycle | 0.0254878 | 1744.200000 | 1618.50 | 238.270555 | 3250.129445 | 20 | 1.0000000 |
| MAPK family signaling cascades | 0.0260248 | 821.672043 | 801.00 | 100.360938 | 1542.983148 | 93 | 1.0000000 |
| Azathioprine ADME | 0.0260430 | 3075.875000 | 3837.00 | 490.042754 | 5661.707247 | 8 | 1.0000000 |
| Metabolism of vitamins and cofactors | 0.0261194 | 1079.867925 | 1001.00 | 133.548608 | 2026.187241 | 53 | 1.0000000 |
| Activation of NMDA receptors and postsynaptic events | 0.0262583 | 1320.413793 | 1317.00 | 167.731471 | 2473.096115 | 29 | 1.0000000 |
| Synthesis of pyrophosphates in the cytosol | 0.0263867 | 2201.214286 | 2710.50 | 361.101249 | 4041.327322 | 7 | 1.0000000 |
| Leishmania infection | 0.0267763 | 1337.906977 | 2062.00 | 161.598508 | 2514.215445 | 43 | 1.0000000 |
| Endogenous sterols | 0.0268277 | 3483.000000 | 4090.00 | 653.814018 | 6312.185982 | 5 | 1.0000000 |
| Unfolded Protein Response (UPR) | 0.0269238 | 1685.076923 | 2488.50 | 208.792400 | 3161.361447 | 26 | 1.0000000 |
| Transport of bile salts and organic acids, metal ions and amine compounds | 0.0272121 | 2114.470588 | 3329.00 | 270.224860 | 3958.716316 | 17 | 1.0000000 |
| FGFR1 ligand binding and activation | 0.0278442 | 3508.200000 | 3841.00 | 624.499399 | 6391.900601 | 5 | 1.0000000 |
| RHOD GTPase cycle | 0.0279506 | 1765.571429 | 2415.00 | 211.659246 | 3319.483611 | 21 | 1.0000000 |
| Antiviral mechanism by IFN-stimulated genes | 0.0286177 | 1665.187500 | 2004.75 | 190.099194 | 3140.275806 | 24 | 1.0000000 |
| ISG15 antiviral mechanism | 0.0286177 | 1665.187500 | 2004.75 | 190.099194 | 3140.275806 | 24 | 1.0000000 |
| Interactions of Rev with host cellular proteins | 0.0295831 | 2096.269231 | 1849.50 | 245.886981 | 3946.651481 | 13 | 1.0000000 |
| Rev-mediated nuclear export of HIV RNA | 0.0295831 | 2096.269231 | 1849.50 | 245.886981 | 3946.651481 | 13 | 1.0000000 |
| Platelet degranulation | 0.0296544 | 1604.230769 | 2226.50 | 171.751931 | 3036.709607 | 26 | 1.0000000 |
| Class A/1 (Rhodopsin-like receptors) | 0.0299652 | 1851.941176 | 1210.00 | 203.861792 | 3500.020561 | 17 | 1.0000000 |
| Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 | 0.0305325 | 2728.400000 | 2673.00 | 418.093251 | 5038.706749 | 5 | 1.0000000 |
| NS1 Mediated Effects on Host Pathways | 0.0305357 | 1827.968750 | 1609.25 | 196.345618 | 3459.591882 | 16 | 1.0000000 |
| Pre-NOTCH Expression and Processing | 0.0307068 | 2128.157895 | 3348.00 | 221.310584 | 4035.005205 | 19 | 1.0000000 |
| p75 NTR receptor-mediated signalling | 0.0308593 | 1450.857143 | 1761.00 | 141.856311 | 2759.857974 | 35 | 1.0000000 |
| PKA activation in glucagon signalling | 0.0315059 | 3424.000000 | 4422.00 | 494.963185 | 6353.036815 | 5 | 1.0000000 |
| Assembly of collagen fibrils and other multimeric structures | 0.0317457 | 2976.166667 | 4320.00 | 312.074664 | 5640.258670 | 12 | 1.0000000 |
| Downstream signaling of activated FGFR1 | 0.0320520 | 2442.700000 | 3243.00 | 261.598130 | 4623.801870 | 10 | 1.0000000 |
| G1/S-Specific Transcription | 0.0323899 | 2789.600000 | 2673.00 | 381.605855 | 5197.594145 | 5 | 1.0000000 |
| Formation of the Early Elongation Complex | 0.0324127 | -2437.142857 | -2855.00 | -4589.844757 | -284.440958 | 7 | 1.0000000 |
| Formation of the HIV-1 Early Elongation Complex | 0.0324127 | -2437.142857 | -2855.00 | -4589.844757 | -284.440958 | 7 | 1.0000000 |
| Collagen biosynthesis and modifying enzymes | 0.0337822 | 3074.300000 | 4298.00 | 294.076205 | 5854.523795 | 10 | 1.0000000 |
| Anti-inflammatory response favouring Leishmania parasite infection | 0.0342670 | 1790.600000 | 2580.00 | 147.479486 | 3433.720514 | 20 | 1.0000000 |
| Leishmania parasite growth and survival | 0.0342670 | 1790.600000 | 2580.00 | 147.479486 | 3433.720514 | 20 | 1.0000000 |
| SARS-CoV-2-host interactions | 0.0343950 | 1123.055556 | 1078.00 | 86.358429 | 2159.752683 | 45 | 1.0000000 |
| trans-Golgi Network Vesicle Budding | 0.0343983 | 2155.866667 | 1781.00 | 182.653757 | 4129.079577 | 15 | 1.0000000 |
| TCF dependent signaling in response to WNT | 0.0346600 | 1271.795455 | 2648.50 | 96.083841 | 2447.507068 | 44 | 1.0000000 |
| MET activates PTK2 signaling | 0.0348865 | 3572.400000 | 4078.00 | 412.457263 | 6732.342737 | 5 | 1.0000000 |
| Mitochondrial translation elongation | 0.0353292 | -1774.000000 | -2596.00 | -3409.950249 | -138.049751 | 17 | 1.0000000 |
| Oncogenic MAPK signaling | 0.0356315 | 1379.884615 | 1633.50 | 100.380328 | 2659.388902 | 26 | 1.0000000 |
| Signaling by PDGF | 0.0359151 | 1896.875000 | 2588.00 | 142.390635 | 3651.359365 | 16 | 1.0000000 |
| PKMTs methylate histone lysines | 0.0365391 | 1935.071429 | 1693.00 | 141.148742 | 3728.994115 | 14 | 1.0000000 |
| Metabolism of non-coding RNA | 0.0366139 | 1929.884615 | 1849.50 | 141.711699 | 3718.057532 | 13 | 1.0000000 |
| snRNP Assembly | 0.0366139 | 1929.884615 | 1849.50 | 141.711699 | 3718.057532 | 13 | 1.0000000 |
| GPER1 signaling | 0.0366583 | 3112.888889 | 4422.00 | 247.226854 | 5978.550924 | 9 | 1.0000000 |
| MAP3K8 (TPL2)-dependent MAPK1/3 activation | 0.0368290 | 2356.200000 | 2552.00 | 234.189252 | 4478.210748 | 5 | 1.0000000 |
| Pyruvate metabolism | 0.0368530 | 2476.583333 | 3912.00 | 181.043269 | 4772.123398 | 12 | 1.0000000 |
| ECM proteoglycans | 0.0376721 | 3684.714286 | 5657.00 | 291.413992 | 7078.014579 | 7 | 1.0000000 |
| Ub-specific processing proteases | 0.0377231 | 1227.775000 | 2230.00 | 73.286250 | 2382.263750 | 40 | 1.0000000 |
| Extra-nuclear estrogen signaling | 0.0381992 | 1660.040000 | 2062.00 | 98.058436 | 3222.021564 | 25 | 1.0000000 |
| Bile acid and bile salt metabolism | 0.0386526 | 2898.800000 | 2743.00 | 245.526817 | 5552.073183 | 5 | 1.0000000 |
| RAF/MAP kinase cascade | 0.0389910 | 853.801370 | 876.00 | 44.345413 | 1663.257327 | 73 | 1.0000000 |
| ERBB2 Regulates Cell Motility | 0.0391846 | -3346.000000 | -4261.00 | -6422.718617 | -269.281383 | 5 | 1.0000000 |
| Beta-catenin independent WNT signaling | 0.0397316 | 1301.305556 | 2718.00 | 64.641621 | 2537.969490 | 36 | 1.0000000 |
| Sialic acid metabolism | 0.0398029 | 1685.727273 | 1971.00 | 95.675577 | 3275.778968 | 11 | 1.0000000 |
| RNA Pol II CTD phosphorylation and interaction with CE | 0.0399283 | -2279.857143 | -2656.00 | -4414.327092 | -145.387193 | 7 | 1.0000000 |
| RNA Pol II CTD phosphorylation and interaction with CE during HIV infection | 0.0399283 | -2279.857143 | -2656.00 | -4414.327092 | -145.387193 | 7 | 1.0000000 |
| mRNA Capping | 0.0399283 | -2279.857143 | -2656.00 | -4414.327092 | -145.387193 | 7 | 1.0000000 |
| ER to Golgi Anterograde Transport | 0.0407342 | 1235.345238 | 2382.50 | 54.634712 | 2416.055765 | 42 | 1.0000000 |
| Ca2+ pathway | 0.0415379 | 1793.736842 | 3672.00 | 76.711156 | 3510.762529 | 19 | 1.0000000 |
| FCGR3A-mediated phagocytosis | 0.0416485 | 1968.833333 | 2106.50 | 83.586597 | 3854.080070 | 18 | 1.0000000 |
| Leishmania phagocytosis | 0.0416485 | 1968.833333 | 2106.50 | 83.586597 | 3854.080070 | 18 | 1.0000000 |
| Parasite infection | 0.0416485 | 1968.833333 | 2106.50 | 83.586597 | 3854.080070 | 18 | 1.0000000 |
| FRS-mediated FGFR2 signaling | 0.0419422 | 2802.142857 | 3672.00 | 141.381868 | 5462.903846 | 7 | 1.0000000 |
| Respiratory electron transport | 0.0437250 | -1615.294118 | -2041.00 | -3179.227126 | -51.361110 | 17 | 1.0000000 |
| Response to elevated platelet cytosolic Ca2+ | 0.0439521 | 1419.250000 | 1923.50 | 41.336393 | 2797.163607 | 28 | 1.0000000 |
| LDL clearance | 0.0442618 | 3867.428571 | 5324.00 | 137.277444 | 7597.579699 | 7 | 1.0000000 |
| Major pathway of rRNA processing in the nucleolus and cytosol | 0.0445529 | 1546.000000 | 1553.00 | 42.848369 | 3049.151631 | 16 | 1.0000000 |
| IRE1alpha activates chaperones | 0.0454568 | 1948.833333 | 3102.00 | 44.175438 | 3853.491229 | 18 | 1.0000000 |
| Signaling by NOTCH | 0.0454753 | 1064.427273 | 2096.00 | 22.213521 | 2106.641024 | 55 | 1.0000000 |
| Signaling by FGFR1 | 0.0455229 | 1883.200000 | 2814.00 | 43.099106 | 3723.300894 | 15 | 1.0000000 |
| SHC-mediated cascade:FGFR1 | 0.0455246 | 2464.375000 | 3243.00 | 64.760933 | 4863.989067 | 8 | 1.0000000 |
| Signal transduction by L1 | 0.0460348 | 3334.000000 | 5736.00 | 74.808353 | 6593.191647 | 9 | 1.0000000 |
| Transport of Ribonucleoproteins into the Host Nucleus | 0.0461787 | 1822.653846 | 1369.00 | 36.325884 | 3608.981808 | 13 | 1.0000000 |
| Neurotransmitter release cycle | 0.0462045 | 2789.571429 | 3898.00 | 64.862639 | 5514.280218 | 7 | 1.0000000 |
| Signaling by WNT in cancer | 0.0469034 | 2440.692308 | 4556.00 | 39.285998 | 4842.098618 | 13 | 1.0000000 |
| Interleukin-12 family signaling | 0.0472028 | 2389.125000 | 3024.00 | 38.923318 | 4739.326682 | 8 | 1.0000000 |
| Cell recruitment (pro-inflammatory response) | 0.0475173 | -3653.200000 | -4900.00 | -7241.804587 | -64.595413 | 5 | 1.0000000 |
| Purinergic signaling in leishmaniasis infection | 0.0475173 | -3653.200000 | -4900.00 | -7241.804587 | -64.595413 | 5 | 1.0000000 |
| Heparan sulfate/heparin (HS-GAG) metabolism | 0.0476759 | 2028.937500 | 2697.00 | 23.646549 | 4034.228451 | 16 | 1.0000000 |
| Phospholipid metabolism | 0.0481154 | 906.132353 | 2283.50 | 7.731617 | 1804.533089 | 68 | 1.0000000 |
| The NLRP3 inflammasome | 0.0485793 | -3582.400000 | -4546.00 | -7128.734607 | -36.065393 | 5 | 1.0000000 |
| PKA-mediated phosphorylation of CREB | 0.0490114 | 2509.571429 | 2877.00 | 14.998422 | 5004.144435 | 7 | 1.0000000 |
| Aberrant regulation of mitotic G1/S transition in cancer due to RB1 defects | 0.0492479 | 2371.625000 | 2840.50 | 10.290839 | 4732.959161 | 8 | 1.0000000 |
| Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) | 0.0492479 | 2371.625000 | 2840.50 | 10.290839 | 4732.959161 | 8 | 1.0000000 |
| Inflammasomes | 0.0498710 | -2666.428571 | -4393.00 | -5330.785571 | -2.071572 | 7 | 1.0000000 |
| RHO GTPases activate CIT | 0.0499061 | 3013.285714 | 3944.00 | 1.704178 | 6024.867251 | 7 | 1.0000000 |
| HS-GAG degradation | 0.0504946 | 3021.000000 | 2242.00 | -10.494617 | 6052.494617 | 5 | 1.0000000 |
| Neurotransmitter receptors and postsynaptic signal transmission | 0.0507769 | 949.140000 | 955.50 | -3.336868 | 1901.616868 | 50 | 1.0000000 |
| Chromatin modifying enzymes | 0.0517573 | 901.958333 | 1271.00 | -7.097502 | 1811.014168 | 60 | 1.0000000 |
| Chromatin organization | 0.0517573 | 901.958333 | 1271.00 | -7.097502 | 1811.014168 | 60 | 1.0000000 |
| Regulation of MECP2 expression and activity | 0.0522428 | 1565.029412 | 2062.00 | -17.123675 | 3147.182499 | 17 | 1.0000000 |
| Complex I biogenesis | 0.0528488 | -2302.375000 | -2352.00 | -4642.001658 | 37.251658 | 8 | 1.0000000 |
| Clathrin-mediated endocytosis | 0.0544061 | 1193.097561 | 1781.00 | -23.663333 | 2409.858455 | 41 | 1.0000000 |
| Interleukin-3, Interleukin-5 and GM-CSF signaling | 0.0544549 | 2049.071429 | 2857.00 | -45.383330 | 4143.526187 | 14 | 1.0000000 |
| Semaphorin interactions | 0.0544708 | 1487.413793 | 1518.00 | -30.546129 | 3005.373715 | 29 | 1.0000000 |
| Nuclear Pore Complex (NPC) Disassembly | 0.0549846 | 1756.423077 | 1369.00 | -43.974877 | 3556.821030 | 13 | 1.0000000 |
| PI-3K cascade:FGFR1 | 0.0556977 | 2955.142857 | 3841.00 | -98.905968 | 6009.191682 | 7 | 1.0000000 |
| L1CAM interactions | 0.0570608 | 1573.285714 | 1947.50 | -50.669864 | 3197.241293 | 28 | 1.0000000 |
| Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer | 0.0579090 | 1559.318182 | 2852.00 | -57.224243 | 3175.860606 | 22 | 1.0000000 |
| SUMOylation of DNA replication proteins | 0.0581339 | 1637.531250 | 1609.25 | -64.039232 | 3339.101732 | 16 | 1.0000000 |
| Constitutive Signaling by AKT1 E17K in Cancer | 0.0592659 | 2416.181818 | 4154.00 | -114.242008 | 4946.605644 | 11 | 1.0000000 |
| Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) | 0.0594626 | 1869.791667 | 1609.25 | -88.668394 | 3828.251728 | 12 | 1.0000000 |
| Export of Viral Ribonucleoproteins from Nucleus | 0.0594626 | 1869.791667 | 1609.25 | -88.668394 | 3828.251728 | 12 | 1.0000000 |
| NEP/NS2 Interacts with the Cellular Export Machinery | 0.0594626 | 1869.791667 | 1609.25 | -88.668394 | 3828.251728 | 12 | 1.0000000 |
| Nuclear import of Rev protein | 0.0594626 | 1869.791667 | 1609.25 | -88.668394 | 3828.251728 | 12 | 1.0000000 |
| Regulation of Glucokinase by Glucokinase Regulatory Protein | 0.0594626 | 1869.791667 | 1609.25 | -88.668394 | 3828.251728 | 12 | 1.0000000 |
| Myogenesis | 0.0596421 | 1995.384615 | 2518.00 | -94.976107 | 4085.745337 | 13 | 1.0000000 |
| Interleukin-6 family signaling | 0.0602595 | 3509.000000 | 4887.00 | -207.794436 | 7225.794436 | 7 | 1.0000000 |
| Cyclin D associated events in G1 | 0.0609509 | 1634.714286 | 2368.50 | -86.897899 | 3356.326471 | 14 | 1.0000000 |
| G1 Phase | 0.0609509 | 1634.714286 | 2368.50 | -86.897899 | 3356.326471 | 14 | 1.0000000 |
| Pre-NOTCH Processing in Golgi | 0.0617435 | 3732.500000 | 5086.50 | -267.972872 | 7732.972872 | 6 | 1.0000000 |
| Signaling by VEGF | 0.0621270 | 1197.487179 | 233.00 | -63.793244 | 2458.767603 | 39 | 1.0000000 |
| Fatty acyl-CoA biosynthesis | 0.0636720 | 2686.636364 | 4819.00 | -184.579994 | 5557.852721 | 11 | 1.0000000 |
| NR1H2 and NR1H3-mediated signaling | 0.0639722 | 1773.656250 | 2495.00 | -116.790297 | 3664.102797 | 16 | 1.0000000 |
| COPII-mediated vesicle transport | 0.0640128 | 1694.657895 | 3117.00 | -109.571119 | 3498.886908 | 19 | 1.0000000 |
| N-glycan trimming in the ER and Calnexin/Calreticulin cycle | 0.0644426 | 2427.700000 | 3534.50 | -179.483015 | 5034.883015 | 10 | 1.0000000 |
| Cellular responses to stimuli | 0.0646827 | 506.124324 | 428.00 | -31.140026 | 1043.388674 | 185 | 1.0000000 |
| Cellular responses to stress | 0.0646827 | 506.124324 | 428.00 | -31.140026 | 1043.388674 | 185 | 1.0000000 |
| Transcriptional Regulation by MECP2 | 0.0649743 | 1131.326923 | 1003.75 | -75.676477 | 2338.330323 | 26 | 1.0000000 |
| Biological oxidations | 0.0659547 | 1369.636364 | 1389.50 | -98.726053 | 2837.998781 | 22 | 1.0000000 |
| Phospholipase C-mediated cascade: FGFR1 | 0.0664412 | 2715.500000 | 3327.50 | -268.526111 | 5699.526111 | 6 | 1.0000000 |
| Cargo concentration in the ER | 0.0664964 | 2672.875000 | 3358.50 | -238.079960 | 5583.829961 | 8 | 1.0000000 |
| Class B/2 (Secretin family receptors) | 0.0678467 | 2045.428571 | 2904.00 | -205.264703 | 4296.121845 | 7 | 1.0000000 |
| Sensory Perception | 0.0682523 | 1304.060606 | 1178.00 | -103.570272 | 2711.691485 | 33 | 1.0000000 |
| Neurexins and neuroligins | 0.0688181 | 1696.277778 | 3144.00 | -146.019526 | 3538.575082 | 18 | 1.0000000 |
| HDACs deacetylate histones | 0.0688236 | 1658.863636 | 2252.00 | -154.351613 | 3472.078886 | 11 | 1.0000000 |
| Downstream signaling of activated FGFR2 | 0.0688837 | 2295.875000 | 3243.00 | -232.315198 | 4824.065198 | 8 | 1.0000000 |
| Basigin interactions | 0.0694808 | 2894.888889 | 4078.00 | -291.639011 | 6081.416789 | 9 | 1.0000000 |
| Signaling by NTRKs | 0.0700138 | 1002.837209 | 816.00 | -85.698406 | 2091.372825 | 43 | 1.0000000 |
| Negative regulation of the PI3K/AKT network | 0.0707872 | 1117.256410 | 2060.00 | -99.414875 | 2333.927696 | 39 | 1.0000000 |
| Plasma lipoprotein assembly, remodeling, and clearance | 0.0723453 | 2116.000000 | 4539.00 | -217.279427 | 4449.279427 | 16 | 1.0000000 |
| Postmitotic nuclear pore complex (NPC) reformation | 0.0728076 | 2358.500000 | 3531.50 | -268.331107 | 4985.331107 | 10 | 1.0000000 |
| Intra-Golgi traffic | 0.0729316 | 1195.736842 | 355.00 | -123.215363 | 2514.689047 | 19 | 1.0000000 |
| PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases | 0.0738886 | 2803.000000 | 3610.00 | -431.811039 | 6037.811039 | 5 | 1.0000000 |
| Diseases of metabolism | 0.0744794 | 747.508621 | 1102.50 | -76.311381 | 1571.328622 | 58 | 1.0000000 |
| Selenoamino acid metabolism | 0.0749162 | 3129.800000 | 3856.00 | -501.374811 | 6760.974811 | 5 | 1.0000000 |
| RAF-independent MAPK1/3 activation | 0.0762767 | 2717.200000 | 1717.00 | -457.241611 | 5891.641612 | 5 | 1.0000000 |
| Phase I - Functionalization of compounds | 0.0771295 | 1896.818182 | 1635.00 | -248.422662 | 4042.059026 | 11 | 1.0000000 |
| Glycolysis | 0.0775373 | 1354.395833 | 2020.75 | -161.908283 | 2870.699950 | 24 | 1.0000000 |
| Oncogene Induced Senescence | 0.0776007 | 1455.000000 | 2417.00 | -180.560994 | 3090.560994 | 17 | 1.0000000 |
| ATF4 activates genes in response to endoplasmic reticulum stress | 0.0782466 | 1978.666667 | 1679.00 | -324.343186 | 4281.676519 | 6 | 1.0000000 |
| Regulated Necrosis | 0.0788999 | -2059.111111 | -3273.00 | -4417.837533 | 299.615311 | 9 | 1.0000000 |
| Metabolism of fat-soluble vitamins | 0.0804267 | 3385.285714 | 5921.00 | -558.376054 | 7328.947483 | 7 | 1.0000000 |
| Retinoid metabolism and transport | 0.0804267 | 3385.285714 | 5921.00 | -558.376054 | 7328.947483 | 7 | 1.0000000 |
| Striated Muscle Contraction | 0.0806749 | -3093.600000 | -4983.00 | -6787.557865 | 600.357866 | 5 | 1.0000000 |
| Formation of HIV elongation complex in the absence of HIV Tat | 0.0808596 | -1989.100000 | -2755.50 | -4277.827464 | 299.627464 | 10 | 1.0000000 |
| Mitotic G1 phase and G1/S transition | 0.0814787 | 1039.848485 | 2018.00 | -137.618451 | 2217.315421 | 33 | 1.0000000 |
| FRS-mediated FGFR3 signaling | 0.0814851 | 2800.166667 | 3756.50 | -507.199467 | 6107.532801 | 6 | 1.0000000 |
