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package loading

function load

Knowles data

The code below is how I wrangled the knowles supplemental lists into entrezgene_ids to overlap with my expressed gene lists

Enrichment of Pairwise

A note on Knowles data sets: the intersection of the Knowles-4 and Knowles-5 sets yielded 104 genes in

backGL <- read.csv("data/backGL.txt")
# drug_palNoVeh <- c("#8B006D","#DF707E","#F1B72B", "#3386DD","#707031")
drug_palc <- c("#8B006D","#DF707E","#F1B72B", "#3386DD","#707031","#41B333")
time <- rep((rep(c("3h", "24h"), c(6,6))), 6)
time <- ordered(time, levels =c("3h", "24h"))
drug <- rep(c("DNR","DOX","EPI","MTX","TRZ", "Vehicle"),12)
mat_drug <- c("DNR","DOX","EPI","MTX")
indv <- as.factor(rep(c(1,2,3,4,5,6), c(12,12,12,12,12,12)))
labeltop <- (interaction(substring(drug, 0, 2), indv, time))
level_order2 <- c('75','87','77','79','78','71')


toplistall <- readRDS("data/toplistall.RDS")
knowles4 <-readRDS("output/knowles4.RDS")
knowles5 <-readRDS("output/knowles5.RDS")
DOXmeSNPs <- readRDS("output/DOXmeSNPs.RDS")
DOXreQTLs <- readRDS("output/DOXreQTLs.RDS")
DNRmeSNPs <- readRDS("output/DNRmeSNPs.RDS")
DNRreQTLs <- readRDS("output/DNRreQTLs.RDS")
EPImeSNPs <- readRDS("output/EPImeSNPs.RDS")
EPIreQTLs <- readRDS("output/EPIreQTLs.RDS")
MTXmeSNPs <- readRDS("output/MTXmeSNPs.RDS")
MTXreQTLs <- readRDS("output/MTXreQTLs.RDS")
cpmcounts <- readRDS("data/cpmcount.RDS")
toplist24hr <-   toplistall %>%
  mutate(id =case_match(id, "Da"~"DNR",
                            "Do"~"DOX",
                            "Ep"~"EPI",
                            "Mi"~"MTX",
                            "Tr"~"TRZ",
                            "Ve"~"VEH", .default = id)) %>% 
      mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  filter(time=="24_hours")

toplist3hr <-   toplistall %>%
  mutate(id =case_match(id, "Da"~"DNR",
                            "Do"~"DOX",
                            "Ep"~"EPI",
                            "Mi"~"MTX",
                            "Tr"~"TRZ",
                            "Ve"~"VEH", .default = id)) %>% 
      mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  filter(time=="3_hours")

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
David A Knowles, Courtney K Burrows†, John D Blischak, Kristen M Patterson, Daniel J Serie, Nadine Norton, Carole Ober, Jonathan K Pritchard, Yoav Gilad

Knowles \(~~et~ al.~\) eLife 2018;7:e33480. DOI: https://doi.org/10.7554/eLife.33480

My first question was about transcriptional response at the 24 hour mark with my treatments. 3 hour RNA-seq had low numbers of DEGs,so my initial focus is at 24 hours. This time also happens to be when the Knowles paper collected their RNA-seq data.

Supplementary 4 contains a list of 518 SNPs within 1 Mb of TSS, which had a detectable marginal effect on expression (5% FDR). When converted from ensembl gene id to entrez gene id, my list of genes for this supplement = 417. I will call these meSNPS for marginal effect QTLs.

Supplementary 5 contains a list of 376 response eQTLs (reQTLs). These are variants that were associated with modulation of transcriptomic response to DOX treatment. After database name conversion, I have 273 genes.

meSNPdf <- toplistall %>% 
   mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  mutate(sigcount = if_else(adj.P.Val < 0.05,'sig','notsig'))%>%
  mutate(meSNP = if_else( ENTREZID %in% knowles4$entrezgene_id, "y" , "no")) %>% 
  dplyr::select(ENTREZID,id,time,meSNP,sigcount) %>%
  group_by(id,time,meSNP,sigcount) %>% 
  tally() %>% 
  pivot_wider(id_cols = c(id,time,sigcount), names_from = meSNP,names_glue = "meSNP_{meSNP}", values_from = n)

meSNPdf %>% 
  kable(., caption= "Number of genes from minimally expressed SNPs found in DEGs (sig and nonsig) broken down by drug,time, and significance") %>% 
  kable_paper("striped", full_width = FALSE) %>% 
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped"),font_size = 18) %>% 
  scroll_box(width = "80%", height = "400px")
Number of genes from minimally expressed SNPs found in DEGs (sig and nonsig) broken down by drug,time, and significance
id time sigcount meSNP_no meSNP_y
DOX 3_hours notsig 13665 400
DOX 3_hours sig 19 NA
DOX 24_hours notsig 7181 258
DOX 24_hours sig 6503 142
EPI 3_hours notsig 13477 397
EPI 3_hours sig 207 3
EPI 24_hours notsig 7484 272
EPI 24_hours sig 6200 128
DNR 3_hours notsig 13156 396
DNR 3_hours sig 528 4
DNR 24_hours notsig 6828 239
DNR 24_hours sig 6856 161
MTX 3_hours notsig 13611 398
MTX 3_hours sig 73 2
MTX 24_hours notsig 12585 384
MTX 24_hours sig 1099 16
TRZ 3_hours notsig 13684 400
TRZ 24_hours notsig 13684 400 
reQTLdf <- toplistall %>% 
   mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  mutate(sigcount = if_else(adj.P.Val < 0.05,'sig','notsig'))%>%
  mutate(reQTL = if_else( ENTREZID %in% knowles5$entrezgene_id, "y" , "no")) %>% 
  dplyr::select(ENTREZID,id,time,reQTL,sigcount) %>%
  group_by(id,time,reQTL,sigcount) %>% 
  tally() %>% 
  pivot_wider(id_cols = c(id,time,sigcount), names_from = reQTL,names_glue = "reQTL_{reQTL}", values_from = n)

reQTLdf %>% 
  kable(., caption= "Number of genes from response eQTLS found in DEGs (sig and nonsig) broken down by drug,time, and significance") %>% 
  kable_paper("striped", full_width = FALSE) %>% 
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped"),font_size = 18) %>% 
  scroll_box(width = "80%", height = "400px")
Number of genes from response eQTLS found in DEGs (sig and nonsig) broken down by drug,time, and significance
id time sigcount reQTL_no reQTL_y
DOX 3_hours notsig 13794 271
DOX 3_hours sig 19 NA
DOX 24_hours notsig 7310 129
DOX 24_hours sig 6503 142
EPI 3_hours notsig 13606 268
EPI 3_hours sig 207 3
EPI 24_hours notsig 7616 140
EPI 24_hours sig 6197 131
DNR 3_hours notsig 13293 259
DNR 3_hours sig 520 12
DNR 24_hours notsig 6944 123
DNR 24_hours sig 6869 148
MTX 3_hours notsig 13739 270
MTX 3_hours sig 74 1
MTX 24_hours notsig 12725 244
MTX 24_hours sig 1088 27
TRZ 3_hours notsig 13813 271
TRZ 24_hours notsig 13813 271 
dataframK_45 <- toplistall %>%
  mutate(id =case_match(id, "Da"~"DNR",
                            "Do"~"DOX",
                            "Ep"~"EPI",
                            "Mi"~"MTX",
                            "Tr"~"TRZ",
                            "Ve"~"VEH", .default = id)) %>%
  mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  mutate(K4 = if_else(ENTREZID %in% knowles4$entrezgene_id,'y','no'))%>%
  mutate(K5 = if_else(ENTREZID %in% knowles5$entrezgene_id,'y','no'))%>%
  filter(adj.P.Val<0.05) %>%
   group_by(time, id) %>%
 dplyr::summarize(n=n(), meSNP=sum(if_else(K4=="y",1,0)), reQTL=sum(if_else(K5=="y",1,0))) %>% 
  as.data.frame()


dataframK_45 %>% 
kable(., caption= "Summary of meSNPs and reQTLs found in my DEGs") %>% 
  kable_paper("striped", full_width = FALSE) %>% 
  kable_styling(font_size = 18) %>% 
  scroll_box(width = "80%", height = "400px")
Summary of meSNPs and reQTLs found in my DEGs
time id n meSNP reQTL
3_hours DOX 19 0 0
3_hours EPI 210 3 3
3_hours DNR 532 4 12
3_hours MTX 75 2 1
24_hours DOX 6645 142 142
24_hours EPI 6328 128 131
24_hours DNR 7017 161 148
24_hours MTX 1115 16 27

Visualization of proportions

toplistall %>%
   mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  mutate(sigcount = if_else(adj.P.Val < 0.05,'sig','notsig'))%>%
  mutate(meSNP=if_else(ENTREZID %in%knowles4$entrezgene_id,"y","no")) %>% 
  mutate(reQTL=if_else(ENTREZID %in%knowles5$entrezgene_id,"a","b")) %>% 
  filter(time =="24_hours") %>% 
  group_by(id,sigcount,meSNP) %>% 
  summarize(K4count=n())%>% 
    pivot_wider(id_cols = c(id,sigcount), names_from=c(meSNP), values_from=K4count) %>% 
   mutate(SNPprop=(y/(y+no)*100)) %>% 
       ggplot(., aes(x=id, y=SNPprop)) +
       geom_col()+
       geom_text(aes(x=id, label = sprintf("%.2f",SNPprop), vjust=-.2))+
       #geom_text(aes(label = expression(paste0("number"~a,"out of",~b))))+
       facet_wrap(~sigcount)+
       ggtitle("non-significant and significant enrichment proportions of Knowles meSNPs ")

toplistall %>%
   mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  mutate(sigcount = if_else(adj.P.Val < 0.05,'sig','notsig'))%>%
  mutate(meSNP=if_else(ENTREZID %in%knowles4$entrezgene_id,"y","no")) %>% 
  mutate(reQTL=if_else(ENTREZID %in%knowles5$entrezgene_id,"a","b")) %>% 
  filter(time =="24_hours") %>% 
  group_by(id,sigcount,reQTL) %>% 
  summarize(K5count=n())%>% 
    pivot_wider(id_cols = c(id,sigcount), names_from=c(reQTL), values_from=K5count) %>% 
   mutate(QTLprop=(a/(a+b)*100)) %>% 
       ggplot(., aes(x=id, y=QTLprop)) +
       geom_col()+
       geom_text(aes(x=id, label = sprintf("%.2f",QTLprop), vjust=-.2))+
       #geom_text(aes(label = expression(paste0("number"~a,"out of",~b))))+
       facet_wrap(~sigcount)+
       ggtitle("non-significant and significant enrichment proportions of Knowles reQTLs ")

chi_squarek4 <- toplistall %>% 
   mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  dplyr::filter(id!="TRZ") %>% 
  mutate(sigcount = if_else(adj.P.Val <0.05,'sig','notsig'))%>%
  mutate(meSNP=if_else(ENTREZID %in%knowles4$entrezgene_id,"y","no")) %>% 
  group_by(id,time) %>% 
  summarise(pvalue= chisq.test(meSNP, sigcount)$p.value) 

chi_squarek5 <-   toplistall %>% 
   mutate(id=factor(id,levels =c('DOX','EPI','DNR','MTX','TRZ','VEH')))%>% 
  dplyr::filter(id!="TRZ") %>% 
  mutate(sigcount = if_else(adj.P.Val <0.05,'sig','notsig'))%>%
  mutate(reQTL=if_else(ENTREZID %in%knowles5$entrezgene_id,"a","b")) %>% 
  group_by(id,time) %>% 
  summarise(pvalue= chisq.test(reQTL, sigcount)$p.value) 

chi_squarek4 %>% 
  kable(., caption= "meSNPs (mininmally expressed QTLS) chi-squared pvalues") %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "right",bootstrap_options = c("striped"),font_size = 18) %>%   scroll_box(width = "50%", height = "400px")
meSNPs (mininmally expressed QTLS) chi-squared pvalues
id time pvalue
DOX 24_hours 0.0000026
DOX 3_hours 0.9563346
EPI 24_hours 0.0000002
EPI 3_hours 0.3023606
DNR 24_hours 0.0001261
DNR 3_hours 0.0047603
MTX 24_hours 0.0043791
MTX 3_hours 1.0000000 
chi_squarek5 %>% 
  kable(., caption= "reQTLS (response eQTLS) chi-squared pvalues") %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "right",bootstrap_options = c("striped"),font_size = 18) %>%   scroll_box(width = "50%", height = "400px")
reQTLS (response eQTLS) chi-squared pvalues
id time pvalue
DOX 24_hours 0.0937665
DOX 3_hours 1.0000000
EPI 24_hours 0.2812223
EPI 3_hours 0.7843268
DNR 24_hours 0.1257321
DNR 3_hours 0.6843822
MTX 24_hours 0.2516965
MTX 3_hours 1.0000000

We can “see” the proportions of SNPs are not enriched significantly in the DE genes compared to the non-DE genes (chi square test).
We do not see significant enrichment of reQTLS in our DE gene sets over the non-DE gene sets.

So what about enrichment of meSNPs in DE compared to reQTLs in significantly DE gene sets?

Knowles_count <- 
  toplistall %>%
  filter(id!='TRZ') %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  group_by(time, id) %>%
  mutate(K4 = if_else(ENTREZID %in% knowles4$entrezgene_id,1,0))%>%
  mutate(K5 = if_else(ENTREZID %in% knowles5$entrezgene_id,1,0))%>%
  filter(adj.P.Val<0.05) %>%
  dplyr::summarize(n=n(), K4=sum(K4), K5=sum(K5)) %>% 
  as.tibble() %>% 
  dplyr::select(time,id,K4,K5) %>% rename("K4_y"='K4',"K5_y"='K5') %>% 
  mutate(time = case_match(time, '3_hours'~'3 hrs',
                           '24_hours'~'24 hrs',.default = time)) %>% 
  mutate(K4_n= 417-K4_y, K5_n=273-K5_y) %>% 
  pivot_longer(!c(time,id), names_to='QTL',values_to="gene_count") %>%
  separate(QTL,into=c("QTL_type",'group'),sep = '_') %>%  
  mutate(QTL_type =case_match(QTL_type, 'K4'~'base\negenes',
                         'K5'~'response\negenes',.default = QTL_type)) %>% 
  mutate(time=factor(time, levels=c("3 hrs","24 hrs"))) %>% 
  group_by(id,time,QTL_type) %>% 
  mutate(percent=gene_count/sum(gene_count)*100) %>% 
  mutate(group=factor(group, levels= c("n","y"), labels=c("not DE","DE")))
  
  ggplot(Knowles_count, aes(x=QTL_type,y=gene_count, group=group,  fill=group))+
    geom_col(position='fill')+
    # guides(fill="none")+
    facet_wrap(time~id,nrow=2,ncol=4)+
    theme_classic()+
   scale_color_manual(values=drug_palc)+
    scale_fill_manual(values=drug_palc)+
       scale_y_continuous(label = scales::percent)+
    theme(strip.text=element_text(size=10, face = "bold"),
          strip.text.x = element_text(margin = margin(2,0,2,0, "pt")),
  strip.background = element_rect (linetype=1, linewidth = 0.5))