| FRS-mediated FGFR4 signaling | 0.0814851 | 2800.166667 | 3756.50 | -507.199467 | 6107.532801 | 6 | 1.0000000 |
| XBP1(S) activates chaperone genes | 0.0824408 | 1712.000000 | 2773.00 | -246.759280 | 3670.759280 | 17 | 1.0000000 |
| Hedgehog ‘off’ state | 0.0829014 | 1481.000000 | 2797.00 | -213.509622 | 3175.509621 | 19 | 1.0000000 |
| Transcriptional regulation by RUNX3 | 0.0839710 | 1262.500000 | 2343.50 | -181.200957 | 2706.200957 | 28 | 1.0000000 |
| Fcgamma receptor (FCGR) dependent phagocytosis | 0.0844079 | 1302.566667 | 584.50 | -188.290136 | 2793.423470 | 30 | 1.0000000 |
| PKA activation | 0.0844530 | 2584.166667 | 3649.50 | -508.318669 | 5676.652002 | 6 | 1.0000000 |
| RUNX2 regulates bone development | 0.0849272 | 2241.428571 | 2106.00 | -419.568706 | 4902.425849 | 7 | 1.0000000 |
| Tie2 Signaling | 0.0852207 | 2620.285714 | 3672.00 | -494.253043 | 5734.824472 | 7 | 1.0000000 |
| Golgi Associated Vesicle Biogenesis | 0.0854184 | 1937.230769 | 1776.00 | -314.617462 | 4189.079001 | 13 | 1.0000000 |
| DAP12 interactions | 0.0874235 | 2143.000000 | 2382.50 | -408.737924 | 4694.737924 | 8 | 1.0000000 |
| Collagen chain trimerization | 0.0880041 | 3345.285714 | 5101.00 | -676.356253 | 7366.927682 | 7 | 1.0000000 |
| Early SARS-CoV-2 Infection Events | 0.0885625 | 2502.000000 | 2594.00 | -512.622970 | 5516.622970 | 7 | 1.0000000 |
| Signaling by Erythropoietin | 0.0892233 | 1428.615385 | 2021.00 | -254.767789 | 3111.998558 | 13 | 1.0000000 |
| FCGR3A-mediated IL10 synthesis | 0.0904174 | 1715.583333 | 2041.50 | -318.860546 | 3750.027213 | 12 | 1.0000000 |
| tRNA modification in the nucleus and cytosol | 0.0908083 | -1856.714286 | -2939.00 | -4113.936121 | 400.507550 | 7 | 1.0000000 |
| Signaling by BRAF and RAF1 fusions | 0.0913010 | 1276.590909 | 1633.50 | -223.577368 | 2776.759186 | 22 | 1.0000000 |
| Signaling by FLT3 ITD and TKD mutants | 0.0935241 | 2156.750000 | 2494.50 | -471.959283 | 4785.459283 | 8 | 1.0000000 |
| Interconversion of nucleotide di- and triphosphates | 0.0937472 | 2872.500000 | 3899.50 | -702.019072 | 6447.019072 | 6 | 1.0000000 |
| HCMV Late Events | 0.0949134 | 1310.125000 | 871.00 | -250.010749 | 2870.260749 | 20 | 1.0000000 |
| HIV elongation arrest and recovery | 0.0949591 | -2598.285714 | -3158.00 | -5808.484934 | 611.913505 | 7 | 1.0000000 |
| Pausing and recovery of HIV elongation | 0.0949591 | -2598.285714 | -3158.00 | -5808.484934 | 611.913505 | 7 | 1.0000000 |
| Late SARS-CoV-2 Infection Events | 0.0953090 | 1353.666667 | 1045.00 | -269.447053 | 2976.780387 | 15 | 1.0000000 |
| Cell-Cell communication | 0.0971759 | 1572.000000 | 3539.00 | -307.598818 | 3451.598819 | 25 | 1.0000000 |
| Downregulation of TGF-beta receptor signaling | 0.0978794 | 1991.307692 | 3451.00 | -425.927492 | 4408.542877 | 13 | 1.0000000 |
| SHC-mediated cascade:FGFR2 | 0.0991945 | 2275.833333 | 3243.00 | -618.324729 | 5169.991395 | 6 | 1.0000000 |
| Nuclear Receptor transcription pathway | 0.1001998 | 1402.052632 | 3031.00 | -297.697253 | 3101.802516 | 19 | 1.0000000 |
| N-glycan antennae elongation in the medial/trans-Golgi | 0.1015363 | 2382.000000 | 3003.50 | -607.340112 | 5371.340112 | 8 | 1.0000000 |
| Smooth Muscle Contraction | 0.1016087 | 1824.500000 | 3659.50 | -423.543310 | 4072.543310 | 12 | 1.0000000 |
| Interferon Signaling | 0.1021239 | 879.900000 | 1369.00 | -182.302947 | 1942.102948 | 45 | 1.0000000 |
| Signaling by PDGFRA extracellular domain mutants | 0.1025660 | 2534.333333 | 2916.00 | -730.854595 | 5799.521261 | 6 | 1.0000000 |
| Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants | 0.1025660 | 2534.333333 | 2916.00 | -730.854595 | 5799.521261 | 6 | 1.0000000 |
| Mitotic Prophase | 0.1038345 | 1087.711538 | 1100.00 | -239.350814 | 2414.773891 | 26 | 1.0000000 |
| Signaling by ERBB2 KD Mutants | 0.1047383 | -2081.125000 | -3021.00 | -4722.506058 | 560.256058 | 8 | 1.0000000 |
| Signaling by ERBB2 TMD/JMD mutants | 0.1047383 | -2081.125000 | -3021.00 | -4722.506058 | 560.256058 | 8 | 1.0000000 |
| Signaling by ERBB2 in Cancer | 0.1047383 | -2081.125000 | -3021.00 | -4722.506058 | 560.256058 | 8 | 1.0000000 |
| Gene Silencing by RNA | 0.1049152 | 1342.738095 | 1369.00 | -306.292174 | 2991.768365 | 21 | 1.0000000 |
| Innate Immune System | 0.1056983 | 423.016129 | 566.00 | -90.186679 | 936.218937 | 217 | 1.0000000 |
| Fatty acid metabolism | 0.1077020 | 1031.100000 | 1935.50 | -235.603942 | 2297.803942 | 40 | 1.0000000 |
| RNA Polymerase II Transcription | 0.1110591 | 340.344595 | 333.50 | -78.747184 | 759.436373 | 296 | 1.0000000 |
| Cilium Assembly | 0.1117475 | 826.070000 | 975.50 | -198.934884 | 1851.074884 | 50 | 1.0000000 |
| CREB1 phosphorylation through the activation of Adenylate Cyclase | 0.1140830 | 2190.833333 | 2469.50 | -754.517558 | 5136.184225 | 6 | 1.0000000 |
| G-protein beta:gamma signalling | 0.1147776 | 2430.000000 | 4127.00 | -794.919133 | 5654.919133 | 7 | 1.0000000 |
| SUMOylation of DNA methylation proteins | 0.1148728 | -2217.750000 | -3307.50 | -5131.051862 | 695.551862 | 8 | 1.0000000 |
| Circadian Clock | 0.1151542 | 1116.750000 | 2373.00 | -292.314580 | 2525.814580 | 26 | 1.0000000 |
| Neuronal System | 0.1156930 | 612.120879 | 627.00 | -153.461654 | 1377.703412 | 91 | 1.0000000 |
| Glucose metabolism | 0.1162783 | 1084.844828 | 1369.00 | -286.243259 | 2455.932915 | 29 | 1.0000000 |
| Post NMDA receptor activation events | 0.1162957 | 1006.920000 | 627.00 | -268.545911 | 2282.385911 | 25 | 1.0000000 |
| Nuclear Envelope Breakdown | 0.1164266 | 1348.205882 | 1369.00 | -373.744991 | 3070.156756 | 17 | 1.0000000 |
| Interactions of Vpr with host cellular proteins | 0.1171827 | 1503.766667 | 1369.00 | -427.907793 | 3435.441126 | 15 | 1.0000000 |
| Vpr-mediated nuclear import of PICs | 0.1171827 | 1503.766667 | 1369.00 | -427.907793 | 3435.441126 | 15 | 1.0000000 |
| Reproduction | 0.1175567 | 1645.000000 | 2619.00 | -470.453866 | 3760.453866 | 15 | 1.0000000 |
| Notch-HLH transcription pathway | 0.1187579 | 1502.730769 | 3031.00 | -446.041339 | 3451.502878 | 13 | 1.0000000 |
| Cellular response to heat stress | 0.1189531 | 1087.104167 | 1100.00 | -301.426986 | 2475.635319 | 24 | 1.0000000 |
| Downstream signaling of activated FGFR3 | 0.1212746 | 2221.857143 | 3672.00 | -791.787765 | 5235.502051 | 7 | 1.0000000 |
| Downstream signaling of activated FGFR4 | 0.1212746 | 2221.857143 | 3672.00 | -791.787765 | 5235.502051 | 7 | 1.0000000 |
| Formation of HIV-1 elongation complex containing HIV-1 Tat | 0.1217924 | -1956.444444 | -2855.00 | -4563.558673 | 650.669784 | 9 | 1.0000000 |
| HIV Transcription Elongation | 0.1217924 | -1956.444444 | -2855.00 | -4563.558673 | 650.669784 | 9 | 1.0000000 |
| Tat-mediated elongation of the HIV-1 transcript | 0.1217924 | -1956.444444 | -2855.00 | -4563.558673 | 650.669784 | 9 | 1.0000000 |
| Antigen processing: Ubiquitination & Proteasome degradation | 0.1219617 | 679.113924 | 1446.00 | -185.569190 | 1543.797038 | 79 | 1.0000000 |
| Hyaluronan metabolism | 0.1237571 | 2053.571429 | 3123.00 | -754.594665 | 4861.737522 | 7 | 1.0000000 |
| Negative regulation of FGFR1 signaling | 0.1238920 | 1877.181818 | 2814.00 | -612.577860 | 4366.941496 | 11 | 1.0000000 |
| Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors | 0.1260526 | -2476.142857 | -4269.00 | -5887.466057 | 935.180343 | 7 | 1.0000000 |
| Metabolism of water-soluble vitamins and cofactors | 0.1276709 | 763.604651 | 974.00 | -227.993981 | 1755.203283 | 43 | 1.0000000 |
| Transport of Mature Transcript to Cytoplasm | 0.1277316 | 1111.586957 | 1369.00 | -344.850564 | 2568.024477 | 23 | 1.0000000 |
| PI-3K cascade:FGFR2 | 0.1278784 | 2925.200000 | 3841.00 | -1313.950852 | 7164.350852 | 5 | 1.0000000 |
| Signaling by NOTCH1 | 0.1304107 | 1116.833333 | 2096.00 | -353.001379 | 2586.668046 | 27 | 1.0000000 |
| Pre-NOTCH Transcription and Translation | 0.1304661 | 1719.857143 | 2849.00 | -581.805387 | 4021.519673 | 14 | 1.0000000 |
| Signaling by FGFR in disease | 0.1313035 | 1227.210526 | 2160.00 | -403.637218 | 2858.058271 | 19 | 1.0000000 |
| Activation of the pre-replicative complex | 0.1319992 | 1696.750000 | 1599.00 | -656.671094 | 4050.171094 | 8 | 1.0000000 |
| VEGFA-VEGFR2 Pathway | 0.1365706 | 966.513514 | 104.00 | -320.792436 | 2253.819463 | 37 | 1.0000000 |
| rRNA processing in the nucleus and cytosol | 0.1369835 | 1182.823529 | 1167.00 | -418.692548 | 2784.339606 | 17 | 1.0000000 |
| GRB2 events in ERBB2 signaling | 0.1370731 | -2200.142857 | -3227.00 | -5338.319443 | 938.033729 | 7 | 1.0000000 |
| Epigenetic regulation of gene expression | 0.1387604 | 1204.280000 | 1999.00 | -418.810676 | 2827.370676 | 25 | 1.0000000 |
| Downregulation of SMAD2/3:SMAD4 transcriptional activity | 0.1396009 | 1472.235294 | 3031.00 | -535.375082 | 3479.845670 | 17 | 1.0000000 |
| Metabolic disorders of biological oxidation enzymes | 0.1426388 | -1500.285714 | -1993.00 | -3676.796610 | 676.225182 | 7 | 1.0000000 |
| Adrenaline,noradrenaline inhibits insulin secretion | 0.1438475 | 2907.833333 | 4299.50 | -1408.251008 | 7223.917675 | 6 | 1.0000000 |
| Regulation of HSF1-mediated heat shock response | 0.1445119 | 1187.175000 | 1100.00 | -445.547251 | 2819.897251 | 20 | 1.0000000 |
| DNA Damage Recognition in GG-NER | 0.1448613 | 1517.600000 | 1542.50 | -632.878782 | 3668.078782 | 10 | 1.0000000 |
| NCAM1 interactions | 0.1462879 | 1794.111111 | 3495.00 | -777.229773 | 4365.451996 | 9 | 1.0000000 |
| Influenza Infection | 0.1463538 | 1119.717391 | 1257.00 | -422.465651 | 2661.900434 | 23 | 1.0000000 |
| Sensory processing of sound by outer hair cells of the cochlea | 0.1466807 | 2006.272727 | 4575.00 | -834.701076 | 4847.246530 | 11 | 1.0000000 |
| Host Interactions of HIV factors | 0.1469318 | 978.532258 | 1369.00 | -363.617315 | 2320.681831 | 31 | 1.0000000 |
| Constitutive Signaling by Aberrant PI3K in Cancer | 0.1471580 | 1333.045455 | 2458.50 | -508.676797 | 3174.767706 | 22 | 1.0000000 |
| Transport of Mature mRNA Derived from an Intronless Transcript | 0.1479591 | 1315.031250 | 1484.50 | -522.438925 | 3152.501425 | 16 | 1.0000000 |
| Transport of Mature mRNAs Derived from Intronless Transcripts | 0.1479591 | 1315.031250 | 1484.50 | -522.438925 | 3152.501425 | 16 | 1.0000000 |
| Pausing and recovery of Tat-mediated HIV elongation | 0.1481394 | -2650.833333 | -3773.00 | -6637.964004 | 1336.297337 | 6 | 1.0000000 |
| Tat-mediated HIV elongation arrest and recovery | 0.1481394 | -2650.833333 | -3773.00 | -6637.964004 | 1336.297337 | 6 | 1.0000000 |
| DAP12 signaling | 0.1487698 | 2057.142857 | 2021.00 | -982.221081 | 5096.506796 | 7 | 1.0000000 |
| Signaling by FGFR | 0.1495160 | 1188.523809 | 1757.00 | -465.487955 | 2842.535574 | 21 | 1.0000000 |
| Generic Transcription Pathway | 0.1541233 | 317.925094 | 165.00 | -120.064536 | 755.914723 | 267 | 1.0000000 |
| Heme signaling | 0.1541428 | 1294.416667 | 2546.50 | -536.562113 | 3125.395446 | 18 | 1.0000000 |
| Signaling by NTRK1 (TRKA) | 0.1542247 | 789.463415 | 705.00 | -309.202578 | 1888.129407 | 41 | 1.0000000 |
| TNF signaling | 0.1546074 | 1546.636364 | 1451.00 | -691.250909 | 3784.523637 | 11 | 1.0000000 |
| TNFR1-induced NFkappaB signaling pathway | 0.1546074 | 1546.636364 | 1451.00 | -691.250909 | 3784.523637 | 11 | 1.0000000 |
| GPVI-mediated activation cascade | 0.1548220 | 2140.200000 | 3152.50 | -977.133881 | 5257.533881 | 10 | 1.0000000 |
| RHO GTPases activate PAKs | 0.1550599 | 1631.181818 | 3838.00 | -731.909731 | 3994.273367 | 11 | 1.0000000 |
| Post-transcriptional silencing by small RNAs | 0.1553565 | 2479.800000 | 2417.00 | -1458.726828 | 6418.326828 | 5 | 1.0000000 |
| Ion channel transport | 0.1554977 | 973.000000 | 1008.00 | -389.455384 | 2335.455384 | 33 | 1.0000000 |
| Signaling by ERBB2 | 0.1555787 | -1292.294118 | -2815.00 | -3130.466582 | 545.878347 | 17 | 1.0000000 |
| Antigen processing-Cross presentation | 0.1565642 | 1795.071429 | 3032.50 | -783.943776 | 4374.086633 | 14 | 1.0000000 |
| PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | 0.1582563 | 972.484848 | 800.00 | -398.630593 | 2343.600290 | 33 | 1.0000000 |
| Disorders of Developmental Biology | 0.1589983 | 1925.300000 | 3031.00 | -1167.616966 | 5018.216967 | 5 | 1.0000000 |
| Disorders of Nervous System Development | 0.1589983 | 1925.300000 | 3031.00 | -1167.616966 | 5018.216967 | 5 | 1.0000000 |
| Loss of function of MECP2 in Rett syndrome | 0.1589983 | 1925.300000 | 3031.00 | -1167.616966 | 5018.216967 | 5 | 1.0000000 |
| Pervasive developmental disorders | 0.1589983 | 1925.300000 | 3031.00 | -1167.616966 | 5018.216967 | 5 | 1.0000000 |
| Calnexin/calreticulin cycle | 0.1593785 | 2261.875000 | 3534.50 | -1135.119914 | 5658.869914 | 8 | 1.0000000 |
| ER Quality Control Compartment (ERQC) | 0.1593785 | 2261.875000 | 3534.50 | -1135.119914 | 5658.869914 | 8 | 1.0000000 |
| FLT3 Signaling | 0.1610223 | 1340.750000 | 1537.50 | -597.345717 | 3278.845717 | 16 | 1.0000000 |
| Transport of Mature mRNA derived from an Intron-Containing Transcript | 0.1628517 | 1101.125000 | 1100.00 | -486.264790 | 2688.514790 | 20 | 1.0000000 |
| RHOBTB GTPase Cycle | 0.1628995 | 1473.833333 | 2150.50 | -695.201323 | 3642.867989 | 12 | 1.0000000 |
| RHO GTPases Activate NADPH Oxidases | 0.1629714 | -1800.000000 | -2721.00 | -4629.955555 | 1029.955555 | 6 | 1.0000000 |
| Regulation of signaling by CBL | 0.1636954 | 1942.444444 | 3016.00 | -978.513473 | 4863.402362 | 9 | 1.0000000 |
| Insulin processing | 0.1637373 | 2157.833333 | 2321.50 | -1242.271443 | 5557.938110 | 6 | 1.0000000 |
| Sensory processing of sound | 0.1644408 | 1714.076923 | 3578.00 | -808.027997 | 4236.181843 | 13 | 1.0000000 |
| Sensory processing of sound by inner hair cells of the cochlea | 0.1644408 | 1714.076923 | 3578.00 | -808.027997 | 4236.181843 | 13 | 1.0000000 |
| SUMOylation of SUMOylation proteins | 0.1660393 | 1275.107143 | 1100.00 | -602.154193 | 3152.368478 | 14 | 1.0000000 |
| Formation of the beta-catenin:TCF transactivating complex | 0.1668691 | 1616.538462 | 3281.00 | -776.906416 | 4009.983339 | 13 | 1.0000000 |
| Metabolism of steroid hormones | 0.1671458 | 2410.750000 | 3653.00 | -1425.471043 | 6246.971043 | 6 | 1.0000000 |
| EPHB-mediated forward signaling | 0.1684508 | 1356.785714 | -494.00 | -652.988787 | 3366.560215 | 14 | 1.0000000 |
| Sealing of the nuclear envelope (NE) by ESCRT-III | 0.1688026 | -2007.200000 | -1013.00 | -5329.868430 | 1315.468429 | 5 | 1.0000000 |
| VEGFR2 mediated vascular permeability | 0.1705322 | 1618.000000 | 233.00 | -800.045294 | 4036.045294 | 13 | 1.0000000 |
| Prolonged ERK activation events | 0.1707806 | 2267.600000 | 3016.00 | -1508.473194 | 6043.673194 | 5 | 1.0000000 |
| CD28 dependent PI3K/Akt signaling | 0.1709607 | 1890.625000 | 1168.00 | -1039.935035 | 4821.185035 | 8 | 1.0000000 |
| Regulation of RUNX1 Expression and Activity | 0.1713439 | 1943.727273 | 2889.00 | -995.162796 | 4882.617342 | 11 | 1.0000000 |
| Signaling by EGFR | 0.1724242 | 1327.705882 | 2955.00 | -642.841551 | 3298.253316 | 17 | 1.0000000 |
| activated TAK1 mediates p38 MAPK activation | 0.1730200 | -1238.928571 | -1797.50 | -3095.348178 | 617.491035 | 14 | 1.0000000 |
| Nicotinamide salvaging | 0.1739394 | 1840.200000 | 2319.00 | -1253.101451 | 4933.501451 | 5 | 1.0000000 |
| Neutrophil degranulation | 0.1748000 | 531.635000 | 727.00 | -240.181551 | 1303.451551 | 100 | 1.0000000 |
| Beta-catenin phosphorylation cascade | 0.1750506 | 2198.000000 | 3308.00 | -1246.403327 | 5642.403327 | 8 | 1.0000000 |
| Meiosis | 0.1755141 | 1691.166667 | 3088.00 | -879.443692 | 4261.777025 | 12 | 1.0000000 |
| Nicotinate metabolism | 0.1764826 | 1334.555556 | 1251.00 | -741.274203 | 3410.385314 | 9 | 1.0000000 |
| SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription | 0.1776147 | 1521.727273 | 2673.00 | -816.199833 | 3859.654379 | 11 | 1.0000000 |
| Negative regulation of MAPK pathway | 0.1781043 | 966.250000 | 1066.50 | -491.420753 | 2423.920753 | 16 | 1.0000000 |
| Alpha-protein kinase 1 signaling pathway | 0.1795146 | 722.600000 | 656.00 | -512.117822 | 1957.317822 | 5 | 1.0000000 |
| UCH proteinases | 0.1801913 | 1135.047619 | 2599.00 | -569.882890 | 2839.978128 | 21 | 1.0000000 |
| Interleukin-10 signaling | 0.1802800 | 1822.200000 | 2103.00 | -1298.364896 | 4942.764896 | 5 | 1.0000000 |
| N-Glycan antennae elongation | 0.1825162 | 2168.285714 | 2129.00 | -1352.217292 | 5688.788721 | 7 | 1.0000000 |
| Translation of Structural Proteins | 0.1830328 | 1407.222222 | 1251.00 | -818.939828 | 3633.384272 | 9 | 1.0000000 |
| Listeria monocytogenes entry into host cells | 0.1853344 | 1972.857143 | 2955.00 | -1254.417923 | 5200.132208 | 7 | 1.0000000 |
| Interleukin-2 family signaling | 0.1854399 | 1351.333333 | 1235.00 | -799.594213 | 3502.260879 | 9 | 1.0000000 |
| G1/S Transition | 0.1866456 | 881.814815 | 1999.00 | -454.548931 | 2218.178561 | 27 | 1.0000000 |
| RNA Polymerase III Transcription Termination | 0.1886015 | -1817.400000 | -2302.00 | -5005.071388 | 1370.271388 | 5 | 1.0000000 |
| Assembly and cell surface presentation of NMDA receptors | 0.1892094 | 1450.571429 | 1553.00 | -946.692253 | 3847.835111 | 7 | 1.0000000 |
| SHC-mediated cascade:FGFR3 | 0.1893392 | 2168.200000 | 3672.00 | -1642.737608 | 5979.137608 | 5 | 1.0000000 |
| SHC-mediated cascade:FGFR4 | 0.1893392 | 2168.200000 | 3672.00 | -1642.737608 | 5979.137608 | 5 | 1.0000000 |
| Transport of the SLBP Dependant Mature mRNA | 0.1912864 | 1345.884615 | 1369.00 | -771.526808 | 3463.296039 | 13 | 1.0000000 |
| Transport of the SLBP independent Mature mRNA | 0.1912864 | 1345.884615 | 1369.00 | -771.526808 | 3463.296039 | 13 | 1.0000000 |
| G2/M Transition | 0.1931116 | 652.804348 | 936.00 | -342.358883 | 1647.967578 | 46 | 1.0000000 |
| Mitotic G2-G2/M phases | 0.1931116 | 652.804348 | 936.00 | -342.358883 | 1647.967578 | 46 | 1.0000000 |
| SOS-mediated signalling | 0.1943785 | 2339.200000 | 3346.00 | -1831.095726 | 6509.495726 | 5 | 1.0000000 |
| MHC class II antigen presentation | 0.1980973 | 1179.000000 | 1664.00 | -671.361370 | 3029.361369 | 20 | 1.0000000 |
| RUNX3 regulates WNT signaling | 0.2011349 | 2842.600000 | 5328.00 | -2321.133912 | 8006.333912 | 5 | 1.0000000 |
| G beta:gamma signalling through PI3Kgamma | 0.2012402 | 2674.200000 | 4308.00 | -2185.034995 | 7533.434995 | 5 | 1.0000000 |
| RHOF GTPase cycle | 0.2037328 | 1372.636364 | 948.00 | -876.384212 | 3621.656939 | 11 | 1.0000000 |
| Metabolism of nucleotides | 0.2037583 | 916.956522 | 2049.00 | -534.845848 | 2368.758892 | 23 | 1.0000000 |
| Organelle biogenesis and maintenance | 0.2042413 | 499.708861 | 558.00 | -277.343423 | 1276.761144 | 79 | 1.0000000 |
| RORA activates gene expression | 0.2048592 | 2257.750000 | 3939.00 | -1725.147353 | 6240.647353 | 6 | 1.0000000 |
| RHO GTPases activate PKNs | 0.2052222 | 1366.250000 | 2034.00 | -866.974285 | 3599.474285 | 12 | 1.0000000 |
| Polymerase switching on the C-strand of the telomere | 0.2061490 | -1788.714286 | -3105.00 | -4876.695839 | 1299.267268 | 7 | 1.0000000 |
| Mitochondrial protein import | 0.2062468 | -1106.181818 | -764.00 | -2929.582567 | 717.218930 | 11 | 1.0000000 |
| CTNNB1 S33 mutants aren’t phosphorylated | 0.2068381 | 2364.285714 | 4556.00 | -1724.469602 | 6453.041030 | 7 | 1.0000000 |
| CTNNB1 S37 mutants aren’t phosphorylated | 0.2068381 | 2364.285714 | 4556.00 | -1724.469602 | 6453.041030 | 7 | 1.0000000 |
| CTNNB1 S45 mutants aren’t phosphorylated | 0.2068381 | 2364.285714 | 4556.00 | -1724.469602 | 6453.041030 | 7 | 1.0000000 |
| CTNNB1 T41 mutants aren’t phosphorylated | 0.2068381 | 2364.285714 | 4556.00 | -1724.469602 | 6453.041030 | 7 | 1.0000000 |
| Signaling by CTNNB1 phospho-site mutants | 0.2068381 | 2364.285714 | 4556.00 | -1724.469602 | 6453.041030 | 7 | 1.0000000 |
| Signaling by GSK3beta mutants | 0.2068381 | 2364.285714 | 4556.00 | -1724.469602 | 6453.041030 | 7 | 1.0000000 |
| Signaling by high-kinase activity BRAF mutants | 0.2076926 | 1637.454545 | 3570.00 | -1071.023762 | 4345.932853 | 11 | 1.0000000 |
| Protein-protein interactions at synapses | 0.2080737 | 1113.240000 | 2968.00 | -662.730286 | 2889.210286 | 25 | 1.0000000 |
| Budding and maturation of HIV virion | 0.2102149 | -1595.714286 | -611.00 | -4378.911001 | 1187.482429 | 7 | 1.0000000 |
| NOTCH1 Intracellular Domain Regulates Transcription | 0.2119814 | 1124.593750 | 2076.50 | -713.993090 | 2963.180590 | 16 | 1.0000000 |
| Signal attenuation | 0.2156869 | 2460.200000 | 3346.00 | -2188.707442 | 7109.107442 | 5 | 1.0000000 |
| Regulation of NF-kappa B signaling | 0.2159871 | 1891.166667 | 2930.50 | -1542.407608 | 5324.740942 | 6 | 1.0000000 |
| Signaling by FGFR3 | 0.2167965 | 1410.545455 | 1317.00 | -973.486037 | 3794.576946 | 11 | 1.0000000 |
| Signaling by FGFR4 | 0.2167965 | 1410.545455 | 1317.00 | -973.486037 | 3794.576946 | 11 | 1.0000000 |
| RAC2 GTPase cycle | 0.2189784 | 902.642857 | 637.50 | -568.984745 | 2374.270459 | 28 | 1.0000000 |
| Pyroptosis | 0.2193306 | -1409.400000 | -428.00 | -4098.604676 | 1279.804676 | 5 | 1.0000000 |
| Disorders of transmembrane transporters | 0.2214517 | 671.756410 | 1086.00 | -422.214629 | 1765.727449 | 39 | 1.0000000 |
| Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 0.2230999 | 759.115385 | 695.50 | -492.253967 | 2010.484736 | 26 | 1.0000000 |
| Signaling by cytosolic FGFR1 fusion mutants | 0.2255659 | 1328.500000 | 1697.50 | -1035.447492 | 3692.447492 | 8 | 1.0000000 |
| Cargo recognition for clathrin-mediated endocytosis | 0.2267738 | 887.379310 | 1386.00 | -583.413351 | 2358.171972 | 29 | 1.0000000 |
| STAT5 activation downstream of FLT3 ITD mutants | 0.2270188 | 2044.166667 | 2880.50 | -1772.364069 | 5860.697402 | 6 | 1.0000000 |
| Signaling by NTRK3 (TRKC) | 0.2271118 | 1982.666667 | 2494.50 | -1719.905612 | 5685.238945 | 6 | 1.0000000 |
| Late endosomal microautophagy | 0.2283146 | -1547.200000 | -611.00 | -4569.865737 | 1475.465737 | 5 | 1.0000000 |
| TRAF6 mediated NF-kB activation | 0.2292083 | 1305.750000 | 1884.00 | -1038.091563 | 3649.591562 | 8 | 1.0000000 |
| Regulation of TNFR1 signaling | 0.2293261 | 1828.250000 | 2930.50 | -1454.410843 | 5110.910843 | 8 | 1.0000000 |
| Visual phototransduction | 0.2313787 | 1376.071429 | 1043.00 | -991.676237 | 3743.819095 | 14 | 1.0000000 |
| NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | 0.2315457 | 1288.192308 | 2417.00 | -938.982630 | 3515.367245 | 13 | 1.0000000 |
| MAP2K and MAPK activation | 0.2325682 | 1219.571429 | 858.50 | -884.556905 | 3323.699762 | 14 | 1.0000000 |
| Ion transport by P-type ATPases | 0.2327879 | 1223.538462 | 1390.00 | -897.845099 | 3344.922022 | 13 | 1.0000000 |
| Positive epigenetic regulation of rRNA expression | 0.2337744 | 1415.642857 | 3154.50 | -1033.442435 | 3864.728149 | 14 | 1.0000000 |
| G0 and Early G1 | 0.2343993 | 1311.875000 | 1436.00 | -1072.262917 | 3696.012917 | 8 | 1.0000000 |
| COPI-mediated anterograde transport | 0.2344556 | 850.785714 | 1631.50 | -584.625994 | 2286.197422 | 28 | 1.0000000 |
| Negative regulation of FGFR2 signaling | 0.2361131 | 1621.000000 | 2814.00 | -1297.296724 | 4539.296724 | 9 | 1.0000000 |
| tRNA processing in the nucleus | 0.2364579 | 1102.031250 | 1100.00 | -802.621593 | 3006.684093 | 16 | 1.0000000 |
| RHOJ GTPase cycle | 0.2365123 | 957.285714 | 953.00 | -678.966868 | 2593.538297 | 21 | 1.0000000 |
| RHOU GTPase cycle | 0.2372204 | 1308.125000 | 3026.00 | -956.581039 | 3572.831039 | 16 | 1.0000000 |
| Negative regulation of MET activity | 0.2377925 | 1290.000000 | 2377.00 | -1041.518911 | 3621.518911 | 9 | 1.0000000 |
| Metal ion SLC transporters | 0.2402770 | 2500.200000 | 4748.00 | -2537.405396 | 7537.805396 | 5 | 1.0000000 |
| IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation | 0.2406739 | 1369.000000 | 656.00 | -1392.169841 | 4130.169841 | 5 | 1.0000000 |
| CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling | 0.2417465 | 1056.461538 | 1317.00 | -812.758197 | 2925.681274 | 13 | 1.0000000 |
| Hedgehog ‘on’ state | 0.2420367 | 1139.117647 | 2599.00 | -848.585472 | 3126.820766 | 17 | 1.0000000 |
| RET signaling | 0.2424566 | 1148.071429 | 341.00 | -877.301279 | 3173.444136 | 14 | 1.0000000 |
| Triglyceride metabolism | 0.2430131 | 1547.833333 | 1809.00 | -1458.900132 | 4554.566799 | 6 | 1.0000000 |
| Autodegradation of Cdh1 by Cdh1:APC/C | 0.2434666 | -1485.272727 | -2359.00 | -4155.251229 | 1184.705774 | 11 | 1.0000000 |
| RHO GTPases Activate ROCKs | 0.2445596 | 1310.200000 | -36.50 | -1070.356352 | 3690.756352 | 10 | 1.0000000 |
| Influenza Viral RNA Transcription and Replication | 0.2514436 | 997.026316 | 831.00 | -770.693548 | 2764.746179 | 19 | 1.0000000 |
| Transcription of the HIV genome | 0.2533990 | -1162.588235 | -2283.00 | -3242.757967 | 917.581497 | 17 | 1.0000000 |
| EGFR Transactivation by Gastrin | 0.2560725 | -1867.000000 | -3225.00 | -5610.644802 | 1876.644802 | 6 | 1.0000000 |
| RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function | 0.2570444 | 1271.909091 | 1178.00 | -1085.766521 | 3629.584703 | 11 | 1.0000000 |
| Translation | 0.2585929 | -660.621622 | -583.00 | -1827.828766 | 506.585523 | 37 | 1.0000000 |
| Muscle contraction | 0.2592225 | 724.275000 | 362.00 | -555.283144 | 2003.833144 | 40 | 1.0000000 |
| Signaling by FGFR3 in disease | 0.2593585 | 1598.833333 | 2494.50 | -1632.533937 | 4830.200604 | 6 | 1.0000000 |
| TBC/RABGAPs | 0.2629550 | -885.588235 | -1525.00 | -2503.611914 | 732.435443 | 17 | 1.0000000 |
| JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 | 0.2643582 | -920.357143 | -593.50 | -2624.836719 | 784.122434 | 14 | 1.0000000 |
| COPI-independent Golgi-to-ER retrograde traffic | 0.2644310 | 1229.062500 | 1575.00 | -1030.524739 | 3488.649738 | 16 | 1.0000000 |
| Hyaluronan uptake and degradation | 0.2650924 | 1433.333333 | 2682.50 | -1503.577407 | 4370.244074 | 6 | 1.0000000 |
| Activation of the AP-1 family of transcription factors | 0.2681662 | -1107.000000 | -535.00 | -3326.903379 | 1112.903379 | 7 | 1.0000000 |
| TNFR2 non-canonical NF-kB pathway | 0.2686280 | 1136.153846 | 2797.00 | -997.961328 | 3270.269020 | 13 | 1.0000000 |
| TP53 Regulates Transcription of DNA Repair Genes | 0.2696392 | -1224.916667 | -2469.50 | -3544.108432 | 1094.275099 | 12 | 1.0000000 |
| Aberrant regulation of mitotic exit in cancer due to RB1 defects | 0.2700208 | -2109.666667 | -3354.00 | -6483.396282 | 2264.062948 | 6 | 1.0000000 |
| Signalling to RAS | 0.2716597 | -1446.875000 | -2943.00 | -4314.223944 | 1420.473945 | 8 | 1.0000000 |
| rRNA modification in the nucleus and cytosol | 0.2716721 | 1056.000000 | 1243.00 | -984.016373 | 3096.016373 | 10 | 1.0000000 |
| PLC beta mediated events | 0.2720230 | 864.055556 | 262.00 | -741.754027 | 2469.865138 | 18 | 1.0000000 |
| Estrogen-dependent nuclear events downstream of ESR-membrane signaling | 0.2740370 | 1342.166667 | 1910.00 | -1223.806046 | 3908.139379 | 12 | 1.0000000 |
| SARS-CoV-1 Infection | 0.2750772 | 902.666667 | 978.00 | -827.023302 | 2632.356635 | 12 | 1.0000000 |
| RND1 GTPase cycle | 0.2752600 | 1534.916667 | 3583.00 | -1407.474655 | 4477.307988 | 12 | 1.0000000 |
| SUMOylation of intracellular receptors | 0.2759016 | 1172.909091 | 2106.00 | -1094.586362 | 3440.404544 | 11 | 1.0000000 |
| RHOBTB1 GTPase cycle | 0.2803468 | 1470.125000 | 1137.50 | -1501.451206 | 4441.701206 | 8 | 1.0000000 |
| Paradoxical activation of RAF signaling by kinase inactive BRAF | 0.2839798 | 978.812500 | 761.50 | -898.709903 | 2856.334904 | 16 | 1.0000000 |
| Signaling by RAS mutants | 0.2839798 | 978.812500 | 761.50 | -898.709903 | 2856.334904 | 16 | 1.0000000 |
| Signaling by moderate kinase activity BRAF mutants | 0.2839798 | 978.812500 | 761.50 | -898.709903 | 2856.334904 | 16 | 1.0000000 |
| Signaling downstream of RAS mutants | 0.2839798 | 978.812500 | 761.50 | -898.709903 | 2856.334904 | 16 | 1.0000000 |
| HS-GAG biosynthesis | 0.2843634 | 2034.875000 | 3999.50 | -2115.819757 | 6185.569757 | 8 | 1.0000000 |
| DDX58/IFIH1-mediated induction of interferon-alpha/beta | 0.2845809 | 996.687500 | 1884.00 | -917.605037 | 2910.980037 | 16 | 1.0000000 |
| HuR (ELAVL1) binds and stabilizes mRNA | 0.2850992 | -1895.583333 | -3531.50 | -5967.726642 | 2176.559975 | 6 | 1.0000000 |
| Keratan sulfate/keratin metabolism | 0.2860975 | 1183.777778 | 1045.00 | -1204.542947 | 3572.098503 | 9 | 1.0000000 |
| Platelet Aggregation (Plug Formation) | 0.2864824 | 1745.400000 | 4020.00 | -1739.391449 | 5230.191449 | 10 | 1.0000000 |
| Sema3A PAK dependent Axon repulsion | 0.2897501 | 1919.571429 | 3888.00 | -2126.190121 | 5965.332978 | 7 | 1.0000000 |
| Processing of Capped Intron-Containing Pre-mRNA | 0.2909395 | 503.372727 | 1096.00 | -442.895017 | 1449.640472 | 55 | 1.0000000 |
| Signaling by RAF1 mutants | 0.2913129 | 1030.866667 | 1317.00 | -985.318967 | 3047.052300 | 15 | 1.0000000 |
| Recruitment of NuMA to mitotic centrosomes | 0.2962943 | 735.400000 | 957.00 | -686.199671 | 2156.999671 | 25 | 1.0000000 |
| Activation of ATR in response to replication stress | 0.2999840 | 1180.142857 | 1180.00 | -1365.889987 | 3726.175701 | 7 | 1.0000000 |
| EPH-Ephrin signaling | 0.3000914 | 759.866667 | -5.00 | -713.077673 | 2232.811006 | 30 | 1.0000000 |
| Nuclear Events (kinase and transcription factor activation) | 0.3002546 | 654.041667 | 445.50 | -622.645642 | 1930.728975 | 24 | 1.0000000 |
| Regulation of PTEN mRNA translation | 0.3016630 | 1479.875000 | 1530.00 | -1658.564224 | 4618.314224 | 8 | 1.0000000 |
| G alpha (q) signalling events | 0.3019864 | 676.848485 | 943.00 | -637.307591 | 1991.004561 | 33 | 1.0000000 |
| DNA Damage Bypass | 0.3023693 | 1443.857143 | 2395.00 | -1688.036883 | 4575.751168 | 7 | 1.0000000 |
| APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 | 0.3033991 | -1163.000000 | -2316.00 | -3519.582125 | 1193.582125 | 13 | 1.0000000 |
| MET activates RAP1 and RAC1 | 0.3057131 | 1869.600000 | 3016.00 | -2553.910953 | 6293.110953 | 5 | 1.0000000 |
| Nuclear events mediated by NFE2L2 | 0.3082942 | 1063.437500 | 2698.00 | -1085.847982 | 3212.722982 | 16 | 1.0000000 |
| Transcriptional regulation by RUNX2 | 0.3102104 | 760.600000 | 1107.00 | -753.634464 | 2274.834464 | 25 | 1.0000000 |
| Nuclear Envelope (NE) Reassembly | 0.3122704 | 959.444444 | 818.00 | -984.315743 | 2903.204632 | 18 | 1.0000000 |
| Intraflagellar transport | 0.3141844 | 1753.937500 | 3254.50 | -2071.241308 | 5579.116308 | 8 | 1.0000000 |
| SUMOylation of chromatin organization proteins | 0.3158595 | 820.847826 | 831.00 | -837.709964 | 2479.405617 | 23 | 1.0000000 |
| Regulation of PLK1 Activity at G2/M Transition | 0.3170013 | 753.166667 | 975.50 | -770.019545 | 2276.352879 | 24 | 1.0000000 |
| Diseases associated with O-glycosylation of proteins | 0.3195465 | 973.846154 | 1142.00 | -1069.477719 | 3017.170027 | 13 | 1.0000000 |
| Regulation of expression of SLITs and ROBOs | 0.3200883 | -1203.500000 | -2059.50 | -3747.357536 | 1340.357536 | 12 | 1.0000000 |
| Downregulation of ERBB2 signaling | 0.3217597 | -1523.444444 | -3923.00 | -4849.832010 | 1802.943121 | 9 | 1.0000000 |
| NRIF signals cell death from the nucleus | 0.3224973 | -1233.555556 | -1127.00 | -3931.359861 | 1464.248750 | 9 | 1.0000000 |
| Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants | 0.3246559 | 789.595238 | 1122.00 | -841.498006 | 2420.688482 | 21 | 1.0000000 |
| Constitutive Signaling by NOTCH1 PEST Domain Mutants | 0.3246559 | 789.595238 | 1122.00 | -841.498006 | 2420.688482 | 21 | 1.0000000 |
| Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer | 0.3246559 | 789.595238 | 1122.00 | -841.498006 | 2420.688482 | 21 | 1.0000000 |
| Signaling by NOTCH1 PEST Domain Mutants in Cancer | 0.3246559 | 789.595238 | 1122.00 | -841.498006 | 2420.688482 | 21 | 1.0000000 |
| Signaling by NOTCH1 in Cancer | 0.3246559 | 789.595238 | 1122.00 | -841.498006 | 2420.688482 | 21 | 1.0000000 |
| Gastrulation | 0.3278317 | 1597.142857 | 3695.00 | -2072.290563 | 5266.576277 | 7 | 1.0000000 |
| Germ layer formation at gastrulation | 0.3278317 | 1597.142857 | 3695.00 | -2072.290563 | 5266.576277 | 7 | 1.0000000 |
| Centrosome maturation | 0.3312533 | 650.769231 | 936.00 | -701.893508 | 2003.431969 | 26 | 1.0000000 |
| Recruitment of mitotic centrosome proteins and complexes | 0.3312533 | 650.769231 | 936.00 | -701.893508 | 2003.431969 | 26 | 1.0000000 |
| Diseases of carbohydrate metabolism | 0.3327096 | 1173.833333 | 1857.00 | -1640.919613 | 3988.586280 | 6 | 1.0000000 |
| AURKA Activation by TPX2 | 0.3330347 | 807.200000 | 975.50 | -893.643153 | 2508.043153 | 20 | 1.0000000 |
| Loss of Nlp from mitotic centrosomes | 0.3330347 | 807.200000 | 975.50 | -893.643153 | 2508.043153 | 20 | 1.0000000 |
| Loss of proteins required for interphase microtubule organization from the centrosome | 0.3330347 | 807.200000 | 975.50 | -893.643153 | 2508.043153 | 20 | 1.0000000 |
| Negative regulation of FGFR3 signaling | 0.3360031 | 1471.875000 | 2023.50 | -1897.640106 | 4841.390106 | 8 | 1.0000000 |
| Negative regulation of FGFR4 signaling | 0.3360031 | 1471.875000 | 2023.50 | -1897.640106 | 4841.390106 | 8 | 1.0000000 |
| Signaling by ERBB2 ECD mutants | 0.3366677 | -1526.833333 | -2031.50 | -5221.303824 | 2167.637157 | 6 | 1.0000000 |
| Transport of vitamins, nucleosides, and related molecules | 0.3382866 | -1441.375000 | -3166.50 | -4757.816811 | 1875.066811 | 8 | 1.0000000 |
| Amino acids regulate mTORC1 | 0.3406905 | 879.411765 | 1372.00 | -1018.923744 | 2777.747273 | 17 | 1.0000000 |
| Meiotic synapsis | 0.3416915 | 1495.888889 | 3557.00 | -1916.688786 | 4908.466564 | 9 | 1.0000000 |
| Neddylation | 0.3440134 | 433.583333 | 981.00 | -475.919732 | 1343.086398 | 60 | 1.0000000 |
| Regulation of TP53 Activity | 0.3457716 | 469.333333 | 384.00 | -521.077476 | 1459.744143 | 51 | 1.0000000 |
| rRNA processing | 0.3459257 | 789.000000 | 857.00 | -928.150552 | 2506.150552 | 18 | 1.0000000 |
| Signaling by FGFR2 | 0.3477499 | 835.611111 | 1537.00 | -990.060916 | 2661.283138 | 18 | 1.0000000 |
| G alpha (i) signalling events | 0.3481481 | 552.842105 | 307.50 | -625.960019 | 1731.644230 | 38 | 1.0000000 |
| Platelet homeostasis | 0.3491539 | 975.100000 | 2700.00 | -1151.027291 | 3101.227291 | 20 | 1.0000000 |
| Rap1 signalling | 0.3494284 | 1602.571429 | 2698.00 | -2262.169320 | 5467.312177 | 7 | 1.0000000 |
| Metabolism of amino acids and derivatives | 0.3494960 | 485.820000 | 144.50 | -547.726667 | 1519.366667 | 50 | 1.0000000 |
| Formation of RNA Pol II elongation complex | 0.3500819 | -1125.692308 | -2656.00 | -3648.179209 | 1396.794594 | 13 | 1.0000000 |
| RNA Polymerase II Transcription Elongation | 0.3500819 | -1125.692308 | -2656.00 | -3648.179209 | 1396.794594 | 13 | 1.0000000 |