  ###This works
  chi_frame <- Knowles_count %>%
  pivot_wider(id_cols = c(time, id,QTL_type), names_from = group, values_from = gene_count) 

testDNR3chi <- matrix(c(4,12,413, 261), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n"))) 
    DNR_3chi <- chisq.test(testDNR3chi,correct=FALSE)$p.value
testDNR24chi <- matrix(c(161,148,256, 125), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n")))  
    DNR_24chi <- chisq.test(testDNR24chi,correct=FALSE)$p.value

testDOX3chi <- matrix(c(0,0,417, 273), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n")))  
    DOX_3chi <- chisq.test(testDOX3chi,correct=FALSE)$p.value
testDOX24chi <- matrix(c(142,142,256, 125), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n"))) 
    DOX_24chi <- chisq.test(testDOX24chi,correct=FALSE)$p.value

testEPI3chi <- matrix(c(3,3,414, 270), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n"))) 
    EPI_3chi <- chisq.test(testEPI3chi,correct=FALSE)$p.value
testEPI24chi <- matrix(c(128,131,289, 142), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n"))) 
    EPI_24chi <- chisq.test(testEPI24chi,correct=FALSE)$p.value
  
testMTX3chi <- matrix(c(2,1,415, 272), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n"))) 
    MTX_3chi <- chisq.test(testMTX3chi,correct=FALSE)$p.value
testMTX24chi <- matrix(c(16,27,401, 246), nrow=2, ncol=2, byrow=FALSE,
dimnames=list(c("k4", "k5"),c( "y", "n"))) 
    MTX_24chi <- chisq.test(testMTX24chi,correct=FALSE)$p.value
K4nK5chi <- data.frame(treatment=c('DNR_3','DNR_24','DOX_3','DOX_24','EPI_3','EPI_24','MTX_3','MTX_24'), chi_p.value=c(DNR_3chi,DNR_24chi,DOX_3chi,DOX_24chi,EPI_3chi,EPI_24chi,MTX_3chi,MTX_24chi))

K4nK5chi %>% 
  separate(treatment, into= c('Drug','time')) %>% 
  pivot_wider(id_cols = Drug, names_from = time, values_from = chi_p.value) %>% 
  kable(., caption= "Chi Square p. values from chi-square test between proportions of sig-DE meQTLs and reQTLS by time and treatment") %>% 
  kable_paper("striped", full_width = TRUE) %>%  
  kable_styling(full_width = FALSE, font_size = 16) %>% 
  scroll_box( height = "500px")
Chi Square p. values from chi-square test between proportions of sig-DE meQTLs and reQTLS by time and treatment
Drug 3 24
DNR 0.0033591 0.0000557
DOX NaN 0.0000077
EPI 0.5995866 0.0000045
MTX 0.8249205 0.0012981

Here we found that 24 hour reQTLs are significantly enriched in sig-DEgens compared to meQTLS, with DNR 3 hour treatment also showing significant enrichment.

toplistall %>% 
  filter(time=="24_hours") %>% 
  group_by(time, id) %>% 
  mutate(sigcount = if_else(adj.P.Val < 0.05,'sig','notsig'))%>%
  ggplot(., aes(x=id, y=abs(logFC)))+
  geom_boxplot(aes(fill=id))+
  ggpubr::fill_palette(palette =drug_palc)+
  guides(fill=guide_legend(title = "Treatment"))+
  facet_wrap(sigcount~time)+
  theme_bw()+
  xlab("")+
  ylab("abs |Log Fold Change|")+
  theme_bw()+
  facet_wrap(~time)+
  #ggtitle("All QTLs from all expressed genes (n=507)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        # axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        strip.background = element_rect(fill = "transparent"),
        axis.text = element_text(size = 8, color = "black", angle = 0),
        strip.text.x = element_text(size = 12, color = "black", face = "bold"))

Dox-reQTLs

When I look ot the reQTLs across treatments at 24 hours, I see that dox has a total of 142 reQTLS. Because this gene set was specifically about DOX response eQTLs, I wanted to see if these reQTLs were only Dox specific, or had more in common with other treatments.

trtonly_24h_genes <- readRDS("data/trtonly_24h_genes.RDS")
list2env(trtonly_24h_genes,.GlobalEnv)
<environment: R_GlobalEnv>
siglist <- readRDS("data/siglist_final.RDS")
list2env(siglist,.GlobalEnv)
<environment: R_GlobalEnv>
reQTLcombine=list(DOXreQTLs$ENTREZID,EPIreQTLs$ENTREZID,DNRreQTLs$ENTREZID,MTXreQTLs$ENTREZID)

length(unique(c(DNRreQTLs$ENTREZID,DOXreQTLs$ENTREZID,EPIreQTLs$ENTREZID,MTXreQTLs$ENTREZID)))
[1] 166
print("number of unique genes expressed in pairwise DE set")
[1] "number of unique genes expressed in pairwise DE set"
QTLoverlaps <- VennDiagram::get.venn.partitions(reQTLcombine)
DoxonlyQTL <-  QTLoverlaps$..values..[[14]]
     ggVennDiagram::ggVennDiagram(reQTLcombine, category.names = c("DOX-142 \nsigDEG\n","EPI-131\nsigDEG\n","DNR-148\nsigDEG","MTX-27\nsigDEG"),label = "count") +scale_x_continuous(expand = expansion(mult = .2))+scale_y_continuous(expand = expansion(mult = .1))+scale_fill_distiller(palette="RdYlGn", direction = -1)

Here, I found 90 reQTLs that were related to only anthracyclines, with 23 reQTLS related to all Top2i drugs at 24 hours.

Venn of DOX egenes and all TOP2i DEGs

library(paletteer)
assignInNamespace(x="plot_venn", value=plot_venn, ns="ggVennDiagram") 

reQTL_overlapDE24 <- list(DOXreQTLs$ENTREZID,sigVDA24$ENTREZID, sigVEP24$ENTREZID, sigVMT24$ENTREZID)
re_incommon <- c(DOXreQTLs$ENTREZID,sigVDA24$ENTREZID, sigVEP24$ENTREZID, sigVMT24$ENTREZID)

names(reQTL_overlapDE24) <- c("Dox_reQTLS", "DNR DEGs","EPI DEGs","MTX DEGs")

ggVennDiagram::ggVennDiagram(reQTL_overlapDE24,
                             category.names = c("DOX\negenes",
                                 "DNR DEGs",
                                 "EPI DEGs",
                                 "MTX DEGs"),
              show_intersect = FALSE,
              set_color = "black",
              category_size = c(6,6,6,6),
              label = "count",
              color =  c("DOX\negenes" = "yellow","DNR DEGs" ="steelblue","EPI DEGs" = 'red', "MTX DEGs" = 'black') ,
          
              label_percent_digit = 1,
              label_size = 4,
              label_alpha = 0,
              label_color = "black",
              edge_lty = "solid", set_size = 4.5)+
  scale_x_continuous(expand = expansion(mult = .3))+
  scale_y_continuous(expand = expansion(mult = .2))+
  # scale_color_paletteer_d(palette = "fishualize::Bodianus_pulchellus")+
  # scale_colour_gradientn(colours = cols, 
  #                      values = rescale(c(0, 20, 75, 1000, 5000)),
  #                      guide = "colorbar", limits=c(0, 100)) +
  scale_fill_distiller(palette="Spectral", direction = -1, limits= c(1,200),oob=scales::squish)+
  # scale_fill_manual(values = cbp1)+
  labs(title = "24 hour DOX egenes in other DEG sets",
       caption = paste("n =", length(unique(re_incommon)),"genes"))+
  theme(plot.title = element_text(size = rel(1.6), hjust = 0.5, vjust =1))

DEG_incommon <-c(sigVDA24$ENTREZID, sigVEP24$ENTREZID, sigVMT24$ENTREZID)
uniqueDEGs_incommon <- unique(DEG_incommon)
two_venn <- list( DOXreQTLs$ENTREZID,uniqueDEGs_incommon)

ggVennDiagram::ggVennDiagram(two_venn,
                             category.names = c("DOX egenes\nn = 142","union of TOP2i DEGs\n     n = 7838"),
              show_intersect = FALSE,
              set_color = "black",
              category_size = c(6,6),
              label = "count",
              # color =  c("DOX\negenes" = "yellow","DNR DEGs" ="steelblue","EPI DEGs" = 'red', "MTX DEGs" = 'black') ,
              # 
              label_percent_digit = 1,
              label_size = 4,
              label_alpha = 0,
              label_color = "black",
              edge_lty = "solid", set_size = 4.5)+
  scale_x_continuous(expand = expansion(mult = .3))+
  scale_y_continuous(expand = expansion(mult = .1))+
   scale_fill_distiller(palette="Spectral", direction = -1, limits= c(1,200),oob=scales::squish)#+

# labs(title = "24 hour DOX egenes in other DEG sets",
#        caption = paste("n =", length(unique(re_incommon)),"genes"))+
#   theme(plot.title = element_text(size = rel(1.6), hjust = 0.5, vjust =1))
 DOXeQTL_table <- toplistall %>% 
  mutate(sigcount = if_else(adj.P.Val < 0.05,'sig','notsig'))%>%
  mutate(DOXreQTLs=if_else(ENTREZID %in%DOXreQTLs$ENTREZID,"y","no")) %>% 
  dplyr::filter(time =="24_hours") %>% 
  dplyr::select(ENTREZID,id,DOXreQTLs,sigcount) %>%
  group_by(id,DOXreQTLs,sigcount) %>% 
  tally() %>% as.data.frame() %>% 
  pivot_wider(.,id_cols = c(id,DOXreQTLs),names_from = sigcount,values_from = n) %>% 
  dplyr::select(id,DOXreQTLs,sig) 

DOXeQTL_table%>% 
  kable(., caption= "All 24 hour sigDEGs broken down by drug and DOXreQTL status") %>% 
  kable_paper("striped", full_width = FALSE) %>% 
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped"),font_size = 18) %>% 
  scroll_box(width = "80%", height = "400px")
All 24 hour sigDEGs broken down by drug and DOXreQTL status
id DOXreQTLs sig
DNR no 6885
DNR y 132
DOX no 6503
DOX y 142
EPI no 6211
EPI y 117
MTX no 1089
MTX y 26
TRZ no NA
TRZ y NA 
DOXeQTL_table %>%
  add_row(id=c("Dox-specific DEGs","Dox-specific DEGs"),DOXreQTLs=c("no","y"), sig = c(62,1)) %>% 
  dplyr::filter(DOXreQTLs=="y") %>% 
  mutate(opp= 142-sig) %>% 
  filter(id !=c('TRZ','DOX')) %>% 
  rename("yes"=sig, "no"=opp) %>% 
  mutate(y_percent= paste0(sprintf("%2.1f", yes/(yes+no)*100), "%"),n_percent = paste0(sprintf("%2.1f", no/(yes+no)*100),"%")) %>% 
  pivot_longer(!c(id,DOXreQTLs,y_percent,n_percent), names_to="group", values_to = "count") %>% 
  mutate(id=factor(id, levels=c("DNR","EPI", "MTX","Dox-specific DEGs"))) %>% 
ggplot(., aes(y=id,x=count,fill=group))+
     geom_col(position='fill')+
    theme_classic()+
   scale_color_manual(values=c("red4","navy"))+
    scale_fill_manual(values=c("#2297E6","red2"))+
  ggtitle("DOXreQTLs overlaps")+
  scale_y_discrete(limits=rev)+
  geom_text(aes(y=id,x=1, label = n_percent,hjust=.8))+

    theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.0),
        axis.line = element_line(linewidth = 1.0),
        axis.text = element_text(size = 10, color = "black", angle = 0),
        strip.text.x = element_text(size = 15, color = "black", face = "bold"))

DOX specific-Dox dE-reqtl

# DoxonlyQTL <-  as.numeric(QTLoverlaps$..values..[[14]])
# geneDoxonlyQTL <- getBM(attributes=my_attributes,filters ='entrezgene_id',
#                   values =DoxonlyQTL, mart = ensembl)
# write.csv(geneDoxonlyQTL,"data/geneDoxonlyQTL.csv")

geneDoxonlyQTL <- read.csv("data/geneDoxonlyQTL.csv",row.names = 1)
cpmcounts <- readRDS("data/cpmcount.RDS")

for (g in seq(from=1, to=length(geneDoxonlyQTL$entrezgene_id))){
  a <- geneDoxonlyQTL$hgnc_symbol[g]
  cpm_boxplot(cpmcounts,GOI=geneDoxonlyQTL[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))

}

### Dox specific DEG examination

#pull list
total24 <-list(sigVDA24$ENTREZID,sigVDX24$ENTREZID,sigVEP24$ENTREZID,sigVMT24$ENTREZID)
## do venn partition and pull doxspe genes
# total24 <- list(sigVDA24$SYMBOL,sigVDX24$SYMBOL,sigVEP24$SYMBOL,sigVMT24$SYMBOL)
trtonly_24h_genes <- readRDS("data/trtonly_24h_genes.RDS")
list2env(trtonly_24h_genes, envir = .GlobalEnv)
<environment: R_GlobalEnv>
# venn_24h <- VennDiagram::get.venn.partitions(total24)
# DoxonlyDEG <- venn_24h$..values..[[14]]# 355
# EpionlyDEG <- venn_24h$..values..[[12]] #444
# DnronlyDEG <- venn_24h$..values..[[15]] #615
# MtxonlyDEG <- venn_24h$..values..[[8]] #122
# trtonly_24h_genes <- list(DnronlyDEG,DoxonlyDEG,EpionlyDEG, MtxonlyDEG)
#   names(trtonly_24h_genes) <-c("DnronlyDEG","DoxonlyDEG","EpionlyDEG", "MtxonlyDEG")

# saveRDS(trtonly_24h_genes,"data/trtonly_24h_genes.RDS")
  
  length(DoxonlyDEG)
[1] 355
intersect(DoxonlyDEG,DOXreQTLs$ENTREZID)
[1] "57338" "29097" "7027"  "10179" "9852" 
Dox24_lfc <- toplist24hr %>% 
  filter(ENTREZID %in% DoxonlyDEG) %>% 
  # group_by(id) %>% 
  # dplyr::filter(adj.P.Val<0.05) #%>% 
  mutate(logFC=logFC*(-1)) %>% 
  ggplot(., aes(x= id, y=logFC))+
  geom_boxplot(aes(fill=id))+
  theme_classic()+
  fill_palette(palette = drug_palc)+
  ggtitle("LogFC of Dox specific DEGs")+
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5,face = "bold"),
    axis.title = element_text(size = 15, color = "black"),
    axis.ticks = element_line(size = 1.5),
    axis.text = element_text(size = 8, color = "black", angle = 20))
    # strip.text.x = element_text(size = 12, color = "black", face = "italic"))
  
  toplist24hr %>% 
  filter(ENTREZID %in% DoxonlyDEG) %>%
  # filter(adj.P.Val<0.05) %>%
  ggplot(., aes(x=adj.P.Val))+
  # geom_histogram(aes(fill=id,position="dodge"))+
    geom_density(aes(fill=id))+
    # facet_wrap(~id)+
    fill_palette(palette = drug_palc)

toplist24hr %>%
  dplyr::filter(ENTREZID %in% DoxonlyDEG) %>%
  # filter(adj.P.Val<0.5) %>%
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)

print(Dox24_lfc)

Plots of some genes:

Dox_eGene_sp <- intersect(DoxonlyDEG,DOXreQTLs$ENTREZID)
### making list
# # 
# Doxonly_deg <- getBM(attributes=my_attributes,filters ='entrezgene_id',
#                   values =DoxonlyDEG, mart = ensembl)
# write.csv(Doxonly_deg,"output/Doxonly_deg.csv")
Doxonly_deg <- read.csv("output/Doxonly_deg.csv", row.names = 1)
set.seed(12345)
sampset <- Doxonly_deg %>% 
  distinct(entrezgene_id,.keep_all = TRUE) %>% 
  sample_n(.,12)
for (g in seq(from=1, to=length(sampset$entrezgene_id))){
  a <- sampset$hgnc_symbol[g]
  cpm_boxplot(cpmcounts,GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))

}

doxsponly <- Doxonly_deg %>% 
  distinct(entrezgene_id,.keep_all = TRUE) %>% 
 dplyr::filter(entrezgene_id %in%Dox_eGene_sp)

for (g in seq(from=1, to=length(doxsponly$entrezgene_id))){
  a <- doxsponly$hgnc_symbol[g]
  cpm_boxplot(cpmcounts,GOI=doxsponly[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))

}

More investigation of 24 hour specific genes

DOX

DOXdeg_sp <- toplist24hr %>% 
  dplyr::filter(ENTREZID %in% DoxonlyDEG) %>%
  dplyr::filter(adj.P.Val<0.01) %>% 
  filter(id=="DOX") %>% 
  dplyr::select(ENTREZID, SYMBOL)  