| Interleukin receptor SHC signaling | 0.3511877 | 1656.000000 | 800.00 | -2704.695766 | 6016.695766 | 5 | 1.0000000 |
| Synthesis of Prostaglandins (PG) and Thromboxanes (TX) | 0.3521443 | 2183.400000 | 2743.00 | -3578.936043 | 7945.736043 | 5 | 1.0000000 |
| mRNA 3’-end processing | 0.3529284 | 940.636364 | 1600.00 | -1210.714073 | 3091.986800 | 11 | 1.0000000 |
| RUNX2 regulates osteoblast differentiation | 0.3539933 | 1452.800000 | 1107.00 | -2397.948137 | 5303.548137 | 5 | 1.0000000 |
| Diseases associated with N-glycosylation of proteins | 0.3547791 | 1133.750000 | 1020.50 | -1725.201721 | 3992.701721 | 6 | 1.0000000 |
| mTORC1-mediated signalling | 0.3562355 | 1003.714286 | -105.00 | -1454.035737 | 3461.464309 | 7 | 1.0000000 |
| Regulation of TP53 Degradation | 0.3575283 | 967.846154 | 384.00 | -1236.027115 | 3171.719423 | 13 | 1.0000000 |
| Regulation of TP53 Expression and Degradation | 0.3575283 | 967.846154 | 384.00 | -1236.027115 | 3171.719423 | 13 | 1.0000000 |
| Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation | 0.3577221 | 1436.200000 | 1945.00 | -2403.803292 | 5276.203292 | 5 | 1.0000000 |
| Interleukin-12 signaling | 0.3577221 | 1436.200000 | 1945.00 | -2403.803292 | 5276.203292 | 5 | 1.0000000 |
| RNA Polymerase I Promoter Escape | 0.3579743 | -1185.125000 | -1851.00 | -4033.561117 | 1663.311117 | 8 | 1.0000000 |
| RNA Polymerase I Transcription Termination | 0.3579743 | -1185.125000 | -1851.00 | -4033.561117 | 1663.311117 | 8 | 1.0000000 |
| Mitochondrial Fatty Acid Beta-Oxidation | 0.3603103 | -1295.285714 | 233.00 | -4496.085981 | 1905.514552 | 7 | 1.0000000 |
| Repression of WNT target genes | 0.3618610 | -1343.333333 | -1685.00 | -4785.837145 | 2099.170478 | 6 | 1.0000000 |
| Effects of PIP2 hydrolysis | 0.3637986 | 1253.666667 | 3497.00 | -1748.697731 | 4256.031064 | 9 | 1.0000000 |
| Amyloid fiber formation | 0.3662216 | 1004.166667 | 1391.50 | -1341.057484 | 3349.390817 | 12 | 1.0000000 |
| Cellular Senescence | 0.3673350 | -441.909091 | -660.00 | -1416.466881 | 532.648699 | 55 | 1.0000000 |
| RUNX3 regulates NOTCH signaling | 0.3683930 | 1666.166667 | 3314.50 | -2667.603896 | 5999.937229 | 6 | 1.0000000 |
| G-protein mediated events | 0.3703305 | 696.904762 | 206.00 | -889.278279 | 2283.087803 | 21 | 1.0000000 |
| Cell junction organization | 0.3728869 | 1052.277778 | 2082.00 | -1373.546627 | 3478.102183 | 18 | 1.0000000 |
| Stimuli-sensing channels | 0.3744331 | 1040.692308 | 1008.00 | -1417.217343 | 3498.601958 | 13 | 1.0000000 |
| Vasopressin regulates renal water homeostasis via Aquaporins | 0.3750355 | 1449.875000 | 3592.50 | -2169.291074 | 5069.041074 | 8 | 1.0000000 |
| NF-kB is activated and signals survival | 0.3760254 | -1067.666667 | -1551.00 | -3893.394981 | 1758.061647 | 6 | 1.0000000 |
| APC/C:Cdc20 mediated degradation of Securin | 0.3768861 | -1194.600000 | -1840.50 | -4101.934172 | 1712.734172 | 10 | 1.0000000 |
| InlB-mediated entry of Listeria monocytogenes into host cell | 0.3781426 | 1291.666667 | 1167.50 | -2143.435204 | 4726.768537 | 6 | 1.0000000 |
| RHOV GTPase cycle | 0.3830190 | 1018.071429 | 869.50 | -1417.945292 | 3454.088149 | 14 | 1.0000000 |
| PTEN Regulation | 0.3832259 | 496.139535 | 715.00 | -640.098260 | 1632.377330 | 43 | 1.0000000 |
| Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase | 0.3832750 | -1669.166667 | -2857.00 | -6160.432804 | 2822.099471 | 6 | 1.0000000 |
| APC truncation mutants have impaired AXIN binding | 0.3851557 | 1748.333333 | 3308.00 | -2976.166273 | 6472.832940 | 6 | 1.0000000 |
| AXIN missense mutants destabilize the destruction complex | 0.3851557 | 1748.333333 | 3308.00 | -2976.166273 | 6472.832940 | 6 | 1.0000000 |
| Signaling by AMER1 mutants | 0.3851557 | 1748.333333 | 3308.00 | -2976.166273 | 6472.832940 | 6 | 1.0000000 |
| Signaling by APC mutants | 0.3851557 | 1748.333333 | 3308.00 | -2976.166273 | 6472.832940 | 6 | 1.0000000 |
| Signaling by AXIN mutants | 0.3851557 | 1748.333333 | 3308.00 | -2976.166273 | 6472.832940 | 6 | 1.0000000 |
| Truncations of AMER1 destabilize the destruction complex | 0.3851557 | 1748.333333 | 3308.00 | -2976.166273 | 6472.832940 | 6 | 1.0000000 |
| SUMOylation of ubiquitinylation proteins | 0.3865850 | 826.633333 | 831.00 | -1157.187206 | 2810.453873 | 15 | 1.0000000 |
| HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand | 0.3885661 | 1020.916667 | 1519.00 | -1482.141982 | 3523.975315 | 12 | 1.0000000 |
| Regulation of TP53 Activity through Phosphorylation | 0.3973596 | 594.038462 | 406.00 | -826.732708 | 2014.809631 | 26 | 1.0000000 |
| TRAF6-mediated induction of TAK1 complex within TLR4 complex | 0.3974090 | 877.833333 | 468.00 | -1561.641914 | 3317.308581 | 6 | 1.0000000 |
| Synthesis of substrates in N-glycan biosythesis | 0.3979347 | 587.476191 | 346.00 | -831.187977 | 2006.140358 | 21 | 1.0000000 |
| Regulation of KIT signaling | 0.3980865 | -1374.833333 | -2669.00 | -5201.384359 | 2451.717692 | 6 | 1.0000000 |
| p38MAPK events | 0.4000529 | -1251.428571 | -3071.00 | -4632.780014 | 2129.922871 | 7 | 1.0000000 |
| APC-Cdc20 mediated degradation of Nek2A | 0.4011897 | -1920.800000 | -3654.00 | -7604.159354 | 3762.559353 | 5 | 1.0000000 |
| Inactivation of APC/C via direct inhibition of the APC/C complex | 0.4011897 | -1920.800000 | -3654.00 | -7604.159354 | 3762.559353 | 5 | 1.0000000 |
| Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components | 0.4011897 | -1920.800000 | -3654.00 | -7604.159354 | 3762.559353 | 5 | 1.0000000 |
| SHC-related events triggered by IGF1R | 0.4027751 | 1199.600000 | 1317.00 | -2363.012238 | 4762.212238 | 5 | 1.0000000 |
| BMAL1:CLOCK,NPAS2 activates circadian gene expression | 0.4030327 | 1477.642857 | 3281.00 | -2541.916835 | 5497.202549 | 7 | 1.0000000 |
| Erythropoietin activates Phosphoinositide-3-kinase (PI3K) | 0.4034974 | 1548.800000 | 2361.00 | -3058.650831 | 6156.250831 | 5 | 1.0000000 |
| Defective Intrinsic Pathway for Apoptosis | 0.4036263 | -1144.714286 | -762.00 | -4262.807859 | 1973.379288 | 7 | 1.0000000 |
| Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models | 0.4036263 | -1144.714286 | -762.00 | -4262.807859 | 1973.379288 | 7 | 1.0000000 |
| Neurodegenerative Diseases | 0.4036263 | -1144.714286 | -762.00 | -4262.807859 | 1973.379288 | 7 | 1.0000000 |
| Negative epigenetic regulation of rRNA expression | 0.4036991 | -850.076923 | -1046.00 | -2989.889778 | 1289.735932 | 13 | 1.0000000 |
| RHOQ GTPase cycle | 0.4042544 | 609.120000 | 709.00 | -871.584509 | 2089.824509 | 25 | 1.0000000 |
| Erythropoietin activates RAS | 0.4078376 | 1120.000000 | 3016.00 | -1959.996612 | 4199.996612 | 7 | 1.0000000 |
| Activated NOTCH1 Transmits Signal to the Nucleus | 0.4081619 | 1105.545455 | 2096.00 | -1747.572213 | 3958.663122 | 11 | 1.0000000 |
| Integrin signaling | 0.4128075 | 1462.555556 | 3749.00 | -2441.557196 | 5366.668307 | 9 | 1.0000000 |
| Signaling by NTRK2 (TRKB) | 0.4129463 | 1174.833333 | 740.00 | -2208.406900 | 4558.073567 | 6 | 1.0000000 |
| Presynaptic depolarization and calcium channel opening | 0.4149007 | 1255.800000 | -5.00 | -2581.116086 | 5092.716086 | 5 | 1.0000000 |
| Signaling by SCF-KIT | 0.4153105 | 779.533333 | 1235.00 | -1212.116862 | 2771.183528 | 15 | 1.0000000 |
| Ras activation upon Ca2+ influx through NMDA receptor | 0.4167584 | 657.500000 | 450.00 | -1144.199099 | 2459.199099 | 8 | 1.0000000 |
| DAG and IP3 signaling | 0.4197898 | 680.250000 | -429.50 | -1067.550016 | 2428.050016 | 16 | 1.0000000 |
| Oxidative Stress Induced Senescence | 0.4202475 | -478.588235 | -853.50 | -1671.572525 | 714.396054 | 34 | 1.0000000 |
| TICAM1, RIP1-mediated IKK complex recruitment | 0.4211733 | -1634.666667 | -2993.50 | -6432.175975 | 3162.842642 | 6 | 1.0000000 |
| Peroxisomal lipid metabolism | 0.4240123 | 1210.666667 | 1732.50 | -2365.833931 | 4787.167264 | 6 | 1.0000000 |
| Protein ubiquitination | 0.4243432 | 858.722222 | 2330.00 | -1354.509830 | 3071.954274 | 18 | 1.0000000 |
| p75NTR signals via NF-kB | 0.4253587 | -821.714286 | -652.00 | -3173.309922 | 1529.881350 | 7 | 1.0000000 |
| Adherens junctions interactions | 0.4274269 | 2095.800000 | 5117.00 | -4499.010019 | 8690.610019 | 5 | 1.0000000 |
| GRB2 events in EGFR signaling | 0.4311335 | -1513.400000 | -2815.00 | -6317.409129 | 3290.609129 | 5 | 1.0000000 |
| SHC1 events in EGFR signaling | 0.4311335 | -1513.400000 | -2815.00 | -6317.409129 | 3290.609129 | 5 | 1.0000000 |
| RIP-mediated NFkB activation via ZBP1 | 0.4312207 | 1342.200000 | 2288.00 | -2919.242975 | 5603.642975 | 5 | 1.0000000 |
| ZBP1(DAI) mediated induction of type I IFNs | 0.4312207 | 1342.200000 | 2288.00 | -2919.242975 | 5603.642975 | 5 | 1.0000000 |
| Signaling by Non-Receptor Tyrosine Kinases | 0.4323532 | 799.000000 | 384.00 | -1303.861314 | 2901.861314 | 17 | 1.0000000 |
| Signaling by PTK6 | 0.4323532 | 799.000000 | 384.00 | -1303.861314 | 2901.861314 | 17 | 1.0000000 |
| Regulation of APC/C activators between G1/S and early anaphase | 0.4323584 | -816.733333 | -1322.00 | -2983.509078 | 1350.042411 | 15 | 1.0000000 |
| FOXO-mediated transcription of cell cycle genes | 0.4359171 | 995.700000 | 2750.00 | -1766.830031 | 3758.230031 | 10 | 1.0000000 |
| Negative regulation of NMDA receptor-mediated neuronal transmission | 0.4368253 | 640.250000 | 252.00 | -1195.871963 | 2476.371963 | 8 | 1.0000000 |
| SUMOylation of DNA damage response and repair proteins | 0.4382385 | 510.790323 | 831.00 | -817.006441 | 1838.587086 | 31 | 1.0000000 |
| PCP/CE pathway | 0.4393352 | 687.789474 | 2599.00 | -1139.376994 | 2514.955942 | 19 | 1.0000000 |
| Transcriptional regulation by RUNX1 | 0.4394361 | 453.577778 | 145.00 | -718.041698 | 1625.197254 | 45 | 1.0000000 |
| Phase II - Conjugation of compounds | 0.4427713 | 842.454545 | 1144.00 | -1506.425610 | 3191.334700 | 11 | 1.0000000 |
| B-WICH complex positively regulates rRNA expression | 0.4430501 | 1138.000000 | 4057.00 | -2036.902208 | 4312.902208 | 11 | 1.0000000 |
| TP53 Regulates Transcription of Genes Involved in Cytochrome C Release | 0.4448090 | 1496.000000 | 2745.00 | -3409.155397 | 6401.155397 | 5 | 1.0000000 |
| Telomere C-strand synthesis initiation | 0.4454732 | -1521.800000 | -3119.00 | -6519.438625 | 3475.838625 | 5 | 1.0000000 |
| HIV Transcription Initiation | 0.4461602 | -976.500000 | -2267.00 | -3696.692433 | 1743.692433 | 12 | 1.0000000 |
| RNA Polymerase II HIV Promoter Escape | 0.4461602 | -976.500000 | -2267.00 | -3696.692433 | 1743.692433 | 12 | 1.0000000 |
| RNA Polymerase II Promoter Escape | 0.4461602 | -976.500000 | -2267.00 | -3696.692433 | 1743.692433 | 12 | 1.0000000 |
| RNA Polymerase II Transcription Initiation | 0.4461602 | -976.500000 | -2267.00 | -3696.692433 | 1743.692433 | 12 | 1.0000000 |
| RNA Polymerase II Transcription Initiation And Promoter Clearance | 0.4461602 | -976.500000 | -2267.00 | -3696.692433 | 1743.692433 | 12 | 1.0000000 |
| RNA Polymerase II Transcription Pre-Initiation And Promoter Opening | 0.4461602 | -976.500000 | -2267.00 | -3696.692433 | 1743.692433 | 12 | 1.0000000 |
| CDK-mediated phosphorylation and removal of Cdc6 | 0.4461920 | -876.461538 | -1322.00 | -3301.006828 | 1548.083751 | 13 | 1.0000000 |
| Signaling by ERBB4 | 0.4466887 | -678.842105 | 478.00 | -2512.050726 | 1154.366515 | 19 | 1.0000000 |
| RHOBTB2 GTPase cycle | 0.4472394 | 875.888889 | 1790.00 | -1651.325346 | 3403.103124 | 9 | 1.0000000 |
| ABC transporter disorders | 0.4506530 | -717.400000 | -320.00 | -2700.190229 | 1265.390229 | 15 | 1.0000000 |
| Role of LAT2/NTAL/LAB on calcium mobilization | 0.4523462 | 1861.800000 | 4850.00 | -4353.402531 | 8077.002532 | 5 | 1.0000000 |
| Keratan sulfate biosynthesis | 0.4524601 | 1053.857143 | 1045.00 | -2156.412005 | 4264.126291 | 7 | 1.0000000 |
| DNA Double Strand Break Response | 0.4531925 | -718.272727 | -1027.00 | -2768.846766 | 1332.301311 | 11 | 1.0000000 |
| Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks | 0.4531925 | -718.272727 | -1027.00 | -2768.846766 | 1332.301311 | 11 | 1.0000000 |
| Citric acid cycle (TCA cycle) | 0.4533565 | 645.625000 | 659.50 | -1277.520426 | 2568.770426 | 8 | 1.0000000 |
| Metabolism of polyamines | 0.4542886 | -856.888889 | 145.00 | -3369.555899 | 1655.778121 | 9 | 1.0000000 |
| APC/C:Cdc20 mediated degradation of mitotic proteins | 0.4557400 | -920.000000 | -1840.50 | -3539.112943 | 1699.112944 | 12 | 1.0000000 |
| APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint | 0.4557400 | -920.000000 | -1840.50 | -3539.112943 | 1699.112944 | 12 | 1.0000000 |
| Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins | 0.4557400 | -920.000000 | -1840.50 | -3539.112943 | 1699.112944 | 12 | 1.0000000 |
| Cdc20:Phospho-APC/C mediated degradation of Cyclin A | 0.4557400 | -920.000000 | -1840.50 | -3539.112943 | 1699.112944 | 12 | 1.0000000 |
| Cargo trafficking to the periciliary membrane | 0.4566833 | 817.615385 | 1284.00 | -1498.521917 | 3133.752686 | 13 | 1.0000000 |
| Cyclin A/B1/B2 associated events during G2/M transition | 0.4571524 | 846.428571 | 1823.00 | -1760.306380 | 3453.163523 | 7 | 1.0000000 |
| S Phase | 0.4578366 | 435.250000 | 782.00 | -738.798079 | 1609.298079 | 40 | 1.0000000 |
| Apoptotic execution phase | 0.4585934 | 728.133333 | 627.00 | -1320.806700 | 2777.073367 | 15 | 1.0000000 |
| Activation of BH3-only proteins | 0.4616205 | 815.500000 | 369.50 | -1537.506076 | 3168.506076 | 12 | 1.0000000 |
| MAPK targets/ Nuclear events mediated by MAP kinases | 0.4642871 | -541.666667 | -428.50 | -2068.121275 | 984.787941 | 18 | 1.0000000 |
| Aquaporin-mediated transport | 0.4654731 | 1073.833333 | 2877.00 | -2157.377093 | 4305.043760 | 9 | 1.0000000 |
| Other semaphorin interactions | 0.4716397 | 1137.777778 | 1518.00 | -2335.330547 | 4610.886102 | 9 | 1.0000000 |
| Cytosolic iron-sulfur cluster assembly | 0.4724522 | -695.200000 | -1046.00 | -3130.948153 | 1740.548153 | 5 | 1.0000000 |
| Telomere C-strand (Lagging Strand) Synthesis | 0.4728377 | -861.222222 | -1807.00 | -3497.499047 | 1775.054603 | 9 | 1.0000000 |
| Autophagy | 0.4739583 | -420.058824 | -989.50 | -1599.905189 | 759.787542 | 34 | 1.0000000 |
| RAF activation | 0.4740290 | 578.857143 | 757.50 | -1117.221482 | 2274.935768 | 14 | 1.0000000 |
| Peptide ligand-binding receptors | 0.4759221 | 920.375000 | 723.00 | -1969.279108 | 3810.029108 | 8 | 1.0000000 |
| Diseases associated with the TLR signaling cascade | 0.4759769 | 1274.285714 | 2552.00 | -2827.756116 | 5376.327545 | 7 | 1.0000000 |
| Diseases of Immune System | 0.4759769 | 1274.285714 | 2552.00 | -2827.756116 | 5376.327545 | 7 | 1.0000000 |
| Nuclear signaling by ERBB4 | 0.4801643 | -780.461538 | 478.00 | -3114.035056 | 1553.111979 | 13 | 1.0000000 |
| Competing endogenous RNAs (ceRNAs) regulate PTEN translation | 0.4801905 | 1106.857143 | 643.00 | -2492.062392 | 4705.776678 | 7 | 1.0000000 |
| Cardiac conduction | 0.4817184 | 565.000000 | -476.50 | -1064.287290 | 2194.287290 | 26 | 1.0000000 |
| Peptide hormone metabolism | 0.4817218 | 855.000000 | 931.50 | -1729.336149 | 3439.336149 | 12 | 1.0000000 |
| Ca-dependent events | 0.4826228 | 593.928571 | -105.50 | -1181.332369 | 2369.189512 | 14 | 1.0000000 |
| Processive synthesis on the C-strand of the telomere | 0.4843028 | -1219.800000 | -1807.00 | -5618.657401 | 3179.057400 | 5 | 1.0000000 |
| Removal of the Flap Intermediate from the C-strand | 0.4843028 | -1219.800000 | -1807.00 | -5618.657401 | 3179.057400 | 5 | 1.0000000 |
| Regulation of PTEN gene transcription | 0.4846103 | 531.952381 | 715.00 | -1026.239778 | 2090.144540 | 21 | 1.0000000 |
| Class I peroxisomal membrane protein import | 0.4862142 | 1142.600000 | 1262.00 | -2997.186965 | 5282.386965 | 5 | 1.0000000 |
| Sensory perception of taste | 0.4863819 | 1473.200000 | 3254.00 | -3866.587350 | 6812.987350 | 5 | 1.0000000 |
| Viral Messenger RNA Synthesis | 0.4864347 | 682.566667 | 831.00 | -1365.276605 | 2730.409938 | 15 | 1.0000000 |
| Nonhomologous End-Joining (NHEJ) | 0.4864597 | -897.375000 | -963.00 | -3785.977216 | 1991.227216 | 8 | 1.0000000 |
| SCF-beta-TrCP mediated degradation of Emi1 | 0.4875897 | -948.875000 | -1107.00 | -4011.481440 | 2113.731440 | 8 | 1.0000000 |
| DSCAM interactions | 0.4897607 | -894.833333 | -807.50 | -3982.211590 | 2192.544923 | 6 | 1.0000000 |
| Asymmetric localization of PCP proteins | 0.4899771 | 756.750000 | 2098.50 | -1575.338947 | 3088.838947 | 12 | 1.0000000 |
| Gastrin-CREB signalling pathway via PKC and MAPK | 0.4904225 | -876.500000 | -1304.50 | -3634.426444 | 1881.426444 | 10 | 1.0000000 |
| Sulfur amino acid metabolism | 0.4926311 | 1051.000000 | 1409.00 | -2600.547705 | 4702.547705 | 6 | 1.0000000 |
| SRP-dependent cotranslational protein targeting to membrane | 0.4932407 | 1018.333333 | 1545.00 | -2524.968186 | 4561.634852 | 6 | 1.0000000 |
| Transferrin endocytosis and recycling | 0.4933062 | 776.500000 | 778.50 | -1635.331417 | 3188.331417 | 12 | 1.0000000 |
| Sema4D induced cell migration and growth-cone collapse | 0.4951303 | 833.363636 | -510.00 | -1789.394055 | 3456.121327 | 11 | 1.0000000 |
| CaM pathway | 0.4953253 | 623.769231 | -417.00 | -1308.826902 | 2556.365364 | 13 | 1.0000000 |
| Calmodulin induced events | 0.4953253 | 623.769231 | -417.00 | -1308.826902 | 2556.365364 | 13 | 1.0000000 |
| Inactivation of CSF3 (G-CSF) signaling | 0.4988925 | -1139.000000 | -1241.50 | -5157.188944 | 2879.188944 | 6 | 1.0000000 |
| RHOH GTPase cycle | 0.5003614 | 822.750000 | 232.50 | -1775.907348 | 3421.407348 | 12 | 1.0000000 |
| NoRC negatively regulates rRNA expression | 0.5022379 | -805.818182 | -1046.00 | -3385.239643 | 1773.603279 | 11 | 1.0000000 |
| Signaling by Retinoic Acid | 0.5035592 | -833.888889 | -552.00 | -3579.557977 | 1911.780199 | 9 | 1.0000000 |
| APC/C-mediated degradation of cell cycle proteins | 0.5073306 | -594.722222 | -588.50 | -2447.312488 | 1257.868043 | 18 | 1.0000000 |
| Regulation of mitotic cell cycle | 0.5073306 | -594.722222 | -588.50 | -2447.312488 | 1257.868043 | 18 | 1.0000000 |
| Stabilization of p53 | 0.5082121 | -898.000000 | -290.00 | -4022.198478 | 2226.198478 | 7 | 1.0000000 |
| Association of TriC/CCT with target proteins during biosynthesis | 0.5088707 | 745.222222 | 813.00 | -1740.253236 | 3230.697681 | 9 | 1.0000000 |
| TP53 Regulates Transcription of Cell Cycle Genes | 0.5095479 | 648.000000 | 643.00 | -1463.038191 | 2759.038191 | 11 | 1.0000000 |
| Recycling pathway of L1 | 0.5099312 | 1061.375000 | 1351.50 | -2553.935476 | 4676.685476 | 8 | 1.0000000 |
| Opioid Signalling | 0.5170493 | 483.166667 | -105.50 | -1035.762054 | 2002.095388 | 24 | 1.0000000 |
| Degradation of AXIN | 0.5174994 | 946.000000 | 2599.00 | -2276.272375 | 4168.272375 | 9 | 1.0000000 |
| Cyclin E associated events during G1/S transition | 0.5186860 | 561.222222 | 1191.50 | -1235.392099 | 2357.836544 | 18 | 1.0000000 |
| Interleukin-1 family signaling | 0.5193112 | 346.829268 | 654.00 | -731.331880 | 1424.990416 | 41 | 1.0000000 |
| SHC1 events in ERBB4 signaling | 0.5223312 | -1062.800000 | -2815.00 | -5276.426102 | 3150.826102 | 5 | 1.0000000 |
| Sema4D in semaphorin signaling | 0.5236571 | 712.250000 | -565.00 | -1667.786627 | 3092.286626 | 12 | 1.0000000 |
| MAP kinase activation | 0.5252906 | -337.142857 | 168.00 | -1404.655854 | 730.370139 | 35 | 1.0000000 |
| Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA | 0.5256608 | 1242.800000 | 111.00 | -3726.429016 | 6212.029016 | 5 | 1.0000000 |
| Orc1 removal from chromatin | 0.5303373 | 693.454545 | 1180.00 | -1683.625243 | 3070.534334 | 11 | 1.0000000 |
| Degradation of the extracellular matrix | 0.5306513 | 587.875000 | 1042.00 | -1364.303947 | 2540.053947 | 16 | 1.0000000 |
| Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways | 0.5320150 | -467.916667 | 467.00 | -1993.460510 | 1057.627177 | 24 | 1.0000000 |
| RNA Polymerase II Pre-transcription Events | 0.5346293 | -655.263158 | -2283.00 | -2829.729482 | 1519.203166 | 19 | 1.0000000 |
| NOTCH2 Activation and Transmission of Signal to the Nucleus | 0.5353740 | 912.200000 | 1287.00 | -2289.915099 | 4114.315099 | 10 | 1.0000000 |
| Autodegradation of the E3 ubiquitin ligase COP1 | 0.5363220 | -999.333333 | -1107.00 | -4870.515707 | 2871.849041 | 6 | 1.0000000 |
| Ubiquitin Mediated Degradation of Phosphorylated Cdc25A | 0.5363220 | -999.333333 | -1107.00 | -4870.515707 | 2871.849041 | 6 | 1.0000000 |
| p53-Independent DNA Damage Response | 0.5363220 | -999.333333 | -1107.00 | -4870.515707 | 2871.849041 | 6 | 1.0000000 |
| p53-Independent G1/S DNA damage checkpoint | 0.5363220 | -999.333333 | -1107.00 | -4870.515707 | 2871.849041 | 6 | 1.0000000 |
| Detoxification of Reactive Oxygen Species | 0.5366128 | -1022.333333 | -1202.00 | -4985.558709 | 2940.892042 | 6 | 1.0000000 |
| Regulation of RUNX3 expression and activity | 0.5368699 | 879.111111 | 2599.00 | -2263.006735 | 4021.228957 | 9 | 1.0000000 |
| Potassium Channels | 0.5375394 | -591.857143 | -1508.00 | -2610.948768 | 1427.234482 | 14 | 1.0000000 |
| Regulation of pyruvate dehydrogenase (PDH) complex | 0.5393388 | 1070.333333 | 885.00 | -3108.056557 | 5248.723223 | 6 | 1.0000000 |
| FCERI mediated NF-kB activation | 0.5400603 | -506.857143 | 280.00 | -2202.828293 | 1189.114008 | 21 | 1.0000000 |
| Regulation of PTEN stability and activity | 0.5418578 | 686.000000 | 1858.50 | -1679.693663 | 3051.693663 | 14 | 1.0000000 |
| Transcriptional regulation by small RNAs | 0.5422267 | 528.088235 | 725.00 | -1269.591891 | 2325.768362 | 17 | 1.0000000 |
| Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA | 0.5428000 | -1179.400000 | -1651.00 | -6108.259773 | 3749.459773 | 5 | 1.0000000 |
| Resolution of Abasic Sites (AP sites) | 0.5430962 | 837.666667 | 1034.00 | -2464.210073 | 4139.543407 | 6 | 1.0000000 |
| Chromosome Maintenance | 0.5439010 | -458.739130 | -294.00 | -2001.947872 | 1084.469611 | 23 | 1.0000000 |
| Signaling by ROBO receptors | 0.5465573 | 417.774194 | 778.00 | -981.287322 | 1816.835709 | 31 | 1.0000000 |
| RUNX3 regulates BCL2L11 (BIM) transcription | 0.5477845 | 1183.800000 | 1758.00 | -3828.375740 | 6195.975740 | 5 | 1.0000000 |
| EGFR downregulation | 0.5477869 | 773.600000 | 2186.00 | -2028.543151 | 3575.743151 | 10 | 1.0000000 |
| Rab regulation of trafficking | 0.5510334 | -351.012500 | -1030.75 | -1531.514164 | 829.489164 | 40 | 1.0000000 |
| PERK regulates gene expression | 0.5528691 | 852.714286 | 1038.00 | -2467.424575 | 4172.853147 | 7 | 1.0000000 |
| Transcription of E2F targets under negative control by DREAM complex | 0.5598132 | 948.600000 | 2064.00 | -3197.659551 | 5094.859551 | 5 | 1.0000000 |
| RUNX1 regulates transcription of genes involved in differentiation of HSCs | 0.5614095 | 714.000000 | 1553.00 | -1964.680210 | 3392.680211 | 10 | 1.0000000 |
| Signal amplification | 0.5639580 | 1230.166667 | 2313.00 | -3891.134842 | 6351.468176 | 6 | 1.0000000 |
| Protein localization | 0.5654064 | -363.166667 | -349.50 | -1640.515493 | 914.182159 | 30 | 1.0000000 |
| Negative regulation of FLT3 | 0.5658864 | 1087.000000 | 916.00 | -3461.585977 | 5635.585977 | 6 | 1.0000000 |
| Platelet sensitization by LDL | 0.5665503 | 1075.571429 | 2060.00 | -3265.445031 | 5416.587889 | 7 | 1.0000000 |
| Vitamin D (calciferol) metabolism | 0.5681805 | 929.166667 | 304.00 | -2982.866773 | 4841.200106 | 6 | 1.0000000 |
| Miscellaneous transport and binding events | 0.5686512 | 925.142857 | -403.00 | -2829.649422 | 4679.935136 | 7 | 1.0000000 |
| MET receptor recycling | 0.5688351 | 885.000000 | 452.00 | -2847.618073 | 4617.618073 | 6 | 1.0000000 |
| Aberrant regulation of mitotic cell cycle due to RB1 defects | 0.5716110 | 663.923077 | 384.00 | -1823.363755 | 3151.209909 | 13 | 1.0000000 |
| Diseases of mitotic cell cycle | 0.5716110 | 663.923077 | 384.00 | -1823.363755 | 3151.209909 | 13 | 1.0000000 |
| Retrograde transport at the Trans-Golgi-Network | 0.5736875 | 377.000000 | 22.50 | -994.709901 | 1748.709901 | 22 | 1.0000000 |
| Interleukin-37 signaling | 0.5769078 | 908.571429 | 801.00 | -2861.470913 | 4678.613771 | 7 | 1.0000000 |
| Regulation of TP53 Activity through Acetylation | 0.5774146 | -635.083333 | -1681.00 | -3069.632101 | 1799.465435 | 12 | 1.0000000 |
| Regulation of mRNA stability by proteins that bind AU-rich elements | 0.5776146 | -443.270833 | -770.00 | -2066.540851 | 1179.999184 | 24 | 1.0000000 |
| Activation of PPARGC1A (PGC-1alpha) by phosphorylation | 0.5784160 | -727.000000 | -1183.00 | -3755.943765 | 2301.943765 | 7 | 1.0000000 |
| TNFR1-induced proapoptotic signaling | 0.5824069 | 1309.800000 | 3309.00 | -4777.428555 | 7397.028555 | 5 | 1.0000000 |
| Telomere Maintenance | 0.5831944 | -505.823529 | -1807.00 | -2420.430073 | 1408.783014 | 17 | 1.0000000 |
| RHO GTPases Activate WASPs and WAVEs | 0.5834872 | 613.700000 | -11.50 | -1827.571408 | 3054.971408 | 10 | 1.0000000 |
| NOTCH4 Activation and Transmission of Signal to the Nucleus | 0.5895993 | 841.285714 | 2096.00 | -2772.517488 | 4455.088916 | 7 | 1.0000000 |
| Chaperonin-mediated protein folding | 0.5913741 | 516.230769 | 813.00 | -1523.029244 | 2555.490783 | 13 | 1.0000000 |
| Cellular response to hypoxia | 0.5927879 | 579.600000 | 1215.00 | -1691.747511 | 2850.947511 | 15 | 1.0000000 |
| Degradation of DVL | 0.5929105 | -749.875000 | -1107.00 | -3916.000170 | 2416.250170 | 8 | 1.0000000 |
| Synthesis of DNA | 0.5931083 | -401.040000 | -294.00 | -1929.389353 | 1127.309353 | 25 | 1.0000000 |
| Glutamate binding, activation of AMPA receptors and synaptic plasticity | 0.5959136 | 607.800000 | 884.00 | -1893.546322 | 3109.146322 | 10 | 1.0000000 |
| Trafficking of AMPA receptors | 0.5959136 | 607.800000 | 884.00 | -1893.546322 | 3109.146322 | 10 | 1.0000000 |
| G1/S DNA Damage Checkpoints | 0.5966723 | -619.400000 | -72.50 | -3173.841655 | 1935.041655 | 10 | 1.0000000 |
| p53-Dependent G1 DNA Damage Response | 0.5966723 | -619.400000 | -72.50 | -3173.841655 | 1935.041655 | 10 | 1.0000000 |
| p53-Dependent G1/S DNA damage checkpoint | 0.5966723 | -619.400000 | -72.50 | -3173.841655 | 1935.041655 | 10 | 1.0000000 |
| Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 0.5969576 | -729.750000 | -1171.50 | -3845.684645 | 2386.184645 | 8 | 1.0000000 |
| Transcriptional activation of mitochondrial biogenesis | 0.6038842 | 374.500000 | 454.50 | -1115.376468 | 1864.376468 | 19 | 1.0000000 |
| Costimulation by the CD28 family | 0.6039012 | 440.952381 | 233.00 | -1303.984927 | 2185.889689 | 21 | 1.0000000 |
| p75NTR recruits signalling complexes | 0.6041350 | -567.800000 | -652.00 | -3373.060065 | 2237.460065 | 5 | 1.0000000 |
| Signaling by NOTCH2 | 0.6088143 | 592.714286 | 1270.00 | -1849.005596 | 3034.434167 | 14 | 1.0000000 |
| Homology Directed Repair | 0.6103018 | 364.550000 | 406.00 | -1107.881375 | 1836.981375 | 20 | 1.0000000 |
| G2/M DNA damage checkpoint | 0.6104925 | -503.666667 | -827.00 | -2618.156928 | 1610.823595 | 12 | 1.0000000 |
| HDR through MMEJ (alt-NHEJ) | 0.6124979 | 826.200000 | 428.00 | -3355.605394 | 5008.005394 | 5 | 1.0000000 |
| VxPx cargo-targeting to cilium | 0.6126025 | 858.375000 | 1363.50 | -2972.426983 | 4689.176983 | 8 | 1.0000000 |
| Toll Like Receptor 9 (TLR9) Cascade | 0.6163898 | 251.955556 | 332.00 | -754.444451 | 1258.355562 | 45 | 1.0000000 |
| Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells | 0.6178760 | -1109.400000 | -484.00 | -6813.773303 | 4594.973303 | 5 | 1.0000000 |
| NOD1/2 Signaling Pathway | 0.6192725 | 437.352941 | 656.00 | -1392.400576 | 2267.106459 | 17 | 1.0000000 |
| Activation of HOX genes during differentiation | 0.6216361 | -451.375000 | -1985.50 | -2360.563032 | 1457.813032 | 16 | 1.0000000 |
| Activation of anterior HOX genes in hindbrain development during early embryogenesis | 0.6216361 | -451.375000 | -1985.50 | -2360.563032 | 1457.813032 | 16 | 1.0000000 |
| Hh mutants are degraded by ERAD | 0.6226664 | -741.375000 | -1107.00 | -4147.939364 | 2665.189364 | 8 | 1.0000000 |
| Interleukin-15 signaling | 0.6232777 | 751.400000 | 1235.00 | -3174.456327 | 4677.256327 | 5 | 1.0000000 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | 0.6251479 | -782.571429 | -1760.00 | -4502.757784 | 2937.614927 | 7 | 1.0000000 |
| L13a-mediated translational silencing of Ceruloplasmin expression | 0.6251479 | -782.571429 | -1760.00 | -4502.757784 | 2937.614927 | 7 | 1.0000000 |
| Ribosomal scanning and start codon recognition | 0.6251479 | -782.571429 | -1760.00 | -4502.757784 | 2937.614927 | 7 | 1.0000000 |
| Translation initiation complex formation | 0.6251479 | -782.571429 | -1760.00 | -4502.757784 | 2937.614927 | 7 | 1.0000000 |
| HDR through Single Strand Annealing (SSA) | 0.6256528 | -433.142857 | 428.00 | -2495.289614 | 1629.003900 | 7 | 1.0000000 |
| Signaling by NODAL | 0.6263723 | 612.571429 | 795.00 | -2310.028686 | 3535.171543 | 7 | 1.0000000 |
| MTOR signalling | 0.6266618 | 377.200000 | -105.00 | -1249.447572 | 2003.847572 | 15 | 1.0000000 |
| NOTCH2 intracellular domain regulates transcription | 0.6291635 | 1042.800000 | 2062.00 | -4502.379834 | 6587.979833 | 5 | 1.0000000 |
| Regulation of beta-cell development | 0.6295487 | -723.777778 | -484.00 | -4052.082470 | 2604.526915 | 9 | 1.0000000 |
| Translocation of SLC2A4 (GLUT4) to the plasma membrane | 0.6300395 | 409.750000 | 1012.50 | -1326.537374 | 2146.037374 | 24 | 1.0000000 |
| TAK1-dependent IKK and NF-kappa-B activation | 0.6301627 | 399.611111 | 1053.50 | -1319.824146 | 2119.046368 | 18 | 1.0000000 |
| RND3 GTPase cycle | 0.6304933 | 685.363636 | 345.00 | -2392.336394 | 3763.063667 | 11 | 1.0000000 |
| Potential therapeutics for SARS | 0.6311525 | 356.260870 | 292.00 | -1161.208943 | 1873.730682 | 23 | 1.0000000 |
| mRNA Splicing - Major Pathway | 0.6319037 | 270.743590 | 1096.00 | -864.144651 | 1405.631831 | 39 | 1.0000000 |
| Insulin receptor recycling | 0.6338822 | 716.333333 | 609.00 | -2620.519657 | 4053.186324 | 9 | 1.0000000 |
| SUMOylation of transcription cofactors | 0.6340804 | -517.142857 | -1475.50 | -2809.273683 | 1774.987969 | 14 | 1.0000000 |
| RAS processing | 0.6345678 | 553.000000 | 80.00 | -2079.258040 | 3185.258040 | 8 | 1.0000000 |
| IKK complex recruitment mediated by RIP1 | 0.6398751 | -784.500000 | -1115.00 | -4579.034626 | 3010.034626 | 8 | 1.0000000 |
| RNA Polymerase II Transcription Termination | 0.6404925 | 440.230769 | 822.00 | -1561.893256 | 2442.354794 | 13 | 1.0000000 |
| Interleukin-7 signaling | 0.6405481 | 888.714286 | 1235.00 | -3535.908283 | 5313.336854 | 7 | 1.0000000 |
| Nucleotide catabolism | 0.6417467 | -549.555556 | -805.00 | -3171.004391 | 2071.893280 | 9 | 1.0000000 |
| Interleukin-1 signaling | 0.6451863 | 272.333333 | 654.00 | -921.007313 | 1465.673980 | 33 | 1.0000000 |
| Toll-like Receptor Cascades | 0.6452221 | 219.924528 | 332.00 | -733.016398 | 1172.865455 | 53 | 1.0000000 |
| Regulation of ornithine decarboxylase (ODC) | 0.6455119 | -640.142857 | 145.00 | -3876.130087 | 2595.844373 | 7 | 1.0000000 |
| Inactivation, recovery and regulation of the phototransduction cascade | 0.6466884 | -781.400000 | -1615.00 | -5166.052846 | 3603.252847 | 5 | 1.0000000 |
| The phototransduction cascade | 0.6466884 | -781.400000 | -1615.00 | -5166.052846 | 3603.252847 | 5 | 1.0000000 |
| Deactivation of the beta-catenin transactivating complex | 0.6512897 | 487.066667 | 1094.00 | -1774.864438 | 2748.997771 | 15 | 1.0000000 |
| The role of GTSE1 in G2/M progression after G2 checkpoint | 0.6514955 | -629.714286 | 145.00 | -3872.725243 | 2613.296672 | 7 | 1.0000000 |
| Transcriptional regulation of white adipocyte differentiation | 0.6524562 | 410.029412 | 1480.00 | -1483.985762 | 2304.044586 | 17 | 1.0000000 |
| Toll Like Receptor 3 (TLR3) Cascade | 0.6569550 | -220.500000 | 187.00 | -1214.803481 | 773.803481 | 44 | 1.0000000 |
| KSRP (KHSRP) binds and destabilizes mRNA | 0.6573135 | 548.800000 | 1038.00 | -2635.954806 | 3733.554806 | 5 | 1.0000000 |
| CD28 co-stimulation | 0.6607740 | 482.846154 | 104.00 | -1855.315272 | 2821.007580 | 13 | 1.0000000 |
| Regulated proteolysis of p75NTR | 0.6610283 | -581.000000 | -87.00 | -3582.557189 | 2420.557189 | 8 | 1.0000000 |
| Degradation of GLI2 by the proteasome | 0.6649361 | 517.200000 | 1372.00 | -2096.000198 | 3130.400198 | 10 | 1.0000000 |
| GLI3 is processed to GLI3R by the proteasome | 0.6649361 | 517.200000 | 1372.00 | -2096.000198 | 3130.400198 | 10 | 1.0000000 |
| Leading Strand Synthesis | 0.6652100 | -691.800000 | -1807.00 | -4810.209260 | 3426.609260 | 5 | 1.0000000 |
| Polymerase switching | 0.6652100 | -691.800000 | -1807.00 | -4810.209260 | 3426.609260 | 5 | 1.0000000 |
| Apoptotic cleavage of cellular proteins | 0.6686566 | 512.916667 | 313.00 | -2054.469555 | 3080.302889 | 12 | 1.0000000 |
| WNT5A-dependent internalization of FZD2, FZD5 and ROR2 | 0.6692243 | 959.000000 | 3937.00 | -4825.756325 | 6743.756325 | 5 | 1.0000000 |
| Ubiquitin-dependent degradation of Cyclin D | 0.6706123 | 694.750000 | 1372.00 | -3007.343182 | 4396.843182 | 8 | 1.0000000 |
| Iron uptake and transport | 0.6712245 | -436.611111 | -424.50 | -2569.317756 | 1696.095533 | 18 | 1.0000000 |
| Apoptosis | 0.6718456 | 247.833333 | 73.00 | -925.203039 | 1420.869705 | 42 | 1.0000000 |
| Deadenylation-dependent mRNA decay | 0.6729494 | 512.916667 | 377.00 | -2090.596743 | 3116.430076 | 12 | 1.0000000 |
| Ion homeostasis | 0.6746047 | 510.153846 | -417.00 | -2073.001971 | 3093.309663 | 13 | 1.0000000 |
| Glycerophospholipid biosynthesis | 0.6750844 | -251.075000 | -911.50 | -1453.488695 | 951.338695 | 40 | 1.0000000 |
| Arachidonic acid metabolism | 0.6761338 | 533.636364 | 1941.00 | -2229.867622 | 3297.140349 | 11 | 1.0000000 |
| Transcriptional regulation of granulopoiesis | 0.6777558 | -522.000000 | -614.50 | -3272.238724 | 2228.238724 | 10 | 1.0000000 |
| Cytosolic sensors of pathogen-associated DNA | 0.6787635 | 457.833333 | 1733.00 | -1911.079253 | 2826.745920 | 12 | 1.0000000 |
| SCF(Skp2)-mediated degradation of p27/p21 | 0.6823127 | 571.444444 | 384.00 | -2532.028659 | 3674.917548 | 9 | 1.0000000 |
| AKT phosphorylates targets in the nucleus | 0.6825488 | 698.833333 | 1910.00 | -3442.769567 | 4840.436234 | 6 | 1.0000000 |
| Dual incision in TC-NER | 0.6833638 | -423.833333 | -1426.50 | -2650.826785 | 1803.160118 | 12 | 1.0000000 |
| Deadenylation of mRNA | 0.6839043 | 758.600000 | 643.00 | -4048.518935 | 5565.718935 | 5 | 1.0000000 |
| Fc epsilon receptor (FCERI) signaling | 0.6870727 | 223.536585 | 206.00 | -889.858376 | 1336.931546 | 41 | 1.0000000 |
| Synthesis of active ubiquitin: roles of E1 and E2 enzymes | 0.6871180 | 698.555556 | 2354.00 | -3157.527721 | 4554.638832 | 9 | 1.0000000 |
| Peroxisomal protein import | 0.6874081 | 403.285714 | 1172.50 | -1713.948296 | 2520.519724 | 14 | 1.0000000 |