DOXdeg_sp %>% 
  kable(., caption= "68 DOX specific genes") %>% 
  kable_paper("striped", full_width = TRUE) %>%  
  kable_styling(full_width = FALSE, font_size = 16) %>% 
  scroll_box( height = "500px")
68 DOX specific genes
ENTREZID SYMBOL
169200 169200 TMEM64
1452 1452 CSNK1A1
653082 653082 ZDHHC11B
202181 202181 LOC202181
8501 8501 SLC43A1
114882 114882 OSBPL8
23108 23108 RAP1GAP2
135154 135154 SDHAF4
5000 5000 ORC4
2130 2130 EWSR1
122553 122553 TRAPPC6B
54165 54165 DCUN1D1
57862 57862 ZNF410
57181 57181 SLC39A10
112858 112858 TP53RK
79065 79065 ATG9A
8515 8515 ITGA10
25842 25842 ASF1A
284900 284900 TTC28-AS1
2230 2230 FDX1
9524 9524 TECR
256586 256586 LYSMD2
57338 57338 JPH3
440944 440944 THUMPD3-AS1
10190 10190 TXNDC9
805 805 CALM2
100131211 100131211 NEMP2
4987 4987 OPRL1
79624 79624 ARMT1
23548 23548 TTC33
27430 27430 MAT2B
81532 81532 MOB2
158234 158234 TRMT10B
147 147 ADRA1B
26001 26001 RNF167
57186 57186 RALGAPA2
5431 5431 POLR2B
8763 8763 CD164
55234 55234 SMU1
84752 84752 B3GNT9
375056 375056 MIA3
7917 7917 BAG6
54629 54629 MINDY2
102723508 102723508 KANTR
26994 26994 RNF11
29944 29944 PNMA3
9446 9446 GSTO1
7881 7881 KCNAB1
6139 6139 RPL17
100133331 100133331 NA
101927720 101927720 ZNF793-AS1
6653 6653 SORL1
5966 5966 REL
5411 5411 PNN
6498 6498 SKIL
8218 8218 CLTCL1
83695 83695 RHNO1
1838 1838 DTNB
347918 347918 EP400P1
9894 9894 TELO2
10973 10973 ASCC3
5598 5598 MAPK7
8241 8241 RBM10
27229 27229 TUBGCP4
2281 2281 FKBP1B
116068 116068 LYSMD3
56998 56998 CTNNBIP1
2551 2551 GABPA 
intersect(DOXreQTLs$ENTREZID, DOXdeg_sp$ENTREZID)
[1] "57338"
#still jph3
##lfc
toplist24hr %>% 
  group_by(time,id) %>% 
  dplyr::filter(ENTREZID %in% DOXdeg_sp$ENTREZID) %>%
  mutate(logFC=logFC*(-1)) %>% 
  ggplot(., aes(x= id, y=logFC))+
  geom_boxplot(aes(fill=id))+
  theme_classic()+
  fill_palette(palette = drug_palc)+
  ggtitle("LogFC of n = 68 Dox specific DEGs")+
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5,face = "bold"),
    axis.title = element_text(size = 15, color = "black"),
    axis.ticks = element_line(size = 1.5),
    axis.text = element_text(size = 8, color = "black", angle = 20))

##histo check

toplist24hr %>% 
  dplyr::filter(ENTREZID %in% DOXdeg_sp$ENTREZID) %>% 
  dplyr::filter(adj.P.Val <0.05) %>%
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id))+
  geom_vline(xintercept=0.01,linetype=2)+
    # geom_histogram(aes(fill=id))+
    facet_wrap(~id)+
  ggtitle("all Dox specific DEG adj p. value <0.01")+
    fill_palette(palette = drug_palc)+
  theme_bw()

toplist24hr %>% 
  filter(ENTREZID %in% DoxonlyDEG) %>% 
  ggplot(., aes(x=adj.P.Val))+
  geom_density(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()

densityDOXsp <- 
  toplist24hr %>% 
  filter(ENTREZID %in% DoxonlyDEG) %>% 
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()

densityDOXsp

set.seed(12345)
sampset <- DOXdeg_sp %>% 
  sample_n(.,12)

for (g in seq(from=1, to=length(sampset$ENTREZID))){
  a <- sampset$SYMBOL[g]
  cpm_boxplot(cpmcounts,GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))
}

##most convincing of these is ZNF793-AS1 101927720

MTX

MTXdeg_sp <- toplist24hr %>% 
   dplyr::filter(ENTREZID %in% MtxonlyDEG) %>%
  dplyr::filter(adj.P.Val<0.01) %>% 
  filter(id=="MTX") %>% 
  dplyr::select(ENTREZID, SYMBOL)  

MTXdeg_sp %>% 
  kable(., caption= "MTX specific genes") %>% 
  kable_paper("striped", full_width = TRUE) %>%  
  kable_styling(full_width = FALSE, font_size = 16) %>% 
  scroll_box( height = "500px")
MTX specific genes
ENTREZID SYMBOL
25894 25894 PLEKHG4
253714 253714 MMS22L
126432 126432 RINL
4001 4001 LMNB1
6240 6240 RRM1
83879 83879 CDCA7
25886 25886 POC1A
100128191 100128191 TMPO-AS1
84892 84892 POMGNT2
27346 27346 TMEM97
63827 63827 BCAN
55723 55723 ASF1B
4173 4173 MCM4
54853 54853 WDR55
8317 8317 CDC7
57699 57699 CPNE5
655 655 BMP7
9401 9401 RECQL4
126382 126382 NR2C2AP
79109 79109 MAPKAP1
441478 441478 NRARP
22950 22950 SLC4A1AP
100996573 100996573 NA
55780 55780 ERMARD
3148 3148 HMGB2
3983 3983 ABLIM1
9134 9134 CCNE2
25981 25981 DNAH1
9811 9811 CTIF
56970 56970 ATXN7L3
79758 79758 DHRS12
55147 55147 RBM23
65057 65057 ACD
645954 645954 SVIL2P
64116 64116 SLC39A8
147645 147645 VSIG10L
23582 23582 CCNDBP1
8321 8321 FZD1
10432 10432 RBM14
9820 9820 CUL7
55706 55706 NDC1 
#intersect(DOXreQTLs$ENTREZID, MTXdeg_sp$ENTREZID)#none

##lfc

toplist24hr %>% 
  group_by(time,id) %>% 
  filter(ENTREZID %in% MtxonlyDEG) %>% 
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment"=id)%>% 

  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  theme_classic()+
  fill_palette(palette = drug_palc)+
  ggtitle("LogFC of MTX specific DEGs (n = 48)")+
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5,face = "bold"),
    axis.title = element_text(size = 15, color = "black"),
    axis.ticks = element_line(size = 1.5),
    axis.text = element_text(size = 8, color = "black", angle = 0))

##histo check

toplist24hr %>% 
  dplyr::filter(ENTREZID %in% MTXdeg_sp$ENTREZID) %>% 
  dplyr::filter(adj.P.Val <0.05) %>%
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id))+
  geom_vline(xintercept=0.01,linetype=2)+
    # geom_histogram(aes(fill=id))+
    facet_wrap(~id)+
  ggtitle("all MTX specific DEG adj p. value <0.01")+
    fill_palette(palette = drug_palc)+
  theme_bw()

toplist24hr %>% 
  filter(ENTREZID %in% MtxonlyDEG) %>% 
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()

densityMTXsp <- toplist24hr %>% 
  filter(ENTREZID %in% MtxonlyDEG) %>% 
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()

densityMTXsp

set.seed(12345)
sampset <- MTXdeg_sp %>% 
  sample_n(.,12)

for (g in seq(from=1, to=length(sampset$ENTREZID))){
  a <- sampset$SYMBOL[g]
  cpm_boxplot(cpmcounts,GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))
}

##most convincing of these is 54853 WDR55

DNR

DNRdeg_sp <- toplist24hr %>% 
  filter(adj.P.Val<0.01) %>% 
  filter(ENTREZID %in% DnronlyDEG) %>% 
  filter(id=="DNR") %>% 
  dplyr::select(ENTREZID, SYMBOL)  

##lfc

toplist24hr %>% 
  filter(ENTREZID %in% DNRdeg_sp$ENTREZID) %>% 
  group_by(time,id) %>% 
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment" = id) %>% 
  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  theme_classic()+
  fill_palette(palette = drug_palc)+
   ggtitle("LogFC of DNR specific DEGs (n = 112)")+
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5,face = "bold"),
    axis.title = element_text(size = 15, color = "black"),
    axis.ticks = element_line(size = 1.5),
    axis.text = element_text(size = 8, color = "black", angle = 0))

##histo check

toplist24hr %>% 
  dplyr::filter(ENTREZID %in% DNRdeg_sp$ENTREZID) %>% 
  dplyr::filter(adj.P.Val <0.05) %>%
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id))+
  geom_vline(xintercept=0.01,linetype=2)+
    # geom_histogram(aes(fill=id))+
    facet_wrap(~id)+
  ggtitle("all DNR specific DEG adj p. value <0.01")+
    fill_palette(palette = drug_palc)+
  theme_bw()

toplist24hr %>% 
  filter(ENTREZID %in% DnronlyDEG) %>% 
  ggplot(., aes(x=adj.P.Val))+
  geom_density(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()

set.seed(12345)
sampset <- DNRdeg_sp %>% 
  sample_n(.,12)

for (g in seq(from=1, to=length(sampset$ENTREZID))){
  a <- sampset$SYMBOL[g]
  cpm_boxplot(cpmcounts,GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))
}

##most convincing of these is 114826 SMYD4

EPI

EPIdeg_sp <- toplist24hr %>% 
  filter(adj.P.Val<0.01) %>% 
  filter(ENTREZID %in% EpionlyDEG) %>% 
  filter(id=="EPI") %>% 
  dplyr::select(ENTREZID, SYMBOL)  

EPIdeg_sp %>% 
  kable(., caption= "EPI specific genes") %>% 
  kable_paper("striped", full_width = TRUE) %>%  
  kable_styling(full_width = FALSE, font_size = 16) %>% 
  scroll_box( height = "500px")
EPI specific genes
ENTREZID SYMBOL
9685 9685 CLINT1
9373 9373 PLAA
55006 55006 TRMT61B
79798 79798 ARMC5
79759 79759 ZNF668
51434 51434 ANAPC7
54508 54508 EPB41L4A-DT
92140 92140 MTDH
11097 11097 NUP42
64781 64781 CERK
57587 57587 CFAP97
57325 57325 KAT14
201627 201627 DENND6A
55702 55702 YJU2
51132 51132 RLIM
55105 55105 GPATCH2
64863 64863 METTL4
90864 90864 SPSB3
8624 8624 PSMG1
60561 60561 RINT1
56252 56252 YLPM1
55339 55339 WDR33
23086 23086 EXPH5
1938 1938 EEF2
493812 493812 HCG11
7110 7110 TMF1
83852 83852 SETDB2
5884 5884 RAD17
64860 64860 ARMCX5
220963 220963 SLC16A9
22796 22796 COG2
11232 11232 POLG2
1385 1385 CREB1
10111 10111 RAD50
10342 10342 TFG
57609 57609 DIP2B
55727 55727 BTBD7
2043 2043 EPHA4
339210 339210 C17orf67
9972 9972 NUP153
285636 285636 RIMOC1
54942 54942 ABITRAM
143282 143282 FGFBP3
340359 340359 KLHL38
339122 339122 RAB43
79038 79038 ZFYVE21
5533 5533 PPP3CC
2966 2966 GTF2H2
105371932 105371932 LOC105371932
55223 55223 TRIM62
84967 84967 LSM10
7592 7592 ZNF41
11282 11282 MGAT4B
7869 7869 SEMA3B
65260 65260 COA7
9967 9967 THRAP3
10240 10240 MRPS31
130507 130507 UBR3
9829 9829 DNAJC6
349136 349136 WDR86
55676 55676 SLC30A6
64844 64844 MARCHF7
23122 23122 CLASP2
26046 26046 LTN1
138241 138241 C9orf85
10021 10021 HCN4
84859 84859 LRCH3
85457 85457 CIPC
79713 79713 IGFLR1
79657 79657 RPAP3
5887 5887 RAD23B
8899 8899 PRPF4B
54904 54904 NSD3
27246 27246 RNF115
23064 23064 SETX
6897 6897 TARS1
55937 55937 APOM
79230 79230 ZNF557
11054 11054 OGFR
1032 1032 CDKN2D
55958 55958 KLHL9
5048 5048 PAFAH1B1
728229 728229 TMEM191B
80176 80176 SPSB1 
##lfc

toplist24hr %>% 
  filter(ENTREZID %in% EPIdeg_sp$ENTREZID) %>% 
  group_by(time,id) %>% 
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment" = id) %>% 

  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  theme_classic()+
  fill_palette(palette = drug_palc)+
 ggtitle("LogFC of EPI specific DEGs (n = 84) ")+
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5,face = "bold"),
    axis.title = element_text(size = 15, color = "black"),
    axis.ticks = element_line(size = 1.5),
    axis.text = element_text(size = 8, color = "black", angle = 0))

##histo check

toplist24hr %>% 
  dplyr::filter(ENTREZID %in% EPIdeg_sp$ENTREZID) %>% 
  dplyr::filter(adj.P.Val <0.05) %>%
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id))+
  geom_vline(xintercept=0.01,linetype=2)+
    # geom_histogram(aes(fill=id))+
    facet_wrap(~id)+
  ggtitle("all DNR specific DEG adj p. value <0.01")+
    fill_palette(palette = drug_palc)+
  theme_bw()

densityEPIsp <- toplist24hr %>% 
  filter(ENTREZID %in% EpionlyDEG) %>% 
  ggplot(., aes(x=adj.P.Val))+
  geom_histogram(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()


densityEPIsp

set.seed(12345)
sampset <- EPIdeg_sp %>% 
  sample_n(.,12)

for (g in seq(from=1, to=length(sampset$ENTREZID))){
  a <- sampset$SYMBOL[g]
  cpm_boxplot(cpmcounts,GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))
}

##most convincing of these is   220963 SLC16A9

GO analysis 24h stringent adj.P.val <0.01 specific analysis

library(gprofiler2)

# 
# DNRdeg_sp had NO enrichment
# EPIdeg_sp had NO enrichment
# MTXdeg_sep had 2, "DNA-templated DNA replication" "nuclear pore localization"     "DNA replication" 

# gostresMTXdeg_sp <- gost(query = c(MTXdeg_sp),
#                       organism = "hsapiens",
#                       ordered_query = FALSE,
#                       domain_scope = "custom",
#                       measure_underrepresentation = FALSE,
#                       evcodes = FALSE,
#                       user_threshold = 0.05,
#                       correction_method = c("fdr"),
#                       custom_bg = backGL$ENTREZID,
#                       sources=c("GO:BP", "KEGG"))
# saveRDS(gostresMTXdeg_sp,"data/DEG-GO/gostresMTXdeg_sp.RDS")
# saveRDS(gostresDOXdeg_sp,"data/DEG-GO/gostresDOXdeg_sp.RDS")
DX_sp_DEGgostres <- readRDS("data/DEG-GO/gostresDOXdeg_sp.RDS")
MT_sp_DEGgostres <- readRDS("data/DEG-GO/gostresMTXdeg_sp.RDS")
DX_spgenes <- gostplot(DX_sp_DEGgostres, capped = FALSE, interactive = TRUE)
DX_spgenes
MT_spgenes <- gostplot(MT_sp_DEGgostres, capped = FALSE, interactive = TRUE)
MT_spgenes
DX_sp_DEGtable <- DX_sp_DEGgostres$result %>%
  dplyr::select(c(source, term_id,term_name,intersection_size, 
                   term_size, p_value))
MT_sp_DEGtable <- MT_sp_DEGgostres$result %>%
  dplyr::select(c(source, term_id,term_name,intersection_size, 
                   term_size, p_value))
  
  
DX_sp_DEGtable  %>% 
    dplyr::filter(source=="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) %>%
   # slice_max(., n=10,order_by = p_value) %>%
   ggplot(., aes(x = log_val, y =reorder(term_name,p_value), col= intersection_size)) +
    geom_point(aes(size = intersection_size)) +
    scale_y_discrete(labels = wrap_format(30))+
    guides(col="none", size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('DOX specific gene set GO:BP terms') +
    xlab(expression(" -"~log[10]~("adj. p-value")))+
    ylab("GO: BP term")+
    theme_bw()+
    theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, color = "black", angle = 0),
        strip.text.x = element_text(size = 12, color = "black", face = "bold"))