| Processing of SMDT1 | 0.6879967 | -591.166667 | -426.50 | -4160.525420 | 2978.192087 | 6 | 1.0000000 |
| Global Genome Nucleotide Excision Repair (GG-NER) | 0.6892132 | 311.315789 | 447.00 | -1297.913736 | 1920.545315 | 19 | 1.0000000 |
| Cellular response to starvation | 0.6909911 | 338.450000 | 660.50 | -1416.581884 | 2093.481884 | 20 | 1.0000000 |
| Interleukin-17 signaling | 0.6915122 | -210.444444 | 187.00 | -1278.231706 | 857.342817 | 36 | 1.0000000 |
| RNA Polymerase III Transcription Initiation | 0.6930218 | 759.333333 | 513.00 | -3905.946686 | 5424.613353 | 6 | 1.0000000 |
| RNA Polymerase III Transcription Initiation From Type 3 Promoter | 0.6930218 | 759.333333 | 513.00 | -3905.946686 | 5424.613353 | 6 | 1.0000000 |
| TP53 Regulates Metabolic Genes | 0.6978100 | 265.689655 | 144.00 | -1121.632122 | 1653.011432 | 29 | 1.0000000 |
| RMTs methylate histone arginines | 0.6996338 | -476.900000 | -1902.00 | -3184.906671 | 2231.106671 | 10 | 1.0000000 |
| TCR signaling | 0.7024418 | 252.156250 | 655.00 | -1081.619739 | 1585.932239 | 32 | 1.0000000 |
| GAB1 signalosome | 0.7050967 | -870.666667 | -3538.00 | -6454.315856 | 4712.982523 | 6 | 1.0000000 |
| RNA polymerase II transcribes snRNA genes | 0.7057968 | -346.380952 | -2283.00 | -2233.150166 | 1540.388261 | 21 | 1.0000000 |
| Base Excision Repair | 0.7093732 | -504.500000 | -1115.50 | -3577.193876 | 2568.193876 | 8 | 1.0000000 |
| Metabolism of RNA | 0.7110116 | 119.549180 | 529.50 | -517.764728 | 756.863088 | 122 | 1.0000000 |
| Caspase-mediated cleavage of cytoskeletal proteins | 0.7187500 | -628.333333 | -428.50 | -4865.983849 | 3609.317183 | 6 | 1.0000000 |
| Anchoring of the basal body to the plasma membrane | 0.7205904 | 224.870968 | 333.00 | -1047.098616 | 1496.840551 | 31 | 1.0000000 |
| Signaling by CSF3 (G-CSF) | 0.7247087 | 483.300000 | 1697.50 | -2525.384127 | 3491.984127 | 10 | 1.0000000 |
| MECP2 regulates neuronal receptors and channels | 0.7256821 | 423.000000 | -620.00 | -2696.558295 | 3542.558295 | 5 | 1.0000000 |
| Degradation of beta-catenin by the destruction complex | 0.7261854 | 301.190476 | 1034.00 | -1467.777315 | 2070.158267 | 21 | 1.0000000 |
| Fanconi Anemia Pathway | 0.7264519 | 263.000000 | 612.00 | -1682.367732 | 2208.367732 | 5 | 1.0000000 |
| Cyclin A:Cdk2-associated events at S phase entry | 0.7267367 | 300.526316 | 384.00 | -1478.162141 | 2079.214773 | 19 | 1.0000000 |
| HIV Life Cycle | 0.7271476 | -205.965116 | -428.00 | -1389.281530 | 977.351297 | 43 | 1.0000000 |
| HATs acetylate histones | 0.7281065 | -300.800000 | -404.00 | -2085.221742 | 1483.621742 | 20 | 1.0000000 |
| HDR through Homologous Recombination (HRR) | 0.7312852 | 280.375000 | 520.00 | -1574.348831 | 2135.098831 | 8 | 1.0000000 |
| Degradation of GLI1 by the proteasome | 0.7317791 | 389.500000 | 1372.00 | -2102.315266 | 2881.315266 | 10 | 1.0000000 |
| Diseases of DNA repair | 0.7318562 | -266.500000 | -163.50 | -2156.760854 | 1623.760854 | 6 | 1.0000000 |
| DARPP-32 events | 0.7328536 | 533.714286 | -452.00 | -3117.819634 | 4185.248205 | 7 | 1.0000000 |
| mRNA Splicing | 0.7329515 | 189.825000 | 959.00 | -927.450095 | 1307.100095 | 40 | 1.0000000 |
| VEGFR2 mediated cell proliferation | 0.7331933 | 413.900000 | -956.00 | -2248.709004 | 3076.509004 | 10 | 1.0000000 |
| RAB geranylgeranylation | 0.7372547 | -236.565217 | -848.00 | -1680.516012 | 1207.385577 | 23 | 1.0000000 |
| Transcriptional regulation of pluripotent stem cells | 0.7397448 | -542.250000 | -1395.00 | -4251.596506 | 3167.096506 | 8 | 1.0000000 |
| Energy dependent regulation of mTOR by LKB1-AMPK | 0.7408623 | 313.444444 | 582.00 | -1797.466855 | 2424.355744 | 9 | 1.0000000 |
| ROBO receptors bind AKAP5 | 0.7408747 | 417.800000 | 778.00 | -2854.555869 | 3690.155869 | 5 | 1.0000000 |
| Late Phase of HIV Life Cycle | 0.7420542 | -205.934211 | -519.50 | -1464.223357 | 1052.354936 | 38 | 1.0000000 |
| Negative regulation of NOTCH4 signaling | 0.7440830 | -471.142857 | 145.00 | -3843.015437 | 2900.729722 | 7 | 1.0000000 |
| Transcription-Coupled Nucleotide Excision Repair (TC-NER) | 0.7443446 | -318.466667 | -1046.00 | -2371.950909 | 1735.017576 | 15 | 1.0000000 |
| Downstream signaling events of B Cell Receptor (BCR) | 0.7452374 | 257.944444 | 1398.50 | -1389.885697 | 1905.774586 | 18 | 1.0000000 |
| Voltage gated Potassium channels | 0.7456433 | 492.333333 | 1063.50 | -3198.848579 | 4183.515245 | 6 | 1.0000000 |
| Interaction between L1 and Ankyrins | 0.7484952 | 584.142857 | 1751.00 | -3673.142777 | 4841.428492 | 7 | 1.0000000 |
| Macroautophagy | 0.7512139 | -195.580645 | -973.00 | -1443.938762 | 1052.777471 | 31 | 1.0000000 |
| Vpu mediated degradation of CD4 | 0.7523850 | -457.000000 | 145.00 | -3842.288049 | 2928.288049 | 7 | 1.0000000 |
| Signaling by FGFR2 IIIa TM | 0.7525727 | -706.400000 | -2855.00 | -6514.284420 | 5101.484420 | 5 | 1.0000000 |
| FGFR2 alternative splicing | 0.7567108 | -548.166667 | -549.00 | -4853.614296 | 3757.280963 | 6 | 1.0000000 |
| Signaling by Hippo | 0.7588262 | 483.000000 | 93.50 | -3094.075546 | 4060.075546 | 8 | 1.0000000 |
| Regulation of localization of FOXO transcription factors | 0.7606000 | 454.000000 | 1758.00 | -3029.348199 | 3937.348199 | 7 | 1.0000000 |
| FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes | 0.7610690 | 322.545455 | 558.00 | -1977.109958 | 2622.200868 | 11 | 1.0000000 |
| Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | 0.7642269 | 353.722222 | 381.00 | -2274.561925 | 2982.006369 | 9 | 1.0000000 |
| Regulation of RAS by GAPs | 0.7680368 | 281.653846 | 1317.00 | -1752.312985 | 2315.620677 | 13 | 1.0000000 |
| Cellular response to chemical stress | 0.7694019 | -181.587500 | -719.00 | -1425.784478 | 1062.609478 | 40 | 1.0000000 |
| Endosomal Sorting Complex Required For Transport (ESCRT) | 0.7697097 | -283.750000 | -55.50 | -2488.322734 | 1920.822734 | 8 | 1.0000000 |
| Nucleotide Excision Repair | 0.7703024 | -210.320000 | -424.00 | -1680.267125 | 1259.627125 | 25 | 1.0000000 |
| Processive synthesis on the lagging strand | 0.7713984 | 453.800000 | -294.00 | -3598.680995 | 4506.280995 | 5 | 1.0000000 |
| Removal of the Flap Intermediate | 0.7713984 | 453.800000 | -294.00 | -3598.680995 | 4506.280995 | 5 | 1.0000000 |
| Defective CFTR causes cystic fibrosis | 0.7729155 | -341.727273 | 145.00 | -2909.747273 | 2226.292728 | 11 | 1.0000000 |
| Transcriptional Regulation by TP53 | 0.7734187 | 102.549020 | 153.50 | -602.142746 | 807.240785 | 102 | 1.0000000 |
| Signaling by Activin | 0.7746268 | 421.666667 | 500.50 | -3164.472054 | 4007.805387 | 6 | 1.0000000 |
| Metabolism of folate and pterines | 0.7746647 | 415.714286 | -415.00 | -2980.700088 | 3812.128659 | 7 | 1.0000000 |
| Defective B3GALTL causes PpS | 0.7748271 | 321.333333 | 1009.00 | -2182.708447 | 2825.375113 | 9 | 1.0000000 |
| O-glycosylation of TSR domain-containing proteins | 0.7748271 | 321.333333 | 1009.00 | -2182.708447 | 2825.375113 | 9 | 1.0000000 |
| Synthesis of IP3 and IP4 in the cytosol | 0.7757865 | 342.777778 | 691.00 | -2340.182272 | 3025.737827 | 9 | 1.0000000 |
| E2F mediated regulation of DNA replication | 0.7762757 | 313.250000 | -146.50 | -2194.463951 | 2820.963951 | 8 | 1.0000000 |
| RAB GEFs exchange GTP for GDP on RABs | 0.7763938 | -212.431035 | -1213.50 | -1729.790182 | 1304.928113 | 29 | 1.0000000 |
| Transcriptional Regulation by VENTX | 0.7769399 | 304.529412 | 114.00 | -1935.968118 | 2545.026942 | 17 | 1.0000000 |
| Activation of GABAB receptors | 0.7770224 | 460.375000 | 970.00 | -3237.900946 | 4158.650946 | 8 | 1.0000000 |
| GABA B receptor activation | 0.7770224 | 460.375000 | 970.00 | -3237.900946 | 4158.650946 | 8 | 1.0000000 |
| Signaling by EGFR in Cancer | 0.7785496 | -460.000000 | -1248.00 | -4286.469381 | 3366.469381 | 7 | 1.0000000 |
| Spry regulation of FGF signaling | 0.7785619 | 518.000000 | -975.00 | -3968.574907 | 5004.574907 | 6 | 1.0000000 |
| CD28 dependent Vav1 pathway | 0.7803364 | -483.800000 | -488.00 | -4986.979081 | 4019.379081 | 5 | 1.0000000 |
| Cap-dependent Translation Initiation | 0.7812099 | -351.111111 | -583.00 | -3169.637720 | 2467.415498 | 9 | 1.0000000 |
| Eukaryotic Translation Initiation | 0.7812099 | -351.111111 | -583.00 | -3169.637720 | 2467.415498 | 9 | 1.0000000 |
| SUMOylation of RNA binding proteins | 0.7835077 | 234.775000 | 618.50 | -1528.557949 | 1998.107949 | 20 | 1.0000000 |
| CTLA4 inhibitory signaling | 0.7847987 | 407.888889 | 2060.00 | -2922.719137 | 3738.496915 | 9 | 1.0000000 |
| Nucleotide salvage | 0.7870055 | -310.714286 | -793.00 | -3001.396750 | 2379.968179 | 7 | 1.0000000 |
| FCERI mediated Ca+2 mobilization | 0.7880403 | 366.777778 | -1248.00 | -2675.315544 | 3408.871100 | 9 | 1.0000000 |
| Cytoprotection by HMOX1 | 0.7892054 | 287.464286 | 1709.00 | -1988.070301 | 2562.998872 | 14 | 1.0000000 |
| Regulation of IFNA/IFNB signaling | 0.7913042 | 575.200000 | 2160.00 | -5070.344268 | 6220.744268 | 5 | 1.0000000 |
| RNA Polymerase I Promoter Clearance | 0.7944103 | -271.153846 | -960.00 | -2488.368333 | 1946.060640 | 13 | 1.0000000 |
| RNA Polymerase I Transcription | 0.7944103 | -271.153846 | -960.00 | -2488.368333 | 1946.060640 | 13 | 1.0000000 |
| Negative regulators of DDX58/IFIH1 signaling | 0.7944163 | 412.250000 | 835.00 | -3188.600593 | 4013.100593 | 8 | 1.0000000 |
| Extension of Telomeres | 0.7962959 | 257.142857 | 45.00 | -1851.107701 | 2365.393416 | 14 | 1.0000000 |
| MyD88 dependent cascade initiated on endosome | 0.7989369 | 126.750000 | 306.00 | -870.557085 | 1124.057086 | 44 | 1.0000000 |
| TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation | 0.7989369 | 126.750000 | 306.00 | -870.557085 | 1124.057086 | 44 | 1.0000000 |
| Toll Like Receptor 7/8 (TLR7/8) Cascade | 0.7989369 | 126.750000 | 306.00 | -870.557085 | 1124.057086 | 44 | 1.0000000 |
| Signaling by the B Cell Receptor (BCR) | 0.8002756 | 173.423077 | 1058.50 | -1223.422282 | 1570.268436 | 26 | 1.0000000 |
| Vif-mediated degradation of APOBEC3G | 0.8008079 | -374.000000 | 145.00 | -3843.935138 | 3095.935138 | 7 | 1.0000000 |
| Regulation of RUNX2 expression and activity | 0.8011147 | -235.666667 | -396.00 | -2204.414575 | 1733.081242 | 15 | 1.0000000 |
| Pyrimidine salvage | 0.8019301 | -353.800000 | -793.00 | -4018.705267 | 3311.105267 | 5 | 1.0000000 |
| Generation of second messenger molecules | 0.8030794 | 257.625000 | 60.50 | -2094.359613 | 2609.609613 | 8 | 1.0000000 |
| Defects in cobalamin (B12) metabolism | 0.8043801 | -383.333333 | -939.00 | -4156.363886 | 3389.697219 | 6 | 1.0000000 |
| MET activates RAS signaling | 0.8103611 | -297.666667 | 128.00 | -3322.412444 | 2727.079111 | 6 | 1.0000000 |
| EPH-ephrin mediated repulsion of cells | 0.8133680 | -292.750000 | -614.00 | -2957.279499 | 2371.779499 | 12 | 1.0000000 |
| The role of Nef in HIV-1 replication and disease pathogenesis | 0.8136139 | 397.857143 | 603.00 | -3553.731270 | 4349.445556 | 7 | 1.0000000 |
| Protein folding | 0.8140199 | 219.857143 | 565.50 | -1758.616724 | 2198.331010 | 14 | 1.0000000 |
| Downregulation of ERBB2:ERBB3 signaling | 0.8143422 | -524.200000 | -3227.00 | -6327.834583 | 5279.434583 | 5 | 1.0000000 |
| Interferon alpha/beta signaling | 0.8154068 | 283.333333 | 1257.00 | -2424.583440 | 2991.250107 | 9 | 1.0000000 |
| Activation of BAD and translocation to mitochondria | 0.8158682 | 381.571429 | 738.00 | -3455.759801 | 4218.902658 | 7 | 1.0000000 |
| Netrin-1 signaling | 0.8160624 | -198.647059 | -908.00 | -1979.414902 | 1582.120785 | 17 | 1.0000000 |
| Dectin-1 mediated noncanonical NF-kB signaling | 0.8174498 | -312.000000 | 145.00 | -3327.997396 | 2703.997396 | 9 | 1.0000000 |
| DNA Repair | 0.8182131 | -98.206897 | -586.50 | -949.870423 | 753.456630 | 58 | 1.0000000 |
| Transport of RCbl within the body | 0.8182581 | -402.000000 | -1920.00 | -4951.107827 | 4147.107827 | 5 | 1.0000000 |
| Regulation of FOXO transcriptional activity by acetylation | 0.8244524 | -327.285714 | 558.00 | -3783.275582 | 3128.704154 | 7 | 1.0000000 |
| Deposition of new CENPA-containing nucleosomes at the centromere | 0.8245264 | -325.333333 | 450.50 | -3904.702512 | 3254.035845 | 6 | 1.0000000 |
| Nucleosome assembly | 0.8245264 | -325.333333 | 450.50 | -3904.702512 | 3254.035845 | 6 | 1.0000000 |
| TP53 Regulates Transcription of Cell Death Genes | 0.8254310 | -358.750000 | 946.50 | -4063.489821 | 3345.989821 | 8 | 1.0000000 |
| Unwinding of DNA | 0.8263919 | 367.333333 | 1410.50 | -3718.503094 | 4453.169761 | 6 | 1.0000000 |
| Synthesis of PC | 0.8273276 | 374.166667 | 21.00 | -3810.711162 | 4559.044495 | 6 | 1.0000000 |
| CaMK IV-mediated phosphorylation of CREB | 0.8283554 | -154.833333 | -429.50 | -1897.161416 | 1587.494749 | 6 | 1.0000000 |
| ABC-family proteins mediated transport | 0.8310262 | -181.000000 | 145.00 | -1937.359642 | 1575.359642 | 19 | 1.0000000 |
| Growth hormone receptor signaling | 0.8325220 | -286.555556 | 206.00 | -3311.015147 | 2737.904036 | 9 | 1.0000000 |
| SARS-CoV-2 targets host intracellular signalling and regulatory pathways | 0.8353954 | 417.833333 | 523.50 | -4489.242947 | 5324.909614 | 6 | 1.0000000 |
| Signalling to ERKs | 0.8358245 | 204.857143 | 761.50 | -1888.276596 | 2297.990882 | 14 | 1.0000000 |
| Synthesis of PA | 0.8364792 | -216.714286 | -1326.00 | -2440.006600 | 2006.578029 | 14 | 1.0000000 |
| Receptor-type tyrosine-protein phosphatases | 0.8366858 | 495.833333 | 1397.00 | -5374.175042 | 6365.841709 | 6 | 1.0000000 |
| HIV Infection | 0.8396685 | -101.594828 | 484.50 | -1102.561984 | 899.372329 | 58 | 1.0000000 |
| Interferon gamma signaling | 0.8424773 | 154.000000 | -140.00 | -1450.737229 | 1758.737229 | 19 | 1.0000000 |
| Regulation of Apoptosis | 0.8425254 | -301.142857 | 145.00 | -3853.297371 | 3251.011656 | 7 | 1.0000000 |
| Regulation of activated PAK-2p34 by proteasome mediated degradation | 0.8425254 | -301.142857 | 145.00 | -3853.297371 | 3251.011656 | 7 | 1.0000000 |
| Dual Incision in GG-NER | 0.8426447 | -245.857143 | -1046.00 | -3148.120527 | 2656.406241 | 7 | 1.0000000 |
| KEAP1-NFE2L2 pathway | 0.8428117 | 175.727273 | -417.00 | -1644.506555 | 1995.961100 | 22 | 1.0000000 |
| NOTCH4 Intracellular Domain Regulates Transcription | 0.8429421 | 394.666667 | 1398.50 | -4467.243488 | 5256.576821 | 6 | 1.0000000 |
| Cell-cell junction organization | 0.8437725 | -341.100000 | -1704.00 | -4145.211991 | 3463.011991 | 10 | 1.0000000 |
| Toll Like Receptor 4 (TLR4) Cascade | 0.8444672 | 94.803922 | 280.00 | -870.790564 | 1060.398408 | 51 | 1.0000000 |
| PINK1-PRKN Mediated Mitophagy | 0.8457929 | 336.500000 | 482.00 | -3886.815168 | 4559.815168 | 6 | 1.0000000 |
| RNA Polymerase III Abortive And Retractive Initiation | 0.8466784 | 322.000000 | -960.00 | -3580.766471 | 4224.766471 | 7 | 1.0000000 |
| RNA Polymerase III Transcription | 0.8466784 | 322.000000 | -960.00 | -3580.766471 | 4224.766471 | 7 | 1.0000000 |
| Telomere Extension By Telomerase | 0.8502626 | 327.000000 | 384.00 | -3732.732306 | 4386.732306 | 7 | 1.0000000 |
| GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 | 0.8526978 | 270.000000 | 1372.00 | -3043.910073 | 3583.910073 | 8 | 1.0000000 |
| Ephrin signaling | 0.8557550 | -305.500000 | 562.00 | -4408.869402 | 3797.869402 | 6 | 1.0000000 |
| AUF1 (hnRNP D0) binds and destabilizes mRNA | 0.8558330 | -266.375000 | -926.50 | -3607.893027 | 3075.143027 | 8 | 1.0000000 |
| Inwardly rectifying K+ channels | 0.8566208 | -332.600000 | -1842.00 | -5126.048617 | 4460.848617 | 5 | 1.0000000 |
| Diseases of programmed cell death | 0.8584998 | -188.769231 | -294.00 | -2446.661703 | 2069.123242 | 13 | 1.0000000 |
| Platelet calcium homeostasis | 0.8587013 | 353.500000 | 862.50 | -4172.179332 | 4879.179332 | 8 | 1.0000000 |
| Activation of AMPK downstream of NMDARs | 0.8613805 | -162.285714 | -442.00 | -2341.031753 | 2016.460325 | 7 | 1.0000000 |
| Transcriptional Regulation by E2F6 | 0.8626413 | 196.583333 | -961.50 | -2246.407435 | 2639.574102 | 12 | 1.0000000 |
| Signaling by NOTCH3 | 0.8662079 | -168.882353 | 478.00 | -2260.010307 | 1922.245601 | 17 | 1.0000000 |
| Switching of origins to a post-replicative state | 0.8670815 | -169.625000 | 264.50 | -2293.136151 | 1953.886151 | 16 | 1.0000000 |
| NOTCH3 Activation and Transmission of Signal to the Nucleus | 0.8698005 | -239.600000 | -601.00 | -3453.412927 | 2974.212927 | 10 | 1.0000000 |
| DNA Double-Strand Break Repair | 0.8712564 | -88.785714 | -586.50 | -1202.243587 | 1024.672159 | 28 | 1.0000000 |
| Assembly of the pre-replicative complex | 0.8745744 | -158.500000 | 662.50 | -2262.468681 | 1945.468681 | 16 | 1.0000000 |
| MAPK6/MAPK4 signaling | 0.8746456 | -114.791667 | -169.00 | -1603.337853 | 1373.754520 | 24 | 1.0000000 |
| Downstream TCR signaling | 0.8753798 | 130.090909 | 655.00 | -1574.051567 | 1834.233386 | 22 | 1.0000000 |
| ERK/MAPK targets | 0.8758073 | -157.416667 | 269.00 | -2323.321426 | 2008.488093 | 12 | 1.0000000 |
| RNA Polymerase I Transcription Initiation | 0.8790045 | 156.416667 | -122.50 | -2053.123129 | 2365.956463 | 12 | 1.0000000 |
| Biotin transport and metabolism | 0.8803153 | 257.400000 | -610.00 | -4197.119788 | 4711.919788 | 5 | 1.0000000 |
| Role of phospholipids in phagocytosis | 0.8806441 | 216.200000 | -322.50 | -2949.875541 | 3382.275541 | 10 | 1.0000000 |
| Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | 0.8811854 | -194.333333 | 650.00 | -3098.400399 | 2709.733732 | 9 | 1.0000000 |
| Inhibition of replication initiation of damaged DNA by RB1/E2F1 | 0.8813346 | 189.428571 | -294.00 | -2786.503640 | 3165.360782 | 7 | 1.0000000 |
| HSF1-dependent transactivation | 0.8847630 | 154.400000 | -417.00 | -2621.835976 | 2930.635975 | 5 | 1.0000000 |
| Signaling by KIT in disease | 0.8852857 | 160.714286 | 1235.00 | -2451.886817 | 2773.315388 | 7 | 1.0000000 |
| Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants | 0.8852857 | 160.714286 | 1235.00 | -2451.886817 | 2773.315388 | 7 | 1.0000000 |
| Mitochondrial calcium ion transport | 0.8884653 | 207.714286 | -89.00 | -3266.027591 | 3681.456163 | 7 | 1.0000000 |
| NIK–>noncanonical NF-kB signaling | 0.8887307 | 198.125000 | 1372.00 | -3030.890985 | 3427.140985 | 8 | 1.0000000 |
| CLEC7A (Dectin-1) signaling | 0.8901624 | -108.541667 | 468.00 | -1716.536722 | 1499.453389 | 24 | 1.0000000 |
| DNA Replication Pre-Initiation | 0.8914092 | 112.285714 | 384.00 | -1581.667064 | 1806.238493 | 21 | 1.0000000 |
| Processing of Capped Intronless Pre-mRNA | 0.8950948 | 199.500000 | 831.00 | -3497.713546 | 3896.713546 | 6 | 1.0000000 |
| Signaling by NOTCH4 | 0.8965638 | 119.000000 | 478.00 | -1777.134697 | 2015.134697 | 19 | 1.0000000 |
| FOXO-mediated transcription of cell death genes | 0.8966510 | 159.125000 | 874.00 | -2634.562737 | 2952.812737 | 8 | 1.0000000 |
| Intrinsic Pathway for Apoptosis | 0.9035081 | 110.888889 | -563.00 | -1790.362540 | 2012.140318 | 18 | 1.0000000 |
| DNA Damage/Telomere Stress Induced Senescence | 0.9035534 | -186.285714 | 384.00 | -3792.824006 | 3420.252578 | 7 | 1.0000000 |
| Defective homologous recombination repair (HRR) due to BRCA2 loss of function | 0.9067145 | -109.800000 | 428.00 | -2552.855467 | 2333.255467 | 5 | 1.0000000 |
| Diseases of DNA Double-Strand Break Repair | 0.9067145 | -109.800000 | 428.00 | -2552.855467 | 2333.255467 | 5 | 1.0000000 |
| Homologous DNA Pairing and Strand Exchange | 0.9067145 | -109.800000 | 428.00 | -2552.855467 | 2333.255467 | 5 | 1.0000000 |
| Impaired BRCA2 binding to RAD51 | 0.9067145 | -109.800000 | 428.00 | -2552.855467 | 2333.255467 | 5 | 1.0000000 |
| Presynaptic phase of homologous DNA pairing and strand exchange | 0.9067145 | -109.800000 | 428.00 | -2552.855467 | 2333.255467 | 5 | 1.0000000 |
| CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde | 0.9075006 | -102.400000 | -442.00 | -2400.293153 | 2195.493153 | 5 | 1.0000000 |
| Programmed Cell Death | 0.9100750 | -60.937500 | -70.50 | -1140.515535 | 1018.640535 | 48 | 1.0000000 |
| DNA strand elongation | 0.9105208 | 114.000000 | 443.00 | -2067.928149 | 2295.928149 | 12 | 1.0000000 |
| FCERI mediated MAPK activation | 0.9114540 | 86.066667 | -488.00 | -1544.161984 | 1716.295318 | 15 | 1.0000000 |
| Noncanonical activation of NOTCH3 | 0.9138862 | -216.600000 | 478.00 | -5439.830890 | 5006.630890 | 5 | 1.0000000 |
| Mitochondrial biogenesis | 0.9163621 | -62.982759 | -339.00 | -1280.449265 | 1154.483748 | 29 | 1.0000000 |
| Cobalamin (Cbl, vitamin B12) transport and metabolism | 0.9195939 | 138.000000 | -417.00 | -2980.375904 | 3256.375904 | 8 | 1.0000000 |
| Lagging Strand Synthesis | 0.9207085 | -139.333333 | -1050.50 | -3561.281257 | 3282.614590 | 6 | 1.0000000 |
| FOXO-mediated transcription | 0.9216490 | 66.230769 | 274.00 | -1306.675546 | 1439.137085 | 26 | 1.0000000 |
| Early Phase of HIV Life Cycle | 0.9222128 | -206.200000 | 1257.00 | -5713.701364 | 5301.301364 | 5 | 1.0000000 |
| Constitutive Signaling by EGFRvIII | 0.9222980 | 173.500000 | 34.50 | -4175.106358 | 4522.106358 | 6 | 1.0000000 |
| Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants | 0.9222980 | 173.500000 | 34.50 | -4175.106358 | 4522.106358 | 6 | 1.0000000 |
| Signaling by EGFRvIII in Cancer | 0.9222980 | 173.500000 | 34.50 | -4175.106358 | 4522.106358 | 6 | 1.0000000 |
| Signaling by Ligand-Responsive EGFR Variants in Cancer | 0.9222980 | 173.500000 | 34.50 | -4175.106358 | 4522.106358 | 6 | 1.0000000 |
| DNA Replication | 0.9244234 | -65.964286 | 264.50 | -1479.461929 | 1347.533358 | 28 | 1.0000000 |
| Metabolism of porphyrins | 0.9251346 | 209.800000 | 2242.00 | -5613.525084 | 6033.125084 | 5 | 1.0000000 |
| Synthesis of glycosylphosphatidylinositol (GPI) | 0.9254751 | 176.600000 | -1401.00 | -4747.691376 | 5100.891376 | 5 | 1.0000000 |
| Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template | 0.9257753 | 131.400000 | -813.00 | -3547.421573 | 3810.221573 | 5 | 1.0000000 |
| Hedgehog ligand biogenesis | 0.9265324 | -134.000000 | 145.00 | -3381.399819 | 3113.399819 | 9 | 1.0000000 |
| Hh mutants abrogate ligand secretion | 0.9265324 | -134.000000 | 145.00 | -3381.399819 | 3113.399819 | 9 | 1.0000000 |
| MicroRNA (miRNA) biogenesis | 0.9313532 | -175.500000 | -1370.50 | -5156.773886 | 4805.773886 | 6 | 1.0000000 |
| GABA receptor activation | 0.9341703 | -93.916667 | -617.00 | -2539.923313 | 2352.089979 | 12 | 1.0000000 |
| Formation of TC-NER Pre-Incision Complex | 0.9345385 | -98.700000 | -299.50 | -2742.211990 | 2544.811990 | 10 | 1.0000000 |
| Gluconeogenesis | 0.9349928 | 124.500000 | 661.00 | -3357.751700 | 3606.751700 | 8 | 1.0000000 |
| Gap-filling DNA repair synthesis and ligation in TC-NER | 0.9358236 | -91.583333 | -1426.50 | -2538.423451 | 2355.256784 | 12 | 1.0000000 |
| E3 ubiquitin ligases ubiquitinate target proteins | 0.9365259 | -109.636364 | 1262.00 | -3101.007412 | 2881.734684 | 11 | 1.0000000 |
| Formation of Incision Complex in GG-NER | 0.9384197 | -83.800000 | 258.00 | -2470.063034 | 2302.463034 | 10 | 1.0000000 |
| ER-Phagosome pathway | 0.9396502 | 103.400000 | 1348.50 | -2901.162217 | 3107.962217 | 10 | 1.0000000 |
| FBXL7 down-regulates AURKA during mitotic entry and in early mitosis | 0.9398667 | -101.875000 | 386.50 | -3182.866018 | 2979.116018 | 8 | 1.0000000 |
| Aggrephagy | 0.9413975 | -198.200000 | -1575.00 | -7231.910560 | 6835.510560 | 5 | 1.0000000 |
| Post-translational modification: synthesis of GPI-anchored proteins | 0.9424563 | -73.714286 | -301.50 | -2237.709560 | 2090.280989 | 14 | 1.0000000 |
| Surfactant metabolism | 0.9437437 | -154.000000 | -320.00 | -5847.645965 | 5539.645965 | 5 | 1.0000000 |
| tRNA processing | 0.9439105 | -52.937500 | 62.50 | -1592.543668 | 1486.668668 | 24 | 1.0000000 |
| Carboxyterminal post-translational modifications of tubulin | 0.9442850 | 99.571429 | 2321.00 | -3244.366375 | 3443.509232 | 7 | 1.0000000 |
| Senescence-Associated Secretory Phenotype (SASP) | 0.9452298 | -72.400000 | 302.00 | -2292.591509 | 2147.791509 | 15 | 1.0000000 |
| Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | 0.9469357 | 142.000000 | -595.50 | -5075.422591 | 5359.422591 | 6 | 1.0000000 |
| Nonsense-Mediated Decay (NMD) | 0.9469357 | 142.000000 | -595.50 | -5075.422591 | 5359.422591 | 6 | 1.0000000 |
| Mitophagy | 0.9474313 | 96.857143 | 372.00 | -3351.004788 | 3544.719074 | 7 | 1.0000000 |
| RNA Polymerase III Transcription Initiation From Type 1 Promoter | 0.9476232 | -135.200000 | -960.00 | -5504.849241 | 5234.449241 | 5 | 1.0000000 |
| RNA Polymerase III Transcription Initiation From Type 2 Promoter | 0.9476232 | -135.200000 | -960.00 | -5504.849241 | 5234.449241 | 5 | 1.0000000 |
| FGFR2 mutant receptor activation | 0.9497368 | -119.666667 | -20.50 | -4762.010718 | 4522.677385 | 6 | 1.0000000 |
| MyD88-independent TLR4 cascade | 0.9531120 | 29.739130 | 243.00 | -983.278512 | 1042.756773 | 46 | 1.0000000 |
| TRIF(TICAM1)-mediated TLR4 signaling | 0.9531120 | 29.739130 | 243.00 | -983.278512 | 1042.756773 | 46 | 1.0000000 |
| Uptake and actions of bacterial toxins | 0.9571451 | -62.777778 | -660.00 | -2673.846554 | 2548.290999 | 9 | 1.0000000 |
| Long-term potentiation | 0.9587815 | 45.166667 | -458.50 | -2092.128645 | 2182.461978 | 6 | 1.0000000 |
| Unblocking of NMDA receptors, glutamate binding and activation | 0.9587815 | 45.166667 | -458.50 | -2092.128645 | 2182.461978 | 6 | 1.0000000 |
| The citric acid (TCA) cycle and respiratory electron transport | 0.9589795 | 29.717949 | -552.00 | -1132.256874 | 1191.692771 | 39 | 1.0000000 |
| IRAK1 recruits IKK complex | 0.9593926 | 80.375000 | 950.00 | -3521.497620 | 3682.247620 | 8 | 1.0000000 |
| IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation | 0.9593926 | 80.375000 | 950.00 | -3521.497620 | 3682.247620 | 8 | 1.0000000 |
| CD209 (DC-SIGN) signaling | 0.9594148 | -51.727273 | 559.00 | -2260.637856 | 2157.183310 | 11 | 1.0000000 |
| Phase 0 - rapid depolarisation | 0.9610735 | 53.222222 | -536.00 | -2384.053119 | 2490.497563 | 9 | 1.0000000 |
| Cross-presentation of soluble exogenous antigens (endosomes) | 0.9618756 | -78.285714 | 145.00 | -3922.554102 | 3765.982674 | 7 | 1.0000000 |
| Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha | 0.9626760 | -57.363636 | 145.00 | -2721.202235 | 2606.474962 | 11 | 1.0000000 |
| NOTCH3 Intracellular Domain Regulates Transcription | 0.9630435 | -67.857143 | 1518.00 | -3505.431715 | 3369.717429 | 7 | 1.0000000 |
| Selective autophagy | 0.9641617 | -42.388889 | -405.50 | -2003.699325 | 1918.921547 | 18 | 1.0000000 |
| mRNA Splicing - Minor Pathway | 0.9657876 | -47.000000 | 791.00 | -2428.240593 | 2334.240593 | 11 | 1.0000000 |
| Glyoxylate metabolism and glycine degradation | 0.9660824 | 42.000000 | -142.50 | -2211.752965 | 2295.752965 | 8 | 1.0000000 |
| RND2 GTPase cycle | 0.9664276 | 56.909091 | -2280.00 | -2881.375008 | 2995.193190 | 11 | 1.0000000 |
| Processing of DNA double-strand break ends | 0.9685064 | -38.666667 | -185.50 | -2145.769270 | 2068.435936 | 12 | 1.0000000 |
| Activation of NF-kappaB in B cells | 0.9702539 | -38.538461 | 1480.00 | -2243.868701 | 2166.791778 | 13 | 1.0000000 |
| CREB phosphorylation | 0.9769060 | -56.200000 | 559.00 | -5122.618153 | 5010.218153 | 5 | 1.0000000 |
| G alpha (z) signalling events | 0.9823465 | -32.100000 | -384.50 | -3224.049599 | 3159.849599 | 10 | 1.0000000 |
| MyD88 cascade initiated on plasma membrane | 0.9824958 | 10.860465 | 280.00 | -982.174661 | 1003.895591 | 43 | 1.0000000 |
| Toll Like Receptor 10 (TLR10) Cascade | 0.9824958 | 10.860465 | 280.00 | -982.174661 | 1003.895591 | 43 | 1.0000000 |
| Toll Like Receptor 5 (TLR5) Cascade | 0.9824958 | 10.860465 | 280.00 | -982.174661 | 1003.895591 | 43 | 1.0000000 |
| Signaling by FGFR2 in disease | 0.9861717 | 20.800000 | 34.50 | -2619.730974 | 2661.330974 | 10 | 1.0000000 |
| ROS and RNS production in phagocytes | 0.9868498 | -22.666667 | 139.00 | -3096.598002 | 3051.264669 | 9 | 1.0000000 |
| Regulation of glycolysis by fructose 2,6-bisphosphate metabolism | 0.9883165 | -28.400000 | -452.00 | -5089.844090 | 5033.044090 | 5 | 1.0000000 |
| C-type lectin receptors (CLRs) | 0.9900772 | -7.909091 | 559.00 | -1293.214197 | 1277.396015 | 33 | 1.0000000 |
| HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA) | 0.9905469 | -9.117647 | 384.00 | -1615.224404 | 1596.989110 | 17 | 1.0000000 |
| Defects in vitamin and cofactor metabolism | 0.9933036 | 9.800000 | 195.50 | -2559.407862 | 2579.007862 | 10 | 1.0000000 |
| MyD88:MAL(TIRAP) cascade initiated on plasma membrane | 0.9943101 | 3.577778 | 280.00 | -1001.802583 | 1008.958139 | 45 | 1.0000000 |
| Toll Like Receptor 2 (TLR2) Cascade | 0.9943101 | 3.577778 | 280.00 | -1001.802583 | 1008.958139 | 45 | 1.0000000 |
| Toll Like Receptor TLR1:TLR2 Cascade | 0.9943101 | 3.577778 | 280.00 | -1001.802583 | 1008.958139 | 45 | 1.0000000 |
| Toll Like Receptor TLR6:TLR2 Cascade | 0.9943101 | 3.577778 | 280.00 | -1001.802583 | 1008.958139 | 45 | 1.0000000 |
| G2/M Checkpoints | 0.9959985 | 3.521739 | 384.00 | -1436.348443 | 1443.391922 | 23 | 1.0000000 |
Now we can take a look at the results
Top significant results.
Take this table with a grain of salt because small p-values don’t always mean a biologically meaningful observation. For example, some of these are very large sets of genes with only a slight change.
head(out,20) %>% kbl(caption = "Top significant pathways") %>%
kable_paper("hover", full_width = F)| p-value | mean | median | lower conf interval | upper conf interval | numgenes | padj | |
|---|---|---|---|---|---|---|---|
| Signal Transduction | 0.00e+00 | 1434.6853 | 2135.50 | 1152.6641 | 1716.706 | 626 | 0.0000000 |
| Post-translational protein modification | 0.00e+00 | 1297.8443 | 2105.50 | 930.7803 | 1664.908 | 366 | 0.0000000 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 0.00e+00 | 1805.3382 | 2904.00 | 1302.8607 | 2307.816 | 204 | 0.0000000 |
| Signaling by Rho GTPases | 0.00e+00 | 1735.7194 | 2777.00 | 1218.9158 | 2252.523 | 196 | 0.0000004 |
| Metabolism | 0.00e+00 | 1062.2299 | 1515.00 | 735.4435 | 1389.016 | 461 | 0.0000005 |
| Metabolism of proteins | 0.00e+00 | 1099.8174 | 1845.25 | 760.9978 | 1438.637 | 438 | 0.0000005 |
| Disease | 0.00e+00 | 1009.9938 | 1254.00 | 659.0021 | 1360.985 | 402 | 0.0000327 |
| Metabolism of lipids | 1.00e-07 | 1496.6772 | 2451.00 | 974.8450 | 2018.509 | 189 | 0.0000628 |
| Hemostasis | 2.00e-07 | 1762.1197 | 3011.50 | 1131.4611 | 2392.778 | 142 | 0.0001725 |
| Post-translational protein phosphorylation | 4.00e-07 | 3920.5909 | 5015.00 | 2787.7339 | 5053.448 | 22 | 0.0004774 |
| Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | 5.00e-07 | 3682.5833 | 4799.50 | 2583.9066 | 4781.260 | 24 | 0.0005053 |
| RHO GTPase cycle | 1.90e-06 | 1605.8456 | 2479.50 | 968.7158 | 2242.975 | 136 | 0.0020742 |
| Immune System | 2.30e-06 | 865.0878 | 1078.00 | 509.8515 | 1220.324 | 433 | 0.0025878 |
| RHOA GTPase cycle | 4.10e-06 | 2580.1522 | 3678.50 | 1589.0310 | 3571.273 | 46 | 0.0045121 |
| Vesicle-mediated transport | 6.10e-06 | 1208.1650 | 1664.00 | 695.5375 | 1720.792 | 197 | 0.0067981 |
| G alpha (12/13) signalling events | 1.00e-05 | 3472.0000 | 4896.00 | 2195.7617 | 4748.238 | 24 | 0.0110150 |
| Metabolism of steroids | 1.03e-05 | 2737.2778 | 3653.00 | 1657.5759 | 3816.980 | 36 | 0.0113625 |
| Synthesis of PIPs at the early endosome membrane | 1.11e-05 | 4014.5000 | 4129.00 | 3154.2235 | 4874.776 | 8 | 0.0122884 |
| Membrane Trafficking | 1.28e-05 | 1169.9768 | 1594.00 | 654.9165 | 1685.037 | 194 | 0.0140567 |
| Diseases of signal transduction by growth factor receptors and second messengers | 1.28e-05 | 1458.4111 | 2599.00 | 821.8805 | 2094.942 | 135 | 0.0141259 |
Biggest effect size (upregulated) with FDR<0.05, ranked by median.
sigup <- subset(out,padj<0.05 & median>0)
nrow(sigup)## [1] 23upreg <- head(sigup[order(-sigup$median),],20)
upreg %>% kbl(caption = "Top upregulated pathways") %>%
kable_paper("hover", full_width = F)| p-value | mean | median | lower conf interval | upper conf interval | numgenes | padj | |
|---|---|---|---|---|---|---|---|
| Post-translational protein phosphorylation | 4.00e-07 | 3920.591 | 5015.00 | 2787.7339 | 5053.448 | 22 | 0.0004774 |
| G alpha (12/13) signalling events | 1.00e-05 | 3472.000 | 4896.00 | 2195.7617 | 4748.238 | 24 | 0.0110150 |
| Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | 5.00e-07 | 3682.583 | 4799.50 | 2583.9066 | 4781.260 | 24 | 0.0005053 |
| Synthesis of PIPs at the early endosome membrane | 1.11e-05 | 4014.500 | 4129.00 | 3154.2235 | 4874.776 | 8 | 0.0122884 |
| RHOA GTPase cycle | 4.10e-06 | 2580.152 | 3678.50 | 1589.0310 | 3571.273 | 46 | 0.0045121 |
| Metabolism of steroids | 1.03e-05 | 2737.278 | 3653.00 | 1657.5759 | 3816.980 | 36 | 0.0113625 |
| Resolution of Sister Chromatid Cohesion | 3.40e-05 | 2709.875 | 3617.00 | 1567.7920 | 3851.958 | 32 | 0.0373665 |
| RHO GTPases Activate Formins | 1.46e-05 | 2563.868 | 3614.00 | 1522.6560 | 3605.081 | 38 | 0.0160397 |
| Hemostasis | 2.00e-07 | 1762.120 | 3011.50 | 1131.4611 | 2392.778 | 142 | 0.0001725 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 0.00e+00 | 1805.338 | 2904.00 | 1302.8607 | 2307.816 | 204 | 0.0000000 |
| Signaling by Rho GTPases | 0.00e+00 | 1735.719 | 2777.00 | 1218.9158 | 2252.523 | 196 | 0.0000004 |
| Diseases of signal transduction by growth factor receptors and second messengers | 1.28e-05 | 1458.411 | 2599.00 | 821.8805 | 2094.942 | 135 | 0.0141259 |
| RHO GTPase cycle | 1.90e-06 | 1605.846 | 2479.50 | 968.7158 | 2242.975 | 136 | 0.0020742 |
| Metabolism of lipids | 1.00e-07 | 1496.677 | 2451.00 | 974.8450 | 2018.509 | 189 | 0.0000628 |
| RHO GTPase Effectors | 1.84e-05 | 1769.634 | 2393.00 | 996.3700 | 2542.898 | 82 | 0.0202084 |
| Signal Transduction | 0.00e+00 | 1434.685 | 2135.50 | 1152.6641 | 1716.706 | 626 | 0.0000000 |
| Post-translational protein modification | 0.00e+00 | 1297.844 | 2105.50 | 930.7803 | 1664.908 | 366 | 0.0000000 |
| Metabolism of proteins | 0.00e+00 | 1099.817 | 1845.25 | 760.9978 | 1438.637 | 438 | 0.0000005 |
| Vesicle-mediated transport | 6.10e-06 | 1208.165 | 1664.00 | 695.5375 | 1720.792 | 197 | 0.0067981 |
| Membrane Trafficking | 1.28e-05 | 1169.977 | 1594.00 | 654.9165 | 1685.037 | 194 | 0.0140567 |
Biggest effect size (downregulated) with FDR<0.05, ranked by median.
sigdn <- subset(out,padj<0.05 & median<0)
nrow(sigdn)## [1] 0dnreg <- head(sigdn[order(sigdn$median),],20)
dnreg %>% kbl(caption = "Top downregulated pathways") %>%
kable_paper("hover", full_width = F)| p-value | mean | median | lower conf interval | upper conf interval | numgenes | padj |
|---|---|---|---|---|---|---|
There were no downregulated sets that met the FDR threshold.
Take a look at a few top sets.