DX_sp_DEGtable %>% 
  mutate_at(.vars = 6, .funs= scientific_format()) %>% 
  kable(., caption= "Significant (adj. P value of <0.01) DOX specific genes (n = 68) and top 10 enriched GO terms") %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped","hover")) %>% 
  scroll_box(width = "100%", height = "400px")
Significant (adj. P value of <0.01) DOX specific genes (n = 68) and top 10 enriched GO terms
source term_id term_name intersection_size term_size p_value
GO:BP GO:2001258 negative regulation of cation channel activity 5 30 4.78e-04
GO:BP GO:0032413 negative regulation of ion transmembrane transporter activity 5 51 1.98e-03
GO:BP GO:1901020 negative regulation of calcium ion transmembrane transporter activity 4 27 1.98e-03
GO:BP GO:0060314 regulation of ryanodine-sensitive calcium-release channel activity 4 23 1.98e-03
GO:BP GO:0032410 negative regulation of transporter activity 5 58 1.98e-03
GO:BP GO:2001257 regulation of cation channel activity 6 100 1.98e-03
GO:BP GO:0034763 negative regulation of transmembrane transport 6 96 1.98e-03
GO:BP GO:0060315 negative regulation of ryanodine-sensitive calcium-release channel activity 3 10 2.51e-03
GO:BP GO:1904063 negative regulation of cation transmembrane transport 5 64 2.51e-03
GO:BP GO:0051280 negative regulation of release of sequestered calcium ion into cytosol 3 11 2.88e-03
GO:BP GO:1901019 regulation of calcium ion transmembrane transporter activity 5 71 2.95e-03
GO:BP GO:1903170 negative regulation of calcium ion transmembrane transport 4 35 2.95e-03
GO:BP GO:0034766 negative regulation of monoatomic ion transmembrane transport 5 70 2.95e-03
GO:BP GO:0051284 positive regulation of sequestering of calcium ion 3 13 3.54e-03
GO:BP GO:0051926 negative regulation of calcium ion transport 4 45 7.02e-03
GO:BP GO:0043271 negative regulation of monoatomic ion transport 5 90 7.39e-03
GO:BP GO:0034762 regulation of transmembrane transport 9 391 9.58e-03
GO:BP GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion 3 20 1.07e-02
GO:BP GO:0051279 regulation of release of sequestered calcium ion into cytosol 4 60 1.72e-02
GO:BP GO:0010882 regulation of cardiac muscle contraction by calcium ion signaling 3 25 1.91e-02
GO:BP GO:1903169 regulation of calcium ion transmembrane transport 5 122 2.16e-02
GO:BP GO:0032412 regulation of monoatomic ion transmembrane transporter activity 6 190 2.16e-02
GO:BP GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum 3 27 2.16e-02
GO:BP GO:1903514 release of sequestered calcium ion into cytosol by endoplasmic reticulum 3 28 2.16e-02
GO:BP GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum 3 28 2.16e-02
GO:BP GO:0055117 regulation of cardiac muscle contraction 4 70 2.28e-02
GO:BP GO:0022898 regulation of transmembrane transporter activity 6 199 2.34e-02
GO:BP GO:0070296 sarcoplasmic reticulum calcium ion transport 3 31 2.62e-02
GO:BP GO:0032409 regulation of transporter activity 6 211 2.88e-02
GO:BP GO:0065009 regulation of molecular function 20 1939 2.88e-02
GO:BP GO:0051209 release of sequestered calcium ion into cytosol 4 82 3.49e-02
GO:BP GO:0051283 negative regulation of sequestering of calcium ion 4 83 3.54e-02
GO:BP GO:0006942 regulation of striated muscle contraction 4 85 3.65e-02
GO:BP GO:0051282 regulation of sequestering of calcium ion 4 85 3.65e-02
GO:BP GO:1904062 regulation of monoatomic cation transmembrane transport 6 230 3.78e-02
GO:BP GO:0060316 positive regulation of ryanodine-sensitive calcium-release channel activity 2 9 3.78e-02
GO:BP GO:0051208 sequestering of calcium ion 4 89 3.98e-02
GO:BP GO:0007204 positive regulation of cytosolic calcium ion concentration 4 90 4.04e-02
GO:BP GO:0051342 regulation of cyclic-nucleotide phosphodiesterase activity 2 10 4.35e-02
GO:BP GO:2001258 negative regulation of cation channel activity 4 30 1.88e-02
GO:BP GO:2001257 regulation of cation channel activity 5 100 4.45e-02
GO:BP GO:0032413 negative regulation of ion transmembrane transporter activity 4 51 4.45e-02
GO:BP GO:0034763 negative regulation of transmembrane transport 5 96 4.45e-02
GO:BP GO:0032410 negative regulation of transporter activity 4 58 4.63e-02
GO:BP GO:0060314 regulation of ryanodine-sensitive calcium-release channel activity 3 23 4.63e-02 
MT_sp_DEGtable %>% 
 mutate_at(.vars = 6, .funs= scientific_format()) %>% 
  kable(., caption= "Significant (adj. P value of <0.01) DOX specific genes (n = 41) and top 10 enriched GO terms") %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped","hover")) %>% 
  scroll_box(width = "100%", height = "400px")
Significant (adj. P value of <0.01) DOX specific genes (n = 41) and top 10 enriched GO terms
source term_id term_name intersection_size term_size p_value
GO:BP GO:0006261 DNA-templated DNA replication 6 148 4.77e-03
GO:BP GO:0051664 nuclear pore localization 2 4 3.13e-02
GO:BP GO:0006260 DNA replication 6 255 3.47e-02
GO:BP GO:0006261 DNA-templated DNA replication 6 148 4.77e-03
GO:BP GO:0051664 nuclear pore localization 2 4 3.13e-02
GO:BP GO:0006260 DNA replication 6 255 3.47e-02
Grid for supplement

3 hour update

siglist <- readRDS("data/siglist_final.RDS")
list2env(siglist,.GlobalEnv)
<environment: R_GlobalEnv>
total3h <-list(sigVDA3$ENTREZID,sigVDX3$ENTREZID,sigVEP3$ENTREZID,sigVMT3$ENTREZID)
## do venn partition and pull doxspe genes
# venn_3h <- VennDiagram::get.venn.partitions(total3h)
# Dox3onlyDEG <- venn_3h$..values..[[14]]## no genes
# Epi3onlyDEG <- venn_3h$..values..[[12]]## 18 genes
# Dnr3onlyDEG <- venn_3h$..values..[[15]]## 322
# Mtx3onlyDEG <- venn_3h$..values..[[8]] ## 16

# trtonly_3h_genes <- list(Dnr3onlyDEG,Dox3onlyDEG,Epi3onlyDEG,Mtx3onlyDEG)
# names(trtonly_3h_genes) <-c("Dnr3onlyDEG","Dox3onlyDEG","Epi3onlyDEG","Mtx3onlyDEG")
# saveRDS(trtonly_3h_genes,"data/trtonly_3h_genes.RDS")
trtonly_3h_genes <- readRDS("data/trtonly_3h_genes.RDS")
list2env(trtonly_3h_genes,.GlobalEnv)
<environment: R_GlobalEnv>
DOX3deg_sp <- toplist3hr %>% 
  dplyr::filter(ENTREZID %in% Dox3onlyDEG) %>%
  dplyr::filter(adj.P.Val<0.01) %>% 
  filter(id=="DOX") %>% 
  dplyr::select(ENTREZID, SYMBOL)  
EPI3deg_sp <- toplist3hr %>% 
  dplyr::filter(ENTREZID %in% Epi3onlyDEG) %>%
  dplyr::filter(adj.P.Val<0.01) %>% 
  filter(id=="EPI") %>% 
  dplyr::select(ENTREZID, SYMBOL)  
DNR3deg_sp <- toplist3hr %>% 
  dplyr::filter(ENTREZID %in% Dnr3onlyDEG) %>%
  dplyr::filter(adj.P.Val<0.01) %>% 
  filter(id=="DNR") %>% 
  dplyr::select(ENTREZID, SYMBOL)  
MTX3deg_sp <- toplist3hr %>% 
  dplyr::filter(ENTREZID %in% Mtx3onlyDEG) %>%
  dplyr::filter(adj.P.Val<0.01) %>% 
  filter(id=="MTX") %>% 
  dplyr::select(ENTREZID, SYMBOL)  

# set.seed(12345)
# sampset <- EPI3deg_sp %>% 
#   sample_n(.,2)
# 
# for (g in seq(from=1, to=length(sampset$ENTREZID))){
#   a <- sampset$SYMBOL[g]
#   cpm_boxplot(cpmcounts,GOI=sampset[g,1],"Dark2",drug_palc,
#                 ylab=bquote(~italic(.(a))~log[2]~"cpm "))
# }

set.seed(12345)
sampset <- DNR3deg_sp %>% 
  sample_n(.,5)
print("DNR specfic")
[1] "DNR specfic"
for (g in seq(from=1, to=length(sampset$ENTREZID))){
  a <- sampset$SYMBOL[g]
  cpm_boxplot_time(cpmcounts,"3h",GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))
}

set.seed(12345)
sampset <- MTX3deg_sp %>% 
  sample_n(.,2)
print("MTX specfic")
[1] "MTX specfic"
for (g in seq(from=1, to=length(sampset$ENTREZID))){
  a <- sampset$SYMBOL[g]
  cpm_boxplot_time(cpmcounts,"3h",GOI=sampset[g,1],"Dark2",drug_palc,
                ylab=bquote(~italic(.(a))~log[2]~"cpm "))
}

library(paletteer)
in_common3sp <- c(Dnr3onlyDEG,Dox3onlyDEG,Epi3onlyDEG,Mtx3onlyDEG)

ggVennDiagram::ggVennDiagram(trtonly_3h_genes,
                             category.names = c("DNR_sp\nn = 322    ",
                                 "DOX_sp\n n = 0\n",
                                 "EPI_sp\n n = 18\n",
                                 " MTX_sp\n   n = 16"),
              show_intersect = FALSE,
              set_color = "black",
              category_size = c(6,6,6,6),
              label = "count",
              label_percent_digit = 1,
              label_size = 4,
              label_alpha = 0,
              label_color = "black",
              edge_lty = "solid", set_size = 4.5)+
  scale_x_continuous(expand = expansion(mult = .3))+
  scale_y_continuous(expand = expansion(mult = .2))+
  scale_color_paletteer_d(palette = "fishualize::Bodianus_pulchellus")+
  scale_fill_distiller(palette="Spectral", direction = -1)+
  labs(title = "3 hour treatment specific genes p.adj. <0.05",
       caption = paste("n =", length(unique(in_common3sp)),"genes"))+
  
  theme(plot.title = element_text(size = rel(1.6), hjust = 0.5, vjust =1))

GO analysis 3h stringent adj.P.val <0.01 specific analysis

# 
# DNRdeg_sp had NO enrichment
# EPIdeg_sp had NO enrichment
# MTXdeg_sep had 3, "DNA-templated DNA replication" "nuclear pore localization"     "DNA replication" 

# gostres3Mtxdeg_sp <- gost(query = MTX3deg_sp$ENTREZID,
#                       organism = "hsapiens",
#                       ordered_query = FALSE,
#                       domain_scope = "custom",
#                       significant = FALSE,
#                       measure_underrepresentation = FALSE,
#                       evcodes = FALSE,
#                       user_threshold = 0.05,
#                       correction_method = c("fdr"),
#                       custom_bg = backGL$ENTREZID,
#                       sources=c("GO:BP", "KEGG"))
# saveRDS(gostres3Dnrdeg_sp,"data/DEG-GO/gostres3Dnrdeg_sp.RDS")
# saveRDS(gostres3Mtxdeg_sp,"data/DEG-GO/gostres3Mtxdeg_sp.RDS")
gostres3Dnrdeg_sp <- readRDS("data/DEG-GO/gostres3Dnrdeg_sp.RDS")
gostres3Mtxdeg_sp <- readRDS("data/DEG-GO/gostres3Mtxdeg_sp.RDS")

Dnr3_spgenes <- gostplot(gostres3Dnrdeg_sp, capped = FALSE, interactive = TRUE)
Dnr3_spgenes
Mtx3_spgenes <- gostplot(gostres3Mtxdeg_sp, capped = FALSE, interactive = TRUE)
Mtx3_spgenes
Mtx3_sp_DEGtable <- gostres3Mtxdeg_sp$result %>%
  dplyr::select(c(source, term_id,term_name,intersection_size, 
                   term_size, p_value))

Dnr3_sp_DEGtable <- gostres3Dnrdeg_sp$result %>%
  dplyr::select(c(source, term_id,term_name,intersection_size, 
                   term_size, p_value))


Dnr3_sp_DEGtable  %>% 
    dplyr::filter(source=="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) %>%
   # slice_max(., n=10,order_by = p_value) %>%
   ggplot(., aes(x = log_val, y =reorder(term_name,p_value), col= intersection_size)) +
    geom_point(aes(size = intersection_size)) +
    scale_y_discrete(labels = wrap_format(30))+
    guides(col="none", size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('DNR 3 hour specific(stringent)\n gene set GO:BP terms') +
    xlab(expression(" -"~log[10]~("adj. p-value")))+
    ylab("GO: BP term")+
    theme_bw()+
    theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, color = "black", angle = 0),
        strip.text.x = element_text(size = 12, color = "black", face = "bold"))