First with some histograms.
gsnames <- head(rownames(upreg),10)
for (gsname in gsnames ) {
gs <- genesets[[gsname]]
z <- y[names(y) %in% gs]
hist(z,xlim=c(MIN,MAX),breaks=10,xlab="generank",main=gsname)
}
for (gsname in gsnames ) {
gs <- genesets[[gsname]]
print(gsname)
z <- y[names(y) %in% gs]
z <- z[order(-z)]
print(z)
}## [1] "Post-translational protein phosphorylation"
## FBN1 CALU PCSK9 FN1 TGOLN2 PDIA6 FSTL1 CSF1
## 6271 6127 6126 6059 6027 5741 5723 5624
## QSOX1 DNAJC3 WFS1 SDC2 FUCA2 TMEM132A MXRA8 CHRDL1
## 5515 5366 5183 4847 4752 4297 4141 3176
## APLP2 VWA1 MFGE8 MGAT4A TF PRSS23
## 1528 1474 1259 341 -988 -2336
## [1] "G alpha (12/13) signalling events"
## ROCK2 KALRN GNA13 ARHGEF12 VAV2 ARHGEF5 FGD3 ABR
## 6006 5996 5980 5964 5890 5849 5770 5764
## ADRA1D MCF2L ARHGEF2 AKAP13 ARHGEF10 GNB1 RHOB ARHGEF7
## 5738 5432 5180 5098 4694 4308 3944 3097
## ARHGEF10L SOS2 ITSN1 ARHGEF39 ROCK1 PLXNB1 ARHGEF9 RHOC
## 3088 2448 1504 60 -1068 -1211 -3034 -3169
## [1] "Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)"
## FBN1 CALU PCSK9 FN1 TGOLN2 PDIA6 FSTL1 CSF1
## 6271 6127 6126 6059 6027 5741 5723 5624
## QSOX1 DNAJC3 WFS1 SDC2 FUCA2 TMEM132A MXRA8 CHRDL1
## 5515 5366 5183 4847 4752 4297 4141 3176
## PAPPA APLP2 VWA1 MFGE8 MGAT4A IGF1 TF PRSS23
## 2416 1528 1474 1259 341 -287 -988 -2336
## [1] "Synthesis of PIPs at the early endosome membrane"
## MTMR4 PI4K2B MTMR10 INPP4A PI4K2A MTM1 MTMR2 MTMR12
## 5500 4785 4691 4681 3577 3263 2967 2652
## [1] "RHOA GTPase cycle"
## IQGAP1 ROCK2 KALRN ARHGEF12 VAV2 ARHGAP5 ARHGEF5 ABR
## 6065 6006 5996 5964 5890 5855 5849 5764
## LMAN1 PLD1 ARHGAP28 MCF2L CIT STARD13 ARHGEF2 AKAP13
## 5749 5554 5461 5432 5315 5209 5180 5098
## ARHGEF10 TEX2 TMPO VAPB PLEKHG3 ARHGAP31 PGRMC2 STK10
## 4694 4434 4167 4063 3936 3759 3710 3647
## ARHGEF7 ARHGEF10L YKT6 ARHGAP32 FAF2 FMNL3 PKN3 ARHGAP22
## 3097 3088 2857 2415 2196 2048 1962 1287
## ARHGAP42 STOM DIAPH1 ARHGAP26 MYO9A DDRGK1 ROCK1 BCR
## 989 953 845 709 562 349 -1068 -2068
## ARHGAP1 FAM13A OPHN1 VANGL1 ARHGAP24 FLOT2
## -2481 -3315 -3323 -4247 -5288 -5677
## [1] "Metabolism of steroids"
## DHCR24 STARD4 HMGCS1 SEC24D MVD ACACA ELOVL6 FASN
## 6230.0 6221.0 6169.0 6115.0 5899.0 5861.0 5654.0 5568.0
## OSBP LDLRAP1 TSPO MED1 VDR GPAM TBL1XR1 SP1
## 5475.0 5324.0 5195.0 5193.0 5122.0 4860.0 4676.0 4542.0
## STARD5 STARD3NL HSD17B12 CREBBP SEC24C PTGIS NFYB HSD3B7
## 4320.0 3970.0 3336.0 3281.0 3117.0 2743.0 2517.0 2028.0
## CYP27B1 TBL1X NFYA OSBPL3 EBP PIAS4 ACACB LRP2
## 1635.0 454.5 -10.0 -72.0 -352.0 -1027.0 -1111.0 -1920.0
## HSD3B2 STARD3 UBE2I CHD9
## -1983.5 -2274.0 -3559.0 -4655.0
## [1] "Resolution of Sister Chromatid Cohesion"
## TAOK1 CENPF DYNC1LI2 PAFAH1B1 AHCTF1 DYNLL2 SEH1L RCC2
## 6171 6067 5904 5827 5629 5609 5124 5004
## RANGAP1 CKAP5 PPP2R5E PDS5A CLASP1 CENPA NUF2 KIF2C
## 4814 4719 4556 4377 4236 3946 3877 3677
## STAG2 AURKB NSL1 ZWILCH RAD21 PPP2R5C CENPO MAPRE1
## 3557 3535 2997 2951 2619 2060 1592 1588
## CLASP2 NUP37 CENPP CENPM PPP2CB BUB3 PPP2R5D ITGB3BP
## 1445 725 470 431 -2156 -3654 -5191 -5790
## [1] "RHO GTPases Activate Formins"
## ITGB1 TAOK1 CENPF DYNC1LI2 PAFAH1B1 AHCTF1 DYNLL2 SEH1L
## 6192 6171 6067 5904 5827 5629 5609 5124
## RCC2 RANGAP1 CKAP5 PPP2R5E CLASP1 DIAPH2 CENPA RHOB
## 5004 4814 4719 4556 4236 4096 3946 3944
## DVL1 NUF2 KIF2C SRF AURKB NSL1 ZWILCH PPP2R5C
## 3927 3877 3677 3551 3535 2997 2951 2060
## FMNL3 CENPO MAPRE1 CLASP2 DIAPH1 NUP37 CENPP CENPM
## 2048 1592 1588 1445 845 725 470 431
## SRGAP2 PPP2CB RHOC BUB3 PPP2R5D ITGB3BP
## -170 -2156 -3169 -3654 -5191 -5790
## [1] "Hemostasis"
## ITGAV THBD ITGB1 DOCK5 ATP2B4 RAPGEF3 SDC1 KIF1B
## 6243 6198 6192 6188 6185 6178 6170 6156
## CRK CALU FN1 KIF21B PDPK1 KLC1 KIF26B GNA13
## 6137 6127 6059 6041 6037 6002 6000 5980
## ITPR3 PTPN11 GATA2 LRP8 SLC7A5 VAV2 GNAI3 SLC16A3
## 5970 5960 5948 5921 5909 5890 5700 5620
## L1CAM PIK3CB QSOX1 PRKAR2B ATP2A2 MAFF CBX5 ANGPT4
## 5612 5563 5515 5330 5314 5280 5181 5125
## CD109 MFN2 KIF13B AKAP10 PRKAR1A SDC2 NHLRC2 MAFG
## 5104 5032 4988 4952 4943 4847 4841 4824
## PSAP RCOR1 ALDOA ITGA2 CD99L2 PDE10A PROS1 PPP2R5E
## 4820 4807 4689 4673 4665 4619 4561 4556
## GNB1 ADRA2A DOCK9 MFN1 ITGA3 PRKG1 RHOB DGKH
## 4308 4291 4201 4170 4078 4024 3944 3866
## DAGLA MGLL TLN1 VTI1B KIF2C KRAS VCL DGKD
## 3806 3787 3749 3694 3677 3672 3570 3497
## DOCK8 SPN ABCC4 ORAI2 SLC16A1 KIF5C CD44 PRKAR2A
## 3471 3444 3342 3340 3329 3200 3146 2877
## YWHAZ CABLES1 PIK3R5 CD47 CHID1 KLC2 ANXA5 KIF1A
## 2698 2541 2361 2283 2270 2268 2183 2109
## PPP2R5C PLCG2 EHD1 CEACAM1 STXBP3 APLP2 LGALS3BP NRAS
## 2060 2021 1927 1916 1664 1528 1509 1317
## PRKCQ PICK1 EHD2 ITPK1 KIF5A CDK2 GNA11 PLEK
## 1178 990 844 691 420 384 318 303
## MAPK1 PIK3R3 IRF1 ENDOD1 IGF1 PRKACB CD63 ANGPT2
## 206 -118 -140 -190 -287 -452 -477 -480
## VPS45 TF GUCY1A2 PLCG1 CALM1 PRKCE PPP2CB PTPN1
## -560 -988 -1071 -1248 -1615 -1947 -2156 -2279
## PHF21A CD84 SH2B3 ATP1B3 KCNMB4 CABLES2 GRB2 HMG20B
## -2333 -2516 -2523 -2660 -2735 -2782 -2815 -3061
## IRF2 OLA1 MAPK14 PRKCA SERPINA3 LYN KIF3A DGKZ
## -3273 -3287 -3621 -3635 -3963 -4326 -4375 -4427
## PRKCD CSK P2RX6 EHD3 PPP2R5D GNAI2 FGB GATA6
## -4447 -4487 -4664 -4687 -5191 -5304 -5416 -5438
## PPIL2 ORAI1 F11R SLC8A1 RHOG PPBP
## -5470 -5774 -5896 -5928 -5930 -5931
## [1] "Signaling by Rho GTPases, Miro GTPases and RHOBTB3"
## DST ITGB1 DOCK5 TAOK1 SRGAP3 SH3PXD2A ABL2 USP9X
## 6226 6192 6188 6171 6149 6116 6105 6070
## CENPF IQGAP1 CTNNB1 PDPK1 ROCK2 KLC1 KALRN GNA13
## 6067 6065 6060 6037 6006 6002 5996 5980
## UACA ARHGEF12 MYH9 DYNC1LI2 VAV2 ARHGAP5 ARHGEF5 CDC42BPA
## 5974 5964 5945 5904 5890 5855 5849 5848
## CPD TRAK2 PAFAH1B1 PLXNA1 FGD3 ABR LMAN1 ACTR2
## 5835 5832 5827 5785 5770 5764 5749 5663
## AHCTF1 DYNLL2 ANKFY1 PLD1 PEAK1 FARP2 ARHGAP28 SLC4A7
## 5629 5609 5562 5554 5519 5484 5461 5439
## MCF2L CIT ACTR3 STARD13 ARHGEF2 TWF1 SEH1L WDR81
## 5432 5315 5311 5209 5180 5154 5124 5111
## AKAP13 MFN2 RCC2 RNF20 KCTD3 RANGAP1 PRC1 CDC42BPB
## 5098 5032 5004 4865 4864 4814 4805 4782
## CKAP5 ARHGEF10 TRAK1 PPP2R5E CTTN MYO6 ALDH3A2 TEX2
## 4719 4694 4636 4556 4510 4488 4449 4434
## NCKAP1 NF2 JAG1 CLASP1 RAP1GDS1 DOCK9 MFN1 TMPO
## 4389 4378 4274 4236 4214 4201 4170 4167
## DIAPH2 VAPB ALS2 MYLK RHOBTB3 CENPA RHOB PLEKHG3
## 4096 4063 4006 3990 3950 3946 3944 3936
## DVL1 PAK2 NUF2 LEMD3 PPP1R12B ARHGAP31 RND3 PGRMC2
## 3927 3888 3877 3843 3838 3759 3745 3710
## KIF2C STK10 SRF AURKB CDC42SE2 MTR DOCK8 RRAS2
## 3677 3647 3551 3535 3499 3494 3471 3323
## ARHGEF7 ARHGEF10L RAPGEF1 NSL1 STAM2 ZWILCH YKT6 CCT7
## 3097 3088 3016 2997 2955 2951 2857 2856
## YWHAZ MAPK11 RHOBTB2 SOS2 ARHGAP32 SPATA13 KLC2 FAF2
## 2698 2518 2511 2448 2415 2372 2268 2196
## AR RHOT1 PPP2R5C FMNL3 ARFGAP2 PKN3 MSI2 CENPO
## 2106 2105 2060 2048 1979 1962 1790 1592
## MAPRE1 PLXND1 ITSN1 CLASP2 ARHGAP22 ZNF512B ARHGAP42 STOM
## 1588 1518 1504 1445 1287 1177 989 953
## STEAP3 DIAPH1 NUP37 ARHGAP26 ABI2 MYO9A CENPP CENPM
## 948 845 725 709 566 562 470 431
## KIF5A PPP1R12A DDRGK1 CCDC88A MAPK1 ARHGEF39 PIK3R3 SRGAP2
## 420 415 349 345 206 60 -118 -170
## WASF2 TAOK3 PAK1 LIMK2 TRA2B CTNNA1 DBN1 ARHGAP17
## -229 -374 -488 -510 -581 -734 -875 -891
## WASL CDC42EP3 ROCK1 PLXNB1 CALM1 YWHAB RHOF LIMK1
## -908 -1000 -1068 -1211 -1615 -1651 -1768 -1811
## PIN1 RHOT2 CHN1 BCR WHAMM WIPF2 PPP2CB RND2
## -1821 -1851 -2067 -2068 -2115 -2128 -2156 -2280
## ARHGAP1 PARD6B GRB2 VANGL2 ARHGEF9 RHOC FAM13A OPHN1
## -2481 -2674 -2815 -3005 -3034 -3169 -3315 -3323
## RHOU PHIP MAPK14 PRKCA BUB3 NCKIPSD CUL3 CDC42EP4
## -3475 -3530 -3621 -3635 -3654 -3918 -3930 -4245
## VANGL1 VRK2 PKP4 PRKCD CSK TRIP10 SH3BP1 NSFL1C
## -4247 -4289 -4313 -4447 -4487 -4589 -4677 -4716
## RALBP1 GIT1 LRRC1 PAK3 PPP2R5D TPM3 YWHAE ARHGAP24
## -4767 -4835 -4939 -5107 -5191 -5199 -5242 -5288
## PLD2 FLOT2 ITGB3BP RHOG
## -5537 -5677 -5790 -5930Now take a look at the downregulated pathways anyway.
sigdn <- subset(out,`p-value`<0.05 & median<0)
nrow(sigdn)## [1] 20dnreg <- head(sigdn[order(sigdn$median),],20)
dnreg %>% kbl(caption = "Top downregulated pathways") %>%
kable_paper("hover", full_width = F)| p-value | mean | median | lower conf interval | upper conf interval | numgenes | padj | |
|---|---|---|---|---|---|---|---|
| Cell recruitment (pro-inflammatory response) | 0.0475173 | -3653.200 | -4900.0 | -7241.805 | -64.595413 | 5 | 1.0000000 |
| Purinergic signaling in leishmaniasis infection | 0.0475173 | -3653.200 | -4900.0 | -7241.805 | -64.595413 | 5 | 1.0000000 |
| The NLRP3 inflammasome | 0.0485793 | -3582.400 | -4546.0 | -7128.735 | -36.065393 | 5 | 1.0000000 |
| Inflammasomes | 0.0498710 | -2666.429 | -4393.0 | -5330.786 | -2.071572 | 7 | 1.0000000 |
| Inhibition of DNA recombination at telomere | 0.0008383 | -4252.200 | -4388.0 | -5561.740 | -2942.660182 | 5 | 0.8953187 |
| PI3K events in ERBB2 signaling | 0.0010483 | -4078.000 | -4261.0 | -5409.291 | -2746.709193 | 5 | 1.0000000 |
| ERBB2 Regulates Cell Motility | 0.0391846 | -3346.000 | -4261.0 | -6422.719 | -269.281383 | 5 | 1.0000000 |
| SHC1 events in ERBB2 signaling | 0.0212520 | -2543.000 | -3431.0 | -4609.133 | -476.866874 | 10 | 1.0000000 |
| Mitochondrial translation termination | 0.0041988 | -2484.812 | -3206.5 | -4055.847 | -913.777898 | 16 | 1.0000000 |
| Mitochondrial translation initiation | 0.0092694 | -2299.467 | -3120.0 | -3935.178 | -663.755766 | 15 | 1.0000000 |
| Mitochondrial translation | 0.0181638 | -1967.944 | -2858.0 | -3556.593 | -379.295540 | 18 | 1.0000000 |
| Formation of the Early Elongation Complex | 0.0324127 | -2437.143 | -2855.0 | -4589.845 | -284.440958 | 7 | 1.0000000 |
| Formation of the HIV-1 Early Elongation Complex | 0.0324127 | -2437.143 | -2855.0 | -4589.845 | -284.440958 | 7 | 1.0000000 |
| RNA Pol II CTD phosphorylation and interaction with CE | 0.0399283 | -2279.857 | -2656.0 | -4414.327 | -145.387193 | 7 | 1.0000000 |
| RNA Pol II CTD phosphorylation and interaction with CE during HIV infection | 0.0399283 | -2279.857 | -2656.0 | -4414.327 | -145.387193 | 7 | 1.0000000 |
| mRNA Capping | 0.0399283 | -2279.857 | -2656.0 | -4414.327 | -145.387193 | 7 | 1.0000000 |
| Mitochondrial translation elongation | 0.0353292 | -1774.000 | -2596.0 | -3409.950 | -138.049751 | 17 | 1.0000000 |
| RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known | 0.0191950 | -2086.400 | -2415.0 | -3777.873 | -394.927234 | 15 | 1.0000000 |
| Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. | 0.0152564 | -1788.300 | -2390.5 | -3192.086 | -384.513981 | 20 | 1.0000000 |
| Respiratory electron transport | 0.0437250 | -1615.294 | -2041.0 | -3179.227 | -51.361110 | 17 | 1.0000000 |
Now some charts for those pathways.
gsnames <- head(rownames(dnreg),20)
for (gsname in gsnames ) {
gs <- genesets[[gsname]]
z <- y[names(y) %in% gs]
hist(z,xlim=c(MIN,MAX),breaks=10,xlab="generank",main=gsname)
}
for (gsname in gsnames ) {
gs <- genesets[[gsname]]
print(gsname)
z <- y[names(y) %in% gs]
z <- z[order(z)]
print(z)
}## [1] "Cell recruitment (pro-inflammatory response)"
## TXNIP SUGT1 ENTPD5 RELA NFKB1
## -5297 -5156 -4900 -4393 1480
## [1] "Purinergic signaling in leishmaniasis infection"
## TXNIP SUGT1 ENTPD5 RELA NFKB1
## -5297 -5156 -4900 -4393 1480
## [1] "The NLRP3 inflammasome"
## TXNIP SUGT1 PANX1 RELA NFKB1
## -5297 -5156 -4546 -4393 1480
## [1] "Inflammasomes"
## TXNIP SUGT1 PANX1 RELA BCL2L1 BCL2 NFKB1
## -5297 -5156 -4546 -4393 -1491 738 1480
## [1] "Inhibition of DNA recombination at telomere"
## TERF2 POLR2L POLR2D TERF2IP POLR2F
## -5487 -4956 -4388 -3575 -2855
## [1] "PI3K events in ERBB2 signaling"
## EGFR ERBB2 HBEGF NRG2 GRB2
## -5480 -4607 -4261 -3227 -2815
## [1] "ERBB2 Regulates Cell Motility"
## EGFR ERBB2 HBEGF NRG2 DIAPH1
## -5480 -4607 -4261 -3227 845
## [1] "SHC1 events in ERBB2 signaling"
## EGFR ERBB2 PRKCD HBEGF PRKCA NRG2 GRB2 PRKCE NRAS KRAS
## -5480 -4607 -4447 -4261 -3635 -3227 -2815 -1947 1317 3672
## [1] "Mitochondrial translation termination"
## GADD45GIP1 MRPS18A MRRF MRPS25 MRPL30 MRPS35 MRPL28
## -5924 -5632 -5265 -4930 -4025 -3998 -3739
## MRPS30 MRPL46 MRPS10 MRPL17 MRPL51 MRPS23 MRPL3
## -3293 -3120 -2596 -2164 -842 -191 -97
## MRPL19 MRPS6
## 474 5585
## [1] "Mitochondrial translation initiation"
## GADD45GIP1 MRPS18A MRPS25 MRPL30 MRPS35 MRPL28 MRPS30
## -5924 -5632 -4930 -4025 -3998 -3739 -3293
## MRPL46 MRPS10 MRPL17 MRPL51 MRPS23 MRPL3 MRPL19
## -3120 -2596 -2164 -842 -191 -97 474
## MRPS6
## 5585
## [1] "Mitochondrial translation"
## GADD45GIP1 MRPS18A MRRF MRPS25 MRPL30 MRPS35 MRPL28
## -5924 -5632 -5265 -4930 -4025 -3998 -3739
## MRPS30 MRPL46 MRPS10 MRPL17 MRPL51 MRPS23 MRPL3
## -3293 -3120 -2596 -2164 -842 -191 -97
## MRPL19 GFM1 TSFM MRPS6
## 474 644 3690 5585
## [1] "Formation of the Early Elongation Complex"
## POLR2L POLR2D SUPT4H1 POLR2F GTF2H5 ERCC2 CDK7
## -4956 -4388 -3158 -2855 -2656 -1046 1999
## [1] "Formation of the HIV-1 Early Elongation Complex"
## POLR2L POLR2D SUPT4H1 POLR2F GTF2H5 ERCC2 CDK7
## -4956 -4388 -3158 -2855 -2656 -1046 1999
## [1] "RNA Pol II CTD phosphorylation and interaction with CE"
## POLR2L POLR2D POLR2F GTF2H5 RNGTT ERCC2 CDK7
## -4956 -4388 -2855 -2656 -2057 -1046 1999
## [1] "RNA Pol II CTD phosphorylation and interaction with CE during HIV infection"
## POLR2L POLR2D POLR2F GTF2H5 RNGTT ERCC2 CDK7
## -4956 -4388 -2855 -2656 -2057 -1046 1999
## [1] "mRNA Capping"
## POLR2L POLR2D POLR2F GTF2H5 RNGTT ERCC2 CDK7
## -4956 -4388 -2855 -2656 -2057 -1046 1999
## [1] "Mitochondrial translation elongation"
## GADD45GIP1 MRPS18A MRPS25 MRPL30 MRPS35 MRPL28 MRPS30
## -5924 -5632 -4930 -4025 -3998 -3739 -3293
## MRPL46 MRPS10 MRPL17 MRPL51 MRPS23 MRPL3 MRPL19
## -3120 -2596 -2164 -842 -191 -97 474
## GFM1 TSFM MRPS6
## 644 3690 5585
## [1] "RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known"
## PHC2 SMARCD1 CBX2 SCMH1 SMARCE1 CBX6 RING1 RYBP SMARCC2 YAF2
## -5572 -4825 -4363 -4221 -3551 -3482 -3056 -2415 -2348 -2345
## ARID1A RNF2 CBX4 SMARCC1 PHC3
## -2044 -1924 -563 3897 5516
## [1] "Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins."
## MT-ATP6 NDUFB5 NDUFB9 NDUFA10 NDUFA4 COX7C COX4I1 UQCRC1
## -5906 -5280 -4944 -4876 -4525 -4273 -3985 -3399
## NDUFA7 SLC25A27 SDHC NDUFAF3 NDUFAF6 NDUFA2 PM20D1 SCO1
## -2982 -2740 -2041 -1722 -894 -575 340 912
## ETFA COX14 NUBPL TACO1
## 2138 2506 2854 3626
## [1] "Respiratory electron transport"
## NDUFB5 NDUFB9 NDUFA10 NDUFA4 COX7C COX4I1 UQCRC1 NDUFA7 SDHC NDUFAF3
## -5280 -4944 -4876 -4525 -4273 -3985 -3399 -2982 -2041 -1722
## NDUFAF6 NDUFA2 SCO1 ETFA COX14 NUBPL TACO1
## -894 -575 912 2138 2506 2854 3626SessionInfo
sessionInfo()## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] RColorBrewer_1.1-3 beeswarm_0.4.0
## [3] kableExtra_1.4.0 biomaRt_2.60.1
## [5] dplyr_1.1.4 mitch_1.19.2
## [7] gplots_3.2.0 DESeq2_1.44.0
## [9] SummarizedExperiment_1.34.0 Biobase_2.64.0
## [11] MatrixGenerics_1.16.0 matrixStats_1.4.1
## [13] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
## [15] IRanges_2.38.1 S4Vectors_0.42.1
## [17] BiocGenerics_0.50.0 reshape2_1.4.4
##
## loaded via a namespace (and not attached):
## [1] DBI_1.2.3 bitops_1.0-9 httr2_1.0.7
## [4] gridExtra_2.3 echarts4r_0.4.5 rlang_1.1.4
## [7] magrittr_2.0.3 compiler_4.4.2 RSQLite_2.3.9
## [10] png_0.1-8 systemfonts_1.1.0 vctrs_0.6.5
## [13] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.3
## [16] fastmap_1.2.0 dbplyr_2.5.0 XVector_0.44.0
## [19] caTools_1.18.3 promises_1.3.2 rmarkdown_2.29
## [22] UCSC.utils_1.0.0 purrr_1.0.2 bit_4.5.0.1
## [25] xfun_0.49 zlibbioc_1.50.0 cachem_1.1.0
## [28] jsonlite_1.8.9 progress_1.2.3 blob_1.2.4
## [31] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0
## [34] prettyunits_1.2.0 parallel_4.4.2 R6_2.5.1
## [37] bslib_0.8.0 stringi_1.8.4 GGally_2.2.1
## [40] jquerylib_0.1.4 Rcpp_1.0.13-1 knitr_1.49
## [43] httpuv_1.6.15 Matrix_1.7-1 tidyselect_1.2.1
## [46] rstudioapi_0.17.1 abind_1.4-8 yaml_2.3.10
## [49] codetools_0.2-20 curl_6.0.1 lattice_0.22-6
## [52] tibble_3.2.1 plyr_1.8.9 shiny_1.10.0
## [55] KEGGREST_1.44.1 evaluate_1.0.1 BiocFileCache_2.12.0
## [58] ggstats_0.7.0 xml2_1.3.6 Biostrings_2.72.1
## [61] filelock_1.0.3 pillar_1.10.0 KernSmooth_2.23-24
## [64] generics_0.1.3 hms_1.1.3 ggplot2_3.5.1
## [67] munsell_0.5.1 scales_1.3.0 gtools_3.9.5
## [70] xtable_1.8-4 glue_1.8.0 tools_4.4.2
## [73] locfit_1.5-9.10 grid_4.4.2 tidyr_1.3.1
## [76] AnnotationDbi_1.66.0 colorspace_2.1-1 GenomeInfoDbData_1.2.12
## [79] cli_3.6.3 rappdirs_0.3.3 S4Arrays_1.4.1
## [82] viridisLite_0.4.2 svglite_2.1.3 gtable_0.3.6
## [85] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
## [88] htmlwidgets_1.6.4 memoise_2.0.1 htmltools_0.5.8.1
## [91] lifecycle_1.0.4 httr_1.4.7 mime_0.12
## [94] bit64_4.5.2 MASS_7.3-61