Dnr3_sp_DEGtable  %>% 
  mutate_at(.vars = 6, .funs= scientific_format()) %>% 
  kable(., caption= "Stringent (adj. P value of <0.01) DNR 3 hour specific genes (n = 100)  enriched GO  and KEGG terms") %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped","hover")) %>% 
  scroll_box(width = "100%", height = "400px")
Stringent (adj. P value of <0.01) DNR 3 hour specific genes (n = 100) enriched GO and KEGG terms
source term_id term_name intersection_size term_size p_value
GO:BP GO:0006351 DNA-templated transcription 43 2683 4.90e-05
GO:BP GO:0097659 nucleic acid-templated transcription 43 2684 4.90e-05
GO:BP GO:0031323 regulation of cellular metabolic process 57 4174 4.90e-05
GO:BP GO:0032774 RNA biosynthetic process 43 2714 5.13e-05
GO:BP GO:0016070 RNA metabolic process 50 3600 1.08e-04
GO:BP GO:0006366 transcription by RNA polymerase II 35 1995 1.08e-04
GO:BP GO:0006355 regulation of DNA-templated transcription 40 2574 1.48e-04
GO:BP GO:0018130 heterocycle biosynthetic process 45 3132 1.48e-04
GO:BP GO:1901362 organic cyclic compound biosynthetic process 46 3237 1.48e-04
GO:BP GO:2001141 regulation of RNA biosynthetic process 40 2593 1.48e-04
GO:BP GO:1903506 regulation of nucleic acid-templated transcription 40 2576 1.48e-04
GO:BP GO:0006357 regulation of transcription by RNA polymerase II 33 1914 1.66e-04
GO:BP GO:0009059 macromolecule biosynthetic process 50 3730 1.66e-04
GO:BP GO:0051252 regulation of RNA metabolic process 42 2845 1.73e-04
GO:BP GO:0019219 regulation of nucleobase-containing compound metabolic process 44 3080 1.88e-04
GO:BP GO:0019222 regulation of metabolic process 60 5017 1.97e-04
GO:BP GO:0090304 nucleic acid metabolic process 52 4048 2.33e-04
GO:BP GO:0010556 regulation of macromolecule biosynthetic process 43 3012 2.33e-04
GO:BP GO:0019438 aromatic compound biosynthetic process 44 3133 2.42e-04
GO:BP GO:0009889 regulation of biosynthetic process 44 3169 3.18e-04
GO:BP GO:0034654 nucleobase-containing compound biosynthetic process 43 3070 3.39e-04
GO:BP GO:0031326 regulation of cellular biosynthetic process 43 3080 3.54e-04
GO:BP GO:1901576 organic substance biosynthetic process 55 4539 4.60e-04
GO:BP GO:0009058 biosynthetic process 55 4590 6.45e-04
GO:BP GO:0080090 regulation of primary metabolic process 53 4417 1.09e-03
GO:BP GO:0046483 heterocycle metabolic process 53 4570 3.06e-03
GO:BP GO:0006139 nucleobase-containing compound metabolic process 52 4455 3.17e-03
GO:BP GO:0010467 gene expression 53 4587 3.19e-03
GO:BP GO:0006725 cellular aromatic compound metabolic process 53 4596 3.27e-03
GO:BP GO:0044271 cellular nitrogen compound biosynthetic process 46 3750 3.48e-03
GO:BP GO:1901360 organic cyclic compound metabolic process 54 4747 3.48e-03
GO:BP GO:0044249 cellular biosynthetic process 50 4245 3.48e-03
GO:BP GO:0051171 regulation of nitrogen compound metabolic process 50 4292 4.63e-03
GO:BP GO:0010468 regulation of gene expression 44 3580 4.98e-03
GO:BP GO:0060255 regulation of macromolecule metabolic process 52 4617 7.08e-03
GO:BP GO:0140467 integrated stress response signaling 4 35 7.50e-03
GO:BP GO:1901522 positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus 3 16 1.23e-02
GO:BP GO:0034641 cellular nitrogen compound metabolic process 53 4946 2.18e-02
GO:BP GO:0044237 cellular metabolic process 68 6996 2.19e-02
GO:BP GO:2000121 regulation of removal of superoxide radicals 2 6 4.47e-02
GO:BP GO:1903507 negative regulation of nucleic acid-templated transcription 17 1017 5.42e-02
GO:BP GO:0072593 reactive oxygen species metabolic process 6 156 5.42e-02
GO:BP GO:0045892 negative regulation of DNA-templated transcription 17 1015 5.42e-02
GO:BP GO:1902679 negative regulation of RNA biosynthetic process 17 1026 5.84e-02
GO:BP GO:2000377 regulation of reactive oxygen species metabolic process 5 108 5.87e-02
GO:BP GO:0050794 regulation of cellular process 70 7552 7.07e-02
GO:BP GO:0034599 cellular response to oxidative stress 7 240 9.07e-02
GO:BP GO:0043618 regulation of transcription from RNA polymerase II promoter in response to stress 3 36 1.08e-01
GO:BP GO:0045934 negative regulation of nucleobase-containing compound metabolic process 18 1209 1.23e-01
GO:BP GO:0010558 negative regulation of macromolecule biosynthetic process 18 1214 1.24e-01
GO:BP GO:0000122 negative regulation of transcription by RNA polymerase II 13 740 1.24e-01
GO:BP GO:0051253 negative regulation of RNA metabolic process 17 1119 1.25e-01
GO:BP GO:0031324 negative regulation of cellular metabolic process 23 1735 1.25e-01
GO:BP GO:0065007 biological regulation 74 8320 1.35e-01
GO:BP GO:0043620 regulation of DNA-templated transcription in response to stress 3 41 1.38e-01
GO:BP GO:0031327 negative regulation of cellular biosynthetic process 18 1239 1.40e-01
GO:BP GO:0050789 regulation of biological process 72 8061 1.52e-01
GO:BP GO:0043170 macromolecule metabolic process 65 7069 1.63e-01
GO:BP GO:2000379 positive regulation of reactive oxygen species metabolic process 3 46 1.78e-01
GO:BP GO:0009890 negative regulation of biosynthetic process 18 1280 1.85e-01
GO:BP GO:0042636 negative regulation of hair cycle 1 1 1.86e-01
GO:BP GO:0035998 7,8-dihydroneopterin 3’-triphosphate biosynthetic process 1 1 1.86e-01
GO:BP GO:0014861 regulation of skeletal muscle contraction via regulation of action potential 1 1 1.86e-01
GO:BP GO:0045667 regulation of osteoblast differentiation 4 99 1.86e-01
GO:BP GO:0036091 positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress 1 1 1.86e-01
GO:BP GO:1990114 RNA polymerase II core complex assembly 1 1 1.86e-01
GO:BP GO:0036003 positive regulation of transcription from RNA polymerase II promoter in response to stress 2 18 1.86e-01
GO:BP GO:0002041 intussusceptive angiogenesis 1 1 1.86e-01
GO:BP GO:0036499 PERK-mediated unfolded protein response 2 17 1.86e-01
GO:BP GO:0100001 regulation of skeletal muscle contraction by action potential 1 1 1.86e-01
GO:BP GO:0060413 atrial septum morphogenesis 2 15 1.86e-01
GO:BP GO:0071241 cellular response to inorganic substance 5 164 1.86e-01
GO:BP GO:2000761 positive regulation of N-terminal peptidyl-lysine acetylation 1 1 1.86e-01
GO:BP GO:0062197 cellular response to chemical stress 7 293 1.86e-01
GO:BP GO:0062000 positive regulation of cardiac endothelial to mesenchymal transition 1 1 1.86e-01
GO:BP GO:0061999 regulation of cardiac endothelial to mesenchymal transition 1 1 1.86e-01
GO:BP GO:2000759 regulation of N-terminal peptidyl-lysine acetylation 1 1 1.86e-01
GO:BP GO:0003179 heart valve morphogenesis 3 55 1.86e-01
GO:BP GO:0019430 removal of superoxide radicals 2 17 1.86e-01
GO:BP GO:0072714 response to selenite ion 1 1 1.86e-01
GO:BP GO:0072715 cellular response to selenite ion 1 1 1.86e-01
GO:BP GO:0008152 metabolic process 74 8518 1.86e-01
GO:BP GO:1903788 positive regulation of glutathione biosynthetic process 1 1 1.86e-01
GO:BP GO:0006913 nucleocytoplasmic transport 7 295 1.86e-01
GO:BP GO:1902217 erythrocyte apoptotic process 1 1 1.86e-01
GO:BP GO:1904574 negative regulation of selenocysteine insertion sequence binding 1 1 1.86e-01
GO:BP GO:1904570 negative regulation of selenocysteine incorporation 1 1 1.86e-01
GO:BP GO:0051169 nuclear transport 7 295 1.86e-01
GO:BP GO:1904572 negative regulation of mRNA binding 1 1 1.86e-01
GO:BP GO:1901327 response to tacrolimus 1 1 1.86e-01
GO:BP GO:1904573 regulation of selenocysteine insertion sequence binding 1 1 1.86e-01
GO:BP GO:1904569 regulation of selenocysteine incorporation 1 1 1.86e-01
GO:BP GO:0009892 negative regulation of metabolic process 27 2293 1.86e-01
GO:BP GO:0090322 regulation of superoxide metabolic process 2 19 2.00e-01
GO:BP GO:0071450 cellular response to oxygen radical 2 19 2.00e-01
GO:BP GO:0071451 cellular response to superoxide 2 19 2.00e-01
GO:BP GO:0006406 mRNA export from nucleus 3 59 2.16e-01
GO:BP GO:0003170 heart valve development 3 65 2.28e-01
GO:BP GO:1901376 organic heteropentacyclic compound metabolic process 1 2 2.28e-01
GO:BP GO:0031325 positive regulation of cellular metabolic process 26 2270 2.28e-01
GO:BP GO:0003283 atrial septum development 2 23 2.28e-01
GO:BP GO:0035026 leading edge cell differentiation 1 2 2.28e-01
GO:BP GO:0043385 mycotoxin metabolic process 1 2 2.28e-01
GO:BP GO:1903508 positive regulation of nucleic acid-templated transcription 17 1315 2.28e-01
GO:BP GO:1902680 positive regulation of RNA biosynthetic process 17 1322 2.28e-01
GO:BP GO:1901377 organic heteropentacyclic compound catabolic process 1 2 2.28e-01
GO:BP GO:0003181 atrioventricular valve morphogenesis 2 25 2.28e-01
GO:BP GO:0030334 regulation of cell migration 11 706 2.28e-01
GO:BP GO:0034614 cellular response to reactive oxygen species 4 121 2.28e-01
GO:BP GO:1903786 regulation of glutathione biosynthetic process 1 2 2.28e-01
GO:BP GO:0043387 mycotoxin catabolic process 1 2 2.28e-01
GO:BP GO:0035544 negative regulation of SNARE complex assembly 1 2 2.28e-01
GO:BP GO:0045065 cytotoxic T cell differentiation 1 2 2.28e-01
GO:BP GO:1901028 regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway 2 25 2.28e-01
GO:BP GO:0009407 toxin catabolic process 1 2 2.28e-01
GO:BP GO:1905215 negative regulation of RNA binding 1 2 2.28e-01
GO:BP GO:0051172 negative regulation of nitrogen compound metabolic process 22 1849 2.28e-01
GO:BP GO:0008334 histone mRNA metabolic process 2 21 2.28e-01
GO:BP GO:2000120 positive regulation of sodium-dependent phosphate transport 1 2 2.28e-01
GO:BP GO:0006542 glutamine biosynthetic process 1 2 2.28e-01
GO:BP GO:0072752 cellular response to rapamycin 1 2 2.28e-01
GO:BP GO:0001174 transcriptional start site selection at RNA polymerase II promoter 1 2 2.28e-01
GO:BP GO:0001173 DNA-templated transcriptional start site selection 1 2 2.28e-01
GO:BP GO:0060689 cell differentiation involved in salivary gland development 1 2 2.28e-01
GO:BP GO:0060819 inactivation of X chromosome by genomic imprinting 1 2 2.28e-01
GO:BP GO:0071704 organic substance metabolic process 71 8169 2.28e-01
GO:BP GO:2000448 positive regulation of macrophage migration inhibitory factor signaling pathway 1 2 2.28e-01
GO:BP GO:0000349 generation of catalytic spliceosome for first transesterification step 1 2 2.28e-01
GO:BP GO:0000305 response to oxygen radical 2 22 2.28e-01
GO:BP GO:0000303 response to superoxide 2 21 2.28e-01
GO:BP GO:2001055 positive regulation of mesenchymal cell apoptotic process 1 2 2.28e-01
GO:BP GO:0006979 response to oxidative stress 7 352 2.28e-01
GO:BP GO:0070982 L-asparagine metabolic process 1 2 2.28e-01
GO:BP GO:0051066 dihydrobiopterin metabolic process 1 2 2.28e-01
GO:BP GO:0001827 inner cell mass cell fate commitment 1 2 2.28e-01
GO:BP GO:0090164 asymmetric Golgi ribbon formation 1 2 2.28e-01
GO:BP GO:1990478 response to ultrasound 1 2 2.28e-01
GO:BP GO:1900407 regulation of cellular response to oxidative stress 3 67 2.28e-01
GO:BP GO:0044238 primary metabolic process 68 7806 2.28e-01
GO:BP GO:0045585 positive regulation of cytotoxic T cell differentiation 1 2 2.28e-01
GO:BP GO:0046223 aflatoxin catabolic process 1 2 2.28e-01
GO:BP GO:0046222 aflatoxin metabolic process 1 2 2.28e-01
GO:BP GO:0001828 inner cell mass cellular morphogenesis 1 2 2.28e-01
GO:BP GO:0045583 regulation of cytotoxic T cell differentiation 1 2 2.28e-01
GO:BP GO:0140074 cardiac endothelial to mesenchymal transition 1 2 2.28e-01
GO:BP GO:0045893 positive regulation of DNA-templated transcription 17 1315 2.28e-01
GO:BP GO:0010632 regulation of epithelial cell migration 5 195 2.28e-01
GO:BP GO:0030855 epithelial cell differentiation 8 442 2.34e-01
GO:BP GO:0071772 response to BMP 4 131 2.34e-01
GO:BP GO:0071773 cellular response to BMP stimulus 4 131 2.34e-01
GO:BP GO:0003209 cardiac atrium morphogenesis 2 26 2.34e-01
GO:BP GO:0036010 protein localization to endosome 2 26 2.34e-01
GO:BP GO:0010634 positive regulation of epithelial cell migration 4 132 2.38e-01
GO:BP GO:0003171 atrioventricular valve development 2 27 2.46e-01
GO:BP GO:0010966 regulation of phosphate transport 1 3 2.51e-01
GO:BP GO:2000446 regulation of macrophage migration inhibitory factor signaling pathway 1 3 2.51e-01
GO:BP GO:0014916 regulation of lung blood pressure 1 3 2.51e-01
GO:BP GO:0010821 regulation of mitochondrion organization 4 135 2.51e-01
GO:BP GO:2000145 regulation of cell motility 11 742 2.51e-01
GO:BP GO:1904906 positive regulation of endothelial cell-matrix adhesion via fibronectin 1 3 2.51e-01
GO:BP GO:1904904 regulation of endothelial cell-matrix adhesion via fibronectin 1 3 2.51e-01
GO:BP GO:0006556 S-adenosylmethionine biosynthetic process 1 3 2.51e-01
GO:BP GO:0008219 cell death 19 1596 2.51e-01
GO:BP GO:2000118 regulation of sodium-dependent phosphate transport 1 3 2.51e-01
GO:BP GO:0010605 negative regulation of macromolecule metabolic process 24 2135 2.51e-01
GO:BP GO:0006405 RNA export from nucleus 3 78 2.51e-01
GO:BP GO:0010499 proteasomal ubiquitin-independent protein catabolic process 1 3 2.51e-01
GO:BP GO:0009891 positive regulation of biosynthetic process 19 1604 2.51e-01
GO:BP GO:1990737 response to manganese-induced endoplasmic reticulum stress 1 3 2.51e-01
GO:BP GO:0010729 positive regulation of hydrogen peroxide biosynthetic process 1 3 2.51e-01
GO:BP GO:0031328 positive regulation of cellular biosynthetic process 19 1564 2.51e-01
GO:BP GO:0006807 nitrogen compound metabolic process 65 7441 2.51e-01
GO:BP GO:1903300 negative regulation of hexokinase activity 1 3 2.51e-01
GO:BP GO:0051094 positive regulation of developmental process 13 957 2.51e-01
GO:BP GO:0140468 HRI-mediated signaling 1 3 2.51e-01
GO:BP GO:0035691 macrophage migration inhibitory factor signaling pathway 1 3 2.51e-01
GO:BP GO:0003007 heart morphogenesis 5 216 2.51e-01
GO:BP GO:0090674 endothelial cell-matrix adhesion via fibronectin 1 3 2.51e-01
GO:BP GO:0048514 blood vessel morphogenesis 8 462 2.51e-01
GO:BP GO:0090162 establishment of epithelial cell polarity 2 29 2.51e-01
GO:BP GO:0038160 CXCL12-activated CXCR4 signaling pathway 1 3 2.51e-01
GO:BP GO:1901355 response to rapamycin 1 3 2.51e-01
GO:BP GO:1901031 regulation of response to reactive oxygen species 2 28 2.51e-01
GO:BP GO:0099578 regulation of translation at postsynapse, modulating synaptic transmission 1 3 2.51e-01
GO:BP GO:0045776 negative regulation of blood pressure 2 30 2.51e-01
GO:BP GO:0031339 negative regulation of vesicle fusion 1 3 2.51e-01
GO:BP GO:0043549 regulation of kinase activity 9 560 2.51e-01
GO:BP GO:0099547 regulation of translation at synapse, modulating synaptic transmission 1 3 2.51e-01
GO:BP GO:0051239 regulation of multicellular organismal process 23 2035 2.51e-01
GO:BP GO:0002065 columnar/cuboidal epithelial cell differentiation 3 80 2.51e-01
GO:BP GO:1902882 regulation of response to oxidative stress 3 76 2.51e-01
GO:BP GO:0090076 relaxation of skeletal muscle 1 3 2.51e-01
GO:BP GO:0051684 maintenance of Golgi location 1 3 2.51e-01
GO:BP GO:0072740 cellular response to anisomycin 1 3 2.51e-01
GO:BP GO:0033132 negative regulation of glucokinase activity 1 3 2.51e-01
GO:BP GO:0060429 epithelium development 12 850 2.51e-01
GO:BP GO:0060591 chondroblast differentiation 1 3 2.51e-01
GO:BP GO:0071363 cellular response to growth factor stimulus 9 551 2.51e-01
GO:BP GO:1903131 mononuclear cell differentiation 6 294 2.51e-01
GO:BP GO:0071630 nuclear protein quality control by the ubiquitin-proteasome system 1 3 2.51e-01
GO:BP GO:0040012 regulation of locomotion 11 763 2.63e-01
GO:BP GO:0010557 positive regulation of macromolecule biosynthetic process 18 1507 2.64e-01
GO:BP GO:0034250 positive regulation of amide metabolic process 4 149 2.64e-01
GO:BP GO:0030510 regulation of BMP signaling pathway 3 84 2.64e-01
GO:BP GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway 6 303 2.64e-01
GO:BP GO:0070848 response to growth factor 9 572 2.64e-01
GO:BP GO:0051168 nuclear export 4 150 2.68e-01
GO:BP GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity 3 85 2.68e-01
GO:BP GO:0045943 positive regulation of transcription by RNA polymerase I 2 34 2.71e-01
GO:BP GO:0045588 positive regulation of gamma-delta T cell differentiation 1 4 2.71e-01
GO:BP GO:0046645 positive regulation of gamma-delta T cell activation 1 4 2.71e-01
GO:BP GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 5 230 2.71e-01
GO:BP GO:0097345 mitochondrial outer membrane permeabilization 2 35 2.71e-01
GO:BP GO:1990441 negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress 1 4 2.71e-01
GO:BP GO:0048732 gland development 6 318 2.71e-01
GO:BP GO:0072739 response to anisomycin 1 4 2.71e-01
GO:BP GO:0009894 regulation of catabolic process 12 875 2.71e-01
GO:BP GO:0090427 activation of meiosis 1 4 2.71e-01
GO:BP GO:0006408 snRNA export from nucleus 1 4 2.71e-01
GO:BP GO:0090673 endothelial cell-matrix adhesion 1 4 2.71e-01
GO:BP GO:0010726 positive regulation of hydrogen peroxide metabolic process 1 4 2.71e-01
GO:BP GO:1902037 negative regulation of hematopoietic stem cell differentiation 1 4 2.71e-01
GO:BP GO:1902512 positive regulation of apoptotic DNA fragmentation 1 4 2.71e-01
GO:BP GO:0003203 endocardial cushion morphogenesis 2 36 2.71e-01
GO:BP GO:1904029 regulation of cyclin-dependent protein kinase activity 3 88 2.71e-01
GO:BP GO:0003137 Notch signaling pathway involved in heart induction 1 4 2.71e-01
GO:BP GO:0035470 positive regulation of vascular wound healing 1 4 2.71e-01
GO:BP GO:0044341 sodium-dependent phosphate transport 1 4 2.71e-01
GO:BP GO:0035480 regulation of Notch signaling pathway involved in heart induction 1 4 2.71e-01
GO:BP GO:0035481 positive regulation of Notch signaling pathway involved in heart induction 1 4 2.71e-01
GO:BP GO:0032447 protein urmylation 1 4 2.71e-01
GO:BP GO:0035880 embryonic nail plate morphogenesis 1 4 2.71e-01
GO:BP GO:1904798 positive regulation of core promoter binding 1 4 2.71e-01
GO:BP GO:0035910 ascending aorta morphogenesis 1 4 2.71e-01
GO:BP GO:0038159 C-X-C chemokine receptor CXCR4 signaling pathway 1 4 2.71e-01
GO:BP GO:0018076 N-terminal peptidyl-lysine acetylation 1 4 2.71e-01
GO:BP GO:1904886 beta-catenin destruction complex disassembly 1 4 2.71e-01
GO:BP GO:0016477 cell migration 14 1081 2.71e-01
GO:BP GO:1905322 positive regulation of mesenchymal stem cell migration 1 4 2.71e-01
GO:BP GO:0002143 tRNA wobble position uridine thiolation 1 4 2.71e-01
GO:BP GO:1905320 regulation of mesenchymal stem cell migration 1 4 2.71e-01
GO:BP GO:0016480 negative regulation of transcription by RNA polymerase III 1 4 2.71e-01
GO:BP GO:0003230 cardiac atrium development 2 34 2.71e-01
GO:BP GO:0043516 regulation of DNA damage response, signal transduction by p53 class mediator 2 35 2.71e-01
GO:BP GO:0030513 positive regulation of BMP signaling pathway 2 34 2.71e-01
GO:BP GO:1905319 mesenchymal stem cell migration 1 4 2.71e-01
GO:BP GO:0071495 cellular response to endogenous stimulus 14 1107 2.74e-01
GO:BP GO:0000302 response to reactive oxygen species 4 160 2.74e-01
GO:BP GO:0010941 regulation of cell death 15 1219 2.81e-01
GO:BP GO:0051254 positive regulation of RNA metabolic process 17 1441 2.83e-01
GO:BP GO:0006915 apoptotic process 17 1443 2.84e-01
GO:BP GO:0032879 regulation of localization 18 1555 2.84e-01
GO:BP GO:1902110 positive regulation of mitochondrial membrane permeability involved in apoptotic process 2 38 2.84e-01
GO:BP GO:0045912 negative regulation of carbohydrate metabolic process 2 38 2.84e-01
GO:BP GO:0008038 neuron recognition 2 39 2.86e-01
GO:BP GO:0061419 positive regulation of transcription from RNA polymerase II promoter in response to hypoxia 1 5 2.86e-01
GO:BP GO:0060536 cartilage morphogenesis 1 5 2.86e-01
GO:BP GO:2000304 positive regulation of ceramide biosynthetic process 1 5 2.86e-01
GO:BP GO:0070169 positive regulation of biomineral tissue development 2 39 2.86e-01
GO:BP GO:2001053 regulation of mesenchymal cell apoptotic process 1 5 2.86e-01
GO:BP GO:0070309 lens fiber cell morphogenesis 1 5 2.86e-01
GO:BP GO:1903202 negative regulation of oxidative stress-induced cell death 2 40 2.86e-01
GO:BP GO:0032057 negative regulation of translational initiation in response to stress 1 5 2.86e-01
GO:BP GO:0045053 protein retention in Golgi apparatus 1 5 2.86e-01
GO:BP GO:0034227 tRNA thio-modification 1 5 2.86e-01
GO:BP GO:0010728 regulation of hydrogen peroxide biosynthetic process 1 5 2.86e-01
GO:BP GO:0045595 regulation of cell differentiation 14 1137 2.86e-01
GO:BP GO:0045900 negative regulation of translational elongation 1 5 2.86e-01
GO:BP GO:1990089 response to nerve growth factor 2 41 2.86e-01
GO:BP GO:1990090 cellular response to nerve growth factor stimulus 2 41 2.86e-01
GO:BP GO:1905166 negative regulation of lysosomal protein catabolic process 1 5 2.86e-01
GO:BP GO:1903626 positive regulation of DNA catabolic process 1 5 2.86e-01
GO:BP GO:0046654 tetrahydrofolate biosynthetic process 1 5 2.86e-01
GO:BP GO:0035905 ascending aorta development 1 5 2.86e-01
GO:BP GO:0009893 positive regulation of metabolic process 29 2880 2.86e-01
GO:BP GO:0090650 cellular response to oxygen-glucose deprivation 1 5 2.86e-01
GO:BP GO:0009250 glucan biosynthetic process 2 39 2.86e-01
GO:BP GO:0090154 positive regulation of sphingolipid biosynthetic process 1 5 2.86e-01
GO:BP GO:1904351 negative regulation of protein catabolic process in the vacuole 1 5 2.86e-01
GO:BP GO:1904796 regulation of core promoter binding 1 5 2.86e-01
GO:BP GO:0090425 acinar cell differentiation 1 5 2.86e-01
GO:BP GO:1902686 mitochondrial outer membrane permeabilization involved in programmed cell death 2 40 2.86e-01
GO:BP GO:0071362 cellular response to ether 1 5 2.86e-01
GO:BP GO:0001826 inner cell mass cell differentiation 1 5 2.86e-01
GO:BP GO:0006528 asparagine metabolic process 1 5 2.86e-01
GO:BP GO:0005978 glycogen biosynthetic process 2 39 2.86e-01
GO:BP GO:0003289 atrial septum primum morphogenesis 1 5 2.86e-01
GO:BP GO:0003274 endocardial cushion fusion 1 5 2.86e-01
GO:BP GO:0003284 septum primum development 1 5 2.86e-01
GO:BP GO:0000393 spliceosomal conformational changes to generate catalytic conformation 1 5 2.86e-01
GO:BP GO:0060070 canonical Wnt signaling pathway 5 251 2.88e-01
GO:BP GO:0050714 positive regulation of protein secretion 3 100 2.88e-01
GO:BP GO:0035295 tube development 11 821 2.88e-01
GO:BP GO:0045597 positive regulation of cell differentiation 9 620 2.89e-01
GO:BP GO:0090132 epithelium migration 5 252 2.89e-01
GO:BP GO:0010631 epithelial cell migration 5 252 2.89e-01
GO:BP GO:0006801 superoxide metabolic process 2 42 2.91e-01
GO:BP GO:1902108 regulation of mitochondrial membrane permeability involved in apoptotic process 2 42 2.91e-01
GO:BP GO:0051030 snRNA transport 1 6 2.92e-01
GO:BP GO:0140245 regulation of translation at postsynapse 1 6 2.92e-01
GO:BP GO:0007023 post-chaperonin tubulin folding pathway 1 6 2.92e-01
GO:BP GO:0140243 regulation of translation at synapse 1 6 2.92e-01
GO:BP GO:0090303 positive regulation of wound healing 2 45 2.92e-01
GO:BP GO:0120183 positive regulation of focal adhesion disassembly 1 6 2.92e-01
GO:BP GO:0050793 regulation of developmental process 20 1835 2.92e-01
GO:BP GO:0051661 maintenance of centrosome location 1 6 2.92e-01
GO:BP GO:0045586 regulation of gamma-delta T cell differentiation 1 6 2.92e-01
GO:BP GO:0045682 regulation of epidermis development 2 45 2.92e-01
GO:BP GO:0007179 transforming growth factor beta receptor signaling pathway 4 179 2.92e-01
GO:BP GO:1902949 positive regulation of tau-protein kinase activity 1 6 2.92e-01
GO:BP GO:0001568 blood vessel development 8 534 2.92e-01
GO:BP GO:2000677 regulation of transcription regulatory region DNA binding 2 43 2.92e-01
GO:BP GO:0090130 tissue migration 5 256 2.92e-01
GO:BP GO:1905710 positive regulation of membrane permeability 2 45 2.92e-01
GO:BP GO:0045944 positive regulation of transcription by RNA polymerase II 12 937 2.92e-01
GO:BP GO:0001649 osteoblast differentiation 4 179 2.92e-01
GO:BP GO:0032324 molybdopterin cofactor biosynthetic process 1 6 2.92e-01
GO:BP GO:0019720 Mo-molybdopterin cofactor metabolic process 1 6 2.92e-01
GO:BP GO:0051189 prosthetic group metabolic process 1 6 2.92e-01
GO:BP GO:0048518 positive regulation of biological process 42 4579 2.92e-01
GO:BP GO:0099562 maintenance of postsynaptic density structure 1 6 2.92e-01
GO:BP GO:0003278 apoptotic process involved in heart morphogenesis 1 6 2.92e-01
GO:BP GO:0051101 regulation of DNA binding 3 104 2.92e-01
GO:BP GO:0046643 regulation of gamma-delta T cell activation 1 6 2.92e-01
GO:BP GO:0006356 regulation of transcription by RNA polymerase I 2 45 2.92e-01
GO:BP GO:0051049 regulation of transport 15 1267 2.92e-01
GO:BP GO:0060075 regulation of resting membrane potential 1 6 2.92e-01
GO:BP GO:0120182 regulation of focal adhesion disassembly 1 6 2.92e-01
GO:BP GO:0043545 molybdopterin cofactor metabolic process 1 6 2.92e-01
GO:BP GO:0035794 positive regulation of mitochondrial membrane permeability 2 43 2.92e-01
GO:BP GO:0043009 chordate embryonic development 8 534 2.92e-01
GO:BP GO:0060710 chorio-allantoic fusion 1 6 2.92e-01
GO:BP GO:1901525 negative regulation of mitophagy 1 6 2.92e-01
GO:BP GO:0061343 cell adhesion involved in heart morphogenesis 1 6 2.92e-01
GO:BP GO:0038146 chemokine (C-X-C motif) ligand 12 signaling pathway 1 6 2.92e-01
GO:BP GO:0006984 ER-nucleus signaling pathway 2 45 2.92e-01
GO:BP GO:0006777 Mo-molybdopterin cofactor biosynthetic process 1 6 2.92e-01
GO:BP GO:0030098 lymphocyte differentiation 5 260 2.92e-01
GO:BP GO:0012501 programmed cell death 17 1479 2.92e-01
GO:BP GO:0042789 mRNA transcription by RNA polymerase II 2 45 2.92e-01
GO:BP GO:0090287 regulation of cellular response to growth factor stimulus 5 265 2.97e-01
GO:BP GO:0003197 endocardial cushion development 2 46 2.97e-01
GO:BP GO:0043392 negative regulation of DNA binding 2 46 2.97e-01
GO:BP GO:0040011 locomotion 12 954 2.97e-01
GO:BP GO:0010823 negative regulation of mitochondrion organization 2 46 2.97e-01
GO:BP GO:0002244 hematopoietic progenitor cell differentiation 3 109 3.02e-01
GO:BP GO:0030217 T cell differentiation 4 185 3.07e-01
GO:BP GO:0050708 regulation of protein secretion 4 185 3.07e-01
GO:BP GO:0046146 tetrahydrobiopterin metabolic process 1 7 3.08e-01
GO:BP GO:0042492 gamma-delta T cell differentiation 1 7 3.08e-01
GO:BP GO:0046543 development of secondary female sexual characteristics 1 7 3.08e-01
GO:BP GO:2000171 negative regulation of dendrite development 1 7 3.08e-01
GO:BP GO:1903147 negative regulation of autophagy of mitochondrion 1 7 3.08e-01
GO:BP GO:0048870 cell motility 14 1182 3.08e-01
GO:BP GO:0035967 cellular response to topologically incorrect protein 3 111 3.08e-01
GO:BP GO:0009396 folic acid-containing compound biosynthetic process 1 7 3.08e-01
GO:BP GO:0097152 mesenchymal cell apoptotic process 1 7 3.08e-01
GO:BP GO:0009404 toxin metabolic process 1 7 3.08e-01
GO:BP GO:0006398 mRNA 3’-end processing by stem-loop binding and cleavage 1 7 3.08e-01
GO:BP GO:0061312 BMP signaling pathway involved in heart development 1 7 3.08e-01
GO:BP GO:0031329 regulation of cellular catabolic process 8 555 3.08e-01
GO:BP GO:0006729 tetrahydrobiopterin biosynthetic process 1 7 3.08e-01
GO:BP GO:0090649 response to oxygen-glucose deprivation 1 7 3.08e-01
GO:BP GO:0030097 hemopoiesis 9 656 3.08e-01
GO:BP GO:0019083 viral transcription 2 48 3.08e-01
GO:BP GO:0045472 response to ether 1 7 3.08e-01
GO:BP GO:1902255 positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator 1 7 3.08e-01
GO:BP GO:0003357 noradrenergic neuron differentiation 1 7 3.08e-01
GO:BP GO:1905461 positive regulation of vascular associated smooth muscle cell apoptotic process 1 7 3.08e-01
GO:BP GO:0060548 negative regulation of cell death 10 756 3.08e-01
GO:BP GO:0009792 embryo development ending in birth or egg hatching 8 551 3.08e-01
GO:BP GO:1900246 positive regulation of RIG-I signaling pathway 1 7 3.08e-01
GO:BP GO:0006370 7-methylguanosine mRNA capping 1 7 3.08e-01
GO:BP GO:0043619 regulation of transcription from RNA polymerase II promoter in response to oxidative stress 1 7 3.08e-01
GO:BP GO:0033131 regulation of glucokinase activity 1 7 3.08e-01
GO:BP GO:0009299 mRNA transcription 2 50 3.14e-01
GO:BP GO:0001944 vasculature development 8 559 3.14e-01
GO:BP GO:0072132 mesenchyme morphogenesis 2 50 3.14e-01
GO:BP GO:0048646 anatomical structure formation involved in morphogenesis 11 870 3.14e-01
GO:BP GO:0035239 tube morphogenesis 9 663 3.18e-01
GO:BP GO:0009896 positive regulation of catabolic process 7 464 3.19e-01
GO:BP GO:0042149 cellular response to glucose starvation 2 51 3.22e-01
GO:BP GO:1902510 regulation of apoptotic DNA fragmentation 1 8 3.24e-01
GO:BP GO:0120181 focal adhesion disassembly 1 8 3.24e-01
GO:BP GO:0042416 dopamine biosynthetic process 1 8 3.24e-01
GO:BP GO:0035878 nail development 1 8 3.24e-01
GO:BP GO:0120180 cell-substrate junction disassembly 1 8 3.24e-01
GO:BP GO:0045607 regulation of inner ear auditory receptor cell differentiation 1 8 3.24e-01
GO:BP GO:0032344 regulation of aldosterone metabolic process 1 8 3.24e-01
GO:BP GO:0032347 regulation of aldosterone biosynthetic process 1 8 3.24e-01
GO:BP GO:1902947 regulation of tau-protein kinase activity 1 8 3.24e-01
GO:BP GO:0045631 regulation of mechanoreceptor differentiation 1 8 3.24e-01
GO:BP GO:1990416 cellular response to brain-derived neurotrophic factor stimulus 1 8 3.24e-01
GO:BP GO:0009452 7-methylguanosine RNA capping 1 8 3.24e-01
GO:BP GO:0034393 positive regulation of smooth muscle cell apoptotic process 1 8 3.24e-01
GO:BP GO:1903071 positive regulation of ER-associated ubiquitin-dependent protein catabolic process 1 8 3.24e-01
GO:BP GO:0043269 regulation of monoatomic ion transport 6 373 3.24e-01
GO:BP GO:0036353 histone H2A-K119 monoubiquitination 1 8 3.24e-01
GO:BP GO:0050966 detection of mechanical stimulus involved in sensory perception of pain 1 8 3.24e-01
GO:BP GO:0071287 cellular response to manganese ion 1 8 3.24e-01
GO:BP GO:0090394 negative regulation of excitatory postsynaptic potential 1 8 3.24e-01
GO:BP GO:2000980 regulation of inner ear receptor cell differentiation 1 8 3.24e-01
GO:BP GO:0071499 cellular response to laminar fluid shear stress 1 8 3.24e-01
GO:BP GO:0051028 mRNA transport 3 117 3.24e-01
GO:BP GO:1903299 regulation of hexokinase activity 1 8 3.24e-01
GO:BP GO:0000271 polysaccharide biosynthetic process 2 53 3.24e-01
GO:BP GO:0001501 skeletal system development 6 377 3.25e-01
GO:BP GO:1902966 positive regulation of protein localization to early endosome 1 9 3.32e-01
GO:BP GO:0051173 positive regulation of nitrogen compound metabolic process 24 2412 3.32e-01
GO:BP GO:0097064 ncRNA export from nucleus 1 9 3.32e-01
GO:BP GO:0046629 gamma-delta T cell activation 1 9 3.32e-01
GO:BP GO:0034214 protein hexamerization 1 9 3.32e-01
GO:BP GO:0032446 protein modification by small protein conjugation 10 787 3.32e-01
GO:BP GO:0060352 cell adhesion molecule production 1 9 3.32e-01
GO:BP GO:2001214 positive regulation of vasculogenesis 1 9 3.32e-01
GO:BP GO:0007021 tubulin complex assembly 1 9 3.32e-01
GO:BP GO:0006705 mineralocorticoid biosynthetic process 1 9 3.32e-01
GO:BP GO:1903036 positive regulation of response to wounding 2 55 3.32e-01
GO:BP GO:0030509 BMP signaling pathway 3 123 3.32e-01
GO:BP GO:1902965 regulation of protein localization to early endosome 1 9 3.32e-01
GO:BP GO:0045859 regulation of protein kinase activity 7 479 3.32e-01
GO:BP GO:0045836 positive regulation of meiotic nuclear division 1 9 3.32e-01
GO:BP GO:0045669 positive regulation of osteoblast differentiation 2 54 3.32e-01
GO:BP GO:0051338 regulation of transferase activity 9 679 3.32e-01
GO:BP GO:0045136 development of secondary sexual characteristics 1 9 3.32e-01
GO:BP GO:0090161 Golgi ribbon formation 1 9 3.32e-01
GO:BP GO:0046902 regulation of mitochondrial membrane permeability 2 54 3.32e-01
GO:BP GO:1905459 regulation of vascular associated smooth muscle cell apoptotic process 1 9 3.32e-01
GO:BP GO:0003129 heart induction 1 9 3.32e-01
GO:BP GO:0048757 pigment granule maturation 1 9 3.32e-01
GO:BP GO:0031953 negative regulation of protein autophosphorylation 1 9 3.32e-01
GO:BP GO:0032342 aldosterone biosynthetic process 1 9 3.32e-01
GO:BP GO:1905288 vascular associated smooth muscle cell apoptotic process 1 9 3.32e-01
GO:BP GO:0061043 regulation of vascular wound healing 1 9 3.32e-01
GO:BP GO:0043067 regulation of programmed cell death 13 1111 3.32e-01
GO:BP GO:0048519 negative regulation of biological process 37 4045 3.32e-01
GO:BP GO:0002521 leukocyte differentiation 6 382 3.32e-01
GO:BP GO:0002407 dendritic cell chemotaxis 1 9 3.32e-01
GO:BP GO:0035646 endosome to melanosome transport 1 9 3.32e-01
GO:BP GO:0010660 regulation of muscle cell apoptotic process 2 56 3.32e-01
GO:BP GO:0043485 endosome to pigment granule transport 1 9 3.32e-01
GO:BP GO:0098880 maintenance of postsynaptic specialization structure 1 9 3.32e-01
GO:BP GO:1903201 regulation of oxidative stress-induced cell death 2 56 3.32e-01
GO:BP GO:0061180 mammary gland epithelium development 2 57 3.37e-01
GO:BP GO:0001525 angiogenesis 6 390 3.39e-01
GO:BP GO:0017015 regulation of transforming growth factor beta receptor signaling pathway 3 128 3.45e-01
GO:BP GO:0031124 mRNA 3’-end processing 2 58 3.45e-01
GO:BP GO:0008544 epidermis development 4 210 3.46e-01
GO:BP GO:0043065 positive regulation of apoptotic process 6 393 3.46e-01
GO:BP GO:0042481 regulation of odontogenesis 1 10 3.48e-01
GO:BP GO:0001514 selenocysteine incorporation 1 10 3.48e-01
GO:BP GO:0060174 limb bud formation 1 10 3.48e-01
GO:BP GO:1903844 regulation of cellular response to transforming growth factor beta stimulus 3 129 3.48e-01
GO:BP GO:0033690 positive regulation of osteoblast proliferation 1 10 3.48e-01
GO:BP GO:1903624 regulation of DNA catabolic process 1 10 3.48e-01
GO:BP GO:0006283 transcription-coupled nucleotide-excision repair 1 10 3.48e-01
GO:BP GO:1902415 regulation of mRNA binding 1 10 3.48e-01
GO:BP GO:0002328 pro-B cell differentiation 1 10 3.48e-01
GO:BP GO:2000826 regulation of heart morphogenesis 1 10 3.48e-01
GO:BP GO:0006451 translational readthrough 1 10 3.48e-01
GO:BP GO:0003211 cardiac ventricle formation 1 10 3.48e-01
GO:BP GO:0097201 negative regulation of transcription from RNA polymerase II promoter in response to stress 1 10 3.48e-01
GO:BP GO:0008212 mineralocorticoid metabolic process 1 10 3.48e-01
GO:BP GO:0048194 Golgi vesicle budding 1 10 3.48e-01
GO:BP GO:1903069 regulation of ER-associated ubiquitin-dependent protein catabolic process 1 10 3.48e-01
GO:BP GO:0007423 sensory organ development 6 396 3.48e-01
GO:BP GO:0050965 detection of temperature stimulus involved in sensory perception of pain 1 10 3.48e-01
GO:BP GO:0032341 aldosterone metabolic process 1 10 3.48e-01
GO:BP GO:0045935 positive regulation of nucleobase-containing compound metabolic process 17 1602 3.48e-01
GO:BP GO:0010657 muscle cell apoptotic process 2 60 3.48e-01
GO:BP GO:0043068 positive regulation of programmed cell death 6 399 3.49e-01
GO:BP GO:0045619 regulation of lymphocyte differentiation 3 132 3.52e-01
GO:BP GO:0061418 regulation of transcription from RNA polymerase II promoter in response to hypoxia 1 11 3.56e-01
GO:BP GO:1904753 negative regulation of vascular associated smooth muscle cell migration 1 11 3.56e-01
GO:BP GO:1902946 protein localization to early endosome 1 11 3.56e-01
GO:BP GO:0048522 positive regulation of cellular process 37 4099 3.56e-01
GO:BP GO:0090280 positive regulation of calcium ion import 1 11 3.56e-01
GO:BP GO:0010508 positive regulation of autophagy 3 133 3.56e-01
GO:BP GO:1905165 regulation of lysosomal protein catabolic process 1 11 3.56e-01
GO:BP GO:0006396 RNA processing 11 929 3.56e-01
GO:BP GO:0030335 positive regulation of cell migration 6 407 3.56e-01
GO:BP GO:0051100 negative regulation of binding 3 135 3.56e-01
GO:BP GO:2000303 regulation of ceramide biosynthetic process 1 11 3.56e-01
GO:BP GO:1990440 positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress 1 11 3.56e-01
GO:BP GO:0051549 positive regulation of keratinocyte migration 1 11 3.56e-01
GO:BP GO:0043482 cellular pigment accumulation 1 11 3.56e-01
GO:BP GO:0071044 histone mRNA catabolic process 1 11 3.56e-01
GO:BP GO:0016567 protein ubiquitination 9 717 3.56e-01
GO:BP GO:0051657 maintenance of organelle location 1 11 3.56e-01
GO:BP GO:0009713 catechol-containing compound biosynthetic process 1 11 3.56e-01
GO:BP GO:0000086 G2/M transition of mitotic cell cycle 3 134 3.56e-01
GO:BP GO:0070307 lens fiber cell development 1 11 3.56e-01
GO:BP GO:0001562 response to protozoan 1 11 3.56e-01
GO:BP GO:0006360 transcription by RNA polymerase I 2 62 3.56e-01
GO:BP GO:0043476 pigment accumulation 1 11 3.56e-01
GO:BP GO:0022604 regulation of cell morphogenesis 4 220 3.56e-01
GO:BP GO:0050665 hydrogen peroxide biosynthetic process 1 11 3.56e-01
GO:BP GO:0042423 catecholamine biosynthetic process 1 11 3.56e-01
GO:BP GO:0030007 intracellular potassium ion homeostasis 1 11 3.56e-01
GO:BP GO:0043922 negative regulation by host of viral transcription 1 11 3.56e-01
GO:BP GO:1901533 negative regulation of hematopoietic progenitor cell differentiation 1 11 3.56e-01
GO:BP GO:0003183 mitral valve morphogenesis 1 11 3.56e-01
GO:BP GO:0065008 regulation of biological quality 21 2102 3.59e-01
GO:BP GO:0001503 ossification 5 313 3.59e-01
GO:BP GO:0010506 regulation of autophagy 5 313 3.59e-01
GO:BP GO:0071560 cellular response to transforming growth factor beta stimulus 4 222 3.60e-01
GO:BP GO:0005977 glycogen metabolic process 2 64 3.60e-01
GO:BP GO:0090559 regulation of membrane permeability 2 64 3.60e-01
GO:BP GO:0044042 glucan metabolic process 2 64 3.60e-01
GO:BP GO:0009719 response to endogenous stimulus 14 1278 3.60e-01
GO:BP GO:0008285 negative regulation of cell population proliferation 7 513 3.64e-01
GO:BP GO:0034309 primary alcohol biosynthetic process 1 12 3.65e-01
GO:BP GO:0050884 neuromuscular process controlling posture 1 12 3.65e-01
GO:BP GO:0071248 cellular response to metal ion 3 139 3.65e-01
GO:BP GO:1905038 regulation of membrane lipid metabolic process 1 12 3.65e-01
GO:BP GO:1903428 positive regulation of reactive oxygen species biosynthetic process 1 12 3.65e-01
GO:BP GO:0007214 gamma-aminobutyric acid signaling pathway 1 12 3.65e-01
GO:BP GO:2000622 regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 1 12 3.65e-01
GO:BP GO:0090153 regulation of sphingolipid biosynthetic process 1 12 3.65e-01
GO:BP GO:1901699 cellular response to nitrogen compound 7 517 3.65e-01
GO:BP GO:0051177 meiotic sister chromatid cohesion 1 12 3.65e-01
GO:BP GO:0098869 cellular oxidant detoxification 2 65 3.65e-01
GO:BP GO:2000009 negative regulation of protein localization to cell surface 1 12 3.65e-01
GO:BP GO:0042559 pteridine-containing compound biosynthetic process 1 12 3.65e-01
GO:BP GO:0051098 regulation of binding 5 317 3.65e-01
GO:BP GO:1901030 positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway 1 12 3.65e-01
GO:BP GO:0010035 response to inorganic substance 6 414 3.65e-01
GO:BP GO:0003174 mitral valve development 1 12 3.65e-01
GO:BP GO:0071559 response to transforming growth factor beta 4 227 3.65e-01
GO:BP GO:0061029 eyelid development in camera-type eye 1 12 3.65e-01
GO:BP GO:0050961 detection of temperature stimulus involved in sensory perception 1 12 3.65e-01
GO:BP GO:0030336 negative regulation of cell migration 4 227 3.65e-01
GO:BP GO:0048523 negative regulation of cellular process 33 3625 3.67e-01
GO:BP GO:0060411 cardiac septum morphogenesis 2 67 3.70e-01
GO:BP GO:0070167 regulation of biomineral tissue development 2 67 3.70e-01
GO:BP GO:0035542 regulation of SNARE complex assembly 1 13 3.70e-01
GO:BP GO:0016048 detection of temperature stimulus 1 13 3.70e-01
GO:BP GO:1905214 regulation of RNA binding 1 13 3.70e-01
GO:BP GO:0031290 retinal ganglion cell axon guidance 1 13 3.70e-01
GO:BP GO:1903206 negative regulation of hydrogen peroxide-induced cell death 1 13 3.70e-01
GO:BP GO:1904350 regulation of protein catabolic process in the vacuole 1 13 3.70e-01
GO:BP GO:0006309 apoptotic DNA fragmentation 1 13 3.70e-01
GO:BP GO:0034248 regulation of amide metabolic process 6 424 3.70e-01
GO:BP GO:0030330 DNA damage response, signal transduction by p53 class mediator 2 69 3.70e-01
GO:BP GO:0003281 ventricular septum development 2 69 3.70e-01
GO:BP GO:1905668 positive regulation of protein localization to endosome 1 13 3.70e-01
GO:BP GO:0006109 regulation of carbohydrate metabolic process 3 144 3.70e-01
GO:BP GO:0051547 regulation of keratinocyte migration 1 13 3.70e-01
GO:BP GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway 1 13 3.70e-01
GO:BP GO:0001682 tRNA 5’-leader removal 1 13 3.70e-01
GO:BP GO:2000147 positive regulation of cell motility 6 421 3.70e-01
GO:BP GO:1990253 cellular response to leucine starvation 1 13 3.70e-01
GO:BP GO:2001212 regulation of vasculogenesis 1 13 3.70e-01
GO:BP GO:0050951 sensory perception of temperature stimulus 1 13 3.70e-01
GO:BP GO:0006750 glutathione biosynthetic process 1 13 3.70e-01
GO:BP GO:0045820 negative regulation of glycolytic process 1 13 3.70e-01
GO:BP GO:0046500 S-adenosylmethionine metabolic process 1 13 3.70e-01
GO:BP GO:0050658 RNA transport 3 144 3.70e-01
GO:BP GO:1901524 regulation of mitophagy 1 13 3.70e-01
GO:BP GO:0010594 regulation of endothelial cell migration 3 143 3.70e-01
GO:BP GO:0098876 vesicle-mediated transport to the plasma membrane 3 143 3.70e-01
GO:BP GO:0042104 positive regulation of activated T cell proliferation 1 13 3.70e-01
GO:BP GO:0048714 positive regulation of oligodendrocyte differentiation 1 13 3.70e-01
GO:BP GO:0050657 nucleic acid transport 3 144 3.70e-01
GO:BP GO:1901032 negative regulation of response to reactive oxygen species 1 13 3.70e-01
GO:BP GO:0042474 middle ear morphogenesis 1 13 3.70e-01
GO:BP GO:0034976 response to endoplasmic reticulum stress 4 234 3.73e-01
GO:BP GO:0030968 endoplasmic reticulum unfolded protein response 2 70 3.74e-01
GO:BP GO:0051236 establishment of RNA localization 3 147 3.74e-01
GO:BP GO:0006813 potassium ion transport 3 147 3.74e-01
GO:BP GO:0040017 positive regulation of locomotion 6 429 3.77e-01
GO:BP GO:0003207 cardiac chamber formation 1 14 3.78e-01
GO:BP GO:0006349 regulation of gene expression by genomic imprinting 1 14 3.78e-01
GO:BP GO:0099505 regulation of presynaptic membrane potential 1 14 3.78e-01
GO:BP GO:2000146 negative regulation of cell motility 4 236 3.78e-01
GO:BP GO:0014819 regulation of skeletal muscle contraction 1 14 3.78e-01
GO:BP GO:0051000 positive regulation of nitric-oxide synthase activity 1 14 3.78e-01
GO:BP GO:0044839 cell cycle G2/M phase transition 3 149 3.78e-01
GO:BP GO:0046184 aldehyde biosynthetic process 1 14 3.78e-01
GO:BP GO:0046653 tetrahydrofolate metabolic process 1 14 3.78e-01
GO:BP GO:0003198 epithelial to mesenchymal transition involved in endocardial cushion formation 1 14 3.78e-01
GO:BP GO:0048485 sympathetic nervous system development 1 14 3.78e-01
GO:BP GO:0060644 mammary gland epithelial cell differentiation 1 14 3.78e-01
GO:BP GO:0003159 morphogenesis of an endothelium 1 14 3.78e-01
GO:BP GO:0035966 response to topologically incorrect protein 3 150 3.78e-01
GO:BP GO:0051645 Golgi localization 1 14 3.78e-01
GO:BP GO:0010310 regulation of hydrogen peroxide metabolic process 1 14 3.78e-01
GO:BP GO:1905666 regulation of protein localization to endosome 1 14 3.78e-01
GO:BP GO:0060021 roof of mouth development 2 71 3.78e-01
GO:BP GO:0023019 signal transduction involved in regulation of gene expression 1 14 3.78e-01
GO:BP GO:0034616 response to laminar fluid shear stress 1 14 3.78e-01
GO:BP GO:0061154 endothelial tube morphogenesis 1 14 3.78e-01
GO:BP GO:0042981 regulation of apoptotic process 12 1088 3.78e-01
GO:BP GO:0071732 cellular response to nitric oxide 1 14 3.78e-01
GO:BP GO:0003085 negative regulation of systemic arterial blood pressure 1 14 3.78e-01
GO:BP GO:0070301 cellular response to hydrogen peroxide 2 73 3.82e-01
GO:BP GO:0006112 energy reserve metabolic process 2 73 3.82e-01
GO:BP GO:0099587 inorganic ion import across plasma membrane 2 73 3.82e-01
GO:BP GO:0098659 inorganic cation import across plasma membrane 2 73 3.82e-01
GO:BP GO:0043266 regulation of potassium ion transport 2 73 3.82e-01
GO:BP GO:0016051 carbohydrate biosynthetic process 3 155 3.86e-01
GO:BP GO:0019184 nonribosomal peptide biosynthetic process 1 15 3.86e-01
GO:BP GO:0060349 bone morphogenesis 2 74 3.86e-01
GO:BP GO:1903861 positive regulation of dendrite extension 1 15 3.86e-01
GO:BP GO:0062149 detection of stimulus involved in sensory perception of pain 1 15 3.86e-01
GO:BP GO:0016973 poly(A)+ mRNA export from nucleus 1 15 3.86e-01
GO:BP GO:0051240 positive regulation of multicellular organismal process 12 1101 3.86e-01
GO:BP GO:2000637 positive regulation of miRNA-mediated gene silencing 1 15 3.86e-01
GO:BP GO:0048705 skeletal system morphogenesis 3 155 3.86e-01
GO:BP GO:0090030 regulation of steroid hormone biosynthetic process 1 15 3.86e-01
GO:BP GO:0051546 keratinocyte migration 1 15 3.86e-01
GO:BP GO:0048598 embryonic morphogenesis 6 440 3.86e-01
GO:BP GO:0036336 dendritic cell migration 1 15 3.86e-01
GO:BP GO:0010042 response to manganese ion 1 15 3.86e-01
GO:BP GO:1902036 regulation of hematopoietic stem cell differentiation 1 15 3.86e-01
GO:BP GO:0010942 positive regulation of cell death 6 441 3.86e-01
GO:BP GO:0036473 cell death in response to oxidative stress 2 75 3.86e-01
GO:BP GO:0043583 ear development 3 153 3.86e-01
GO:BP GO:0034390 smooth muscle cell apoptotic process 1 15 3.86e-01
GO:BP GO:0006474 N-terminal protein amino acid acetylation 1 15 3.86e-01
GO:BP GO:0034391 regulation of smooth muscle cell apoptotic process 1 15 3.86e-01
GO:BP GO:0043217 myelin maintenance 1 15 3.86e-01
GO:BP GO:0045582 positive regulation of T cell differentiation 2 74 3.86e-01
GO:BP GO:0009790 embryo development 10 875 3.86e-01
GO:BP GO:0060148 positive regulation of post-transcriptional gene silencing 1 16 3.92e-01
GO:BP GO:0043278 response to morphine 1 16 3.92e-01
GO:BP GO:1902170 cellular response to reactive nitrogen species 1 16 3.92e-01
GO:BP GO:2000042 negative regulation of double-strand break repair via homologous recombination 1 16 3.92e-01
GO:BP GO:0010226 response to lithium ion 1 16 3.92e-01
GO:BP GO:0006044 N-acetylglucosamine metabolic process 1 16 3.92e-01
GO:BP GO:0071731 response to nitric oxide 1 16 3.92e-01
GO:BP GO:0010566 regulation of ketone biosynthetic process 1 16 3.92e-01
GO:BP GO:0035269 protein O-linked mannosylation 1 16 3.92e-01
GO:BP GO:0042633 hair cycle 2 78 3.92e-01
GO:BP GO:0042325 regulation of phosphorylation 10 881 3.92e-01
GO:BP GO:0042303 molting cycle 2 78 3.92e-01
GO:BP GO:1904294 positive regulation of ERAD pathway 1 16 3.92e-01
GO:BP GO:0003128 heart field specification 1 16 3.92e-01
GO:BP GO:0060716 labyrinthine layer blood vessel development 1 16 3.92e-01
GO:BP GO:0072359 circulatory system development 10 884 3.92e-01
GO:BP GO:0009636 response to toxic substance 3 158 3.92e-01
GO:BP GO:0099116 tRNA 5’-end processing 1 16 3.92e-01
GO:BP GO:0009084 glutamine family amino acid biosynthetic process 1 16 3.92e-01
GO:BP GO:0050901 leukocyte tethering or rolling 1 16 3.92e-01
GO:BP GO:0009612 response to mechanical stimulus 3 158 3.92e-01
GO:BP GO:0014072 response to isoquinoline alkaloid 1 16 3.92e-01
GO:BP GO:0051446 positive regulation of meiotic cell cycle 1 16 3.92e-01
GO:BP GO:0002098 tRNA wobble uridine modification 1 16 3.92e-01
GO:BP GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator 1 16 3.92e-01
GO:BP GO:1905114 cell surface receptor signaling pathway involved in cell-cell signaling 6 448 3.92e-01
GO:BP GO:1990748 cellular detoxification 2 76 3.92e-01
GO:BP GO:0001701 in utero embryonic development 5 344 3.92e-01
GO:BP GO:1900370 positive regulation of post-transcriptional gene silencing by RNA 1 16 3.92e-01
GO:BP GO:1903828 negative regulation of protein localization 3 160 3.93e-01
GO:BP GO:0030308 negative regulation of cell growth 3 160 3.93e-01
GO:BP GO:0048265 response to pain 1 17 3.98e-01
GO:BP GO:0035795 negative regulation of mitochondrial membrane permeability 1 17 3.98e-01
GO:BP GO:0003215 cardiac right ventricle morphogenesis 1 17 3.98e-01
GO:BP GO:0097284 hepatocyte apoptotic process 1 17 3.98e-01
GO:BP GO:0002320 lymphoid progenitor cell differentiation 1 17 3.98e-01
GO:BP GO:0032456 endocytic recycling 2 80 3.98e-01
GO:BP GO:1903859 regulation of dendrite extension 1 17 3.98e-01
GO:BP GO:0001759 organ induction 1 17 3.98e-01
GO:BP GO:0055119 relaxation of cardiac muscle 1 17 3.98e-01
GO:BP GO:0035115 embryonic forelimb morphogenesis 1 17 3.98e-01
GO:BP GO:0061042 vascular wound healing 1 17 3.98e-01
GO:BP GO:0060996 dendritic spine development 2 80 3.98e-01
GO:BP GO:0120255 olefinic compound biosynthetic process 1 17 3.98e-01
GO:BP GO:0060713 labyrinthine layer morphogenesis 1 17 3.98e-01
GO:BP GO:0031338 regulation of vesicle fusion 1 17 3.98e-01
GO:BP GO:0060575 intestinal epithelial cell differentiation 1 17 3.98e-01
GO:BP GO:0051050 positive regulation of transport 8 667 3.98e-01
GO:BP GO:0035116 embryonic hindlimb morphogenesis 1 17 3.98e-01
GO:BP GO:0005976 polysaccharide metabolic process 2 80 3.98e-01
GO:BP GO:0039535 regulation of RIG-I signaling pathway 1 17 3.98e-01
GO:BP GO:0015693 magnesium ion transport 1 17 3.98e-01
GO:BP GO:2000678 negative regulation of transcription regulatory region DNA binding 1 17 3.98e-01
GO:BP GO:0006817 phosphate ion transport 1 17 3.98e-01
GO:BP GO:0006700 C21-steroid hormone biosynthetic process 1 17 3.98e-01
GO:BP GO:0070647 protein modification by small protein conjugation or removal 10 898 4.02e-01
GO:BP GO:0001558 regulation of cell growth 5 357 4.05e-01
GO:BP GO:0030282 bone mineralization 2 82 4.07e-01
GO:BP GO:0097237 cellular response to toxic substance 2 82 4.07e-01
GO:BP GO:0001667 ameboidal-type cell migration 5 358 4.07e-01
GO:BP GO:0002089 lens morphogenesis in camera-type eye 1 18 4.07e-01
GO:BP GO:0009653 anatomical structure morphogenesis 19 1974 4.07e-01
GO:BP GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway 1 18 4.07e-01
GO:BP GO:0006607 NLS-bearing protein import into nucleus 1 18 4.07e-01
GO:BP GO:0010575 positive regulation of vascular endothelial growth factor production 1 18 4.07e-01
GO:BP GO:0106030 neuron projection fasciculation 1 18 4.07e-01
GO:BP GO:0007413 axonal fasciculation 1 18 4.07e-01
GO:BP GO:0045947 negative regulation of translational initiation 1 18 4.07e-01
GO:BP GO:0045185 maintenance of protein location 2 83 4.07e-01
GO:BP GO:0051963 regulation of synapse assembly 2 83 4.07e-01
GO:BP GO:0086013 membrane repolarization during cardiac muscle cell action potential 1 18 4.07e-01
GO:BP GO:0043923 positive regulation by host of viral transcription 1 18 4.07e-01
GO:BP GO:1902883 negative regulation of response to oxidative stress 1 18 4.07e-01
GO:BP GO:0009967 positive regulation of signal transduction 12 1133 4.07e-01
GO:BP GO:0021522 spinal cord motor neuron differentiation 1 18 4.07e-01
GO:BP GO:0071280 cellular response to copper ion 1 18 4.07e-01
GO:BP GO:2000679 positive regulation of transcription regulatory region DNA binding 1 18 4.07e-01
GO:BP GO:0097193 intrinsic apoptotic signaling pathway 4 262 4.08e-01
GO:BP GO:0035592 establishment of protein localization to extracellular region 4 262 4.08e-01
GO:BP GO:0009306 protein secretion 4 262 4.08e-01
GO:BP GO:0071692 protein localization to extracellular region 4 266 4.15e-01
GO:BP GO:1903319 positive regulation of protein maturation 1 19 4.15e-01
GO:BP GO:0035162 embryonic hemopoiesis 1 19 4.15e-01
GO:BP GO:1903204 negative regulation of oxidative stress-induced neuron death 1 19 4.15e-01
GO:BP GO:0002027 regulation of heart rate 2 86 4.15e-01
GO:BP GO:0010001 glial cell differentiation 3 170 4.15e-01
GO:BP GO:0035518 histone H2A monoubiquitination 1 19 4.15e-01
GO:BP GO:0006448 regulation of translational elongation 1 19 4.15e-01
GO:BP GO:1905146 lysosomal protein catabolic process 1 19 4.15e-01
GO:BP GO:0001774 microglial cell activation 1 19 4.15e-01
GO:BP GO:0002097 tRNA wobble base modification 1 19 4.15e-01
GO:BP GO:0060341 regulation of cellular localization 9 798 4.15e-01
GO:BP GO:1905709 negative regulation of membrane permeability 1 19 4.15e-01
GO:BP GO:1901071 glucosamine-containing compound metabolic process 1 19 4.15e-01
GO:BP GO:0045621 positive regulation of lymphocyte differentiation 2 86 4.15e-01
GO:BP GO:0040013 negative regulation of locomotion 4 265 4.15e-01
GO:BP GO:0040020 regulation of meiotic nuclear division 1 19 4.15e-01
GO:BP GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway 2 86 4.15e-01
GO:BP GO:0071498 cellular response to fluid shear stress 1 19 4.15e-01
GO:BP GO:0006308 DNA catabolic process 1 19 4.15e-01
GO:BP GO:0022603 regulation of anatomical structure morphogenesis 8 691 4.17e-01
GO:BP GO:0008037 cell recognition 2 87 4.21e-01
GO:BP GO:0061484 hematopoietic stem cell homeostasis 1 20 4.26e-01
GO:BP GO:0036260 RNA capping 1 20 4.26e-01
GO:BP GO:0010574 regulation of vascular endothelial growth factor production 1 20 4.26e-01
GO:BP GO:0010661 positive regulation of muscle cell apoptotic process 1 20 4.26e-01
GO:BP GO:0035137 hindlimb morphogenesis 1 20 4.26e-01
GO:BP GO:0034312 diol biosynthetic process 1 20 4.26e-01
GO:BP GO:0150146 cell junction disassembly 1 20 4.26e-01
GO:BP GO:1903205 regulation of hydrogen peroxide-induced cell death 1 20 4.26e-01
GO:BP GO:0050974 detection of mechanical stimulus involved in sensory perception 1 20 4.26e-01
GO:BP GO:0022038 corpus callosum development 1 20 4.26e-01
GO:BP GO:0030262 apoptotic nuclear changes 1 20 4.26e-01
GO:BP GO:0003156 regulation of animal organ formation 1 20 4.26e-01
GO:BP GO:0032770 positive regulation of monooxygenase activity 1 20 4.26e-01
GO:BP GO:0043267 negative regulation of potassium ion transport 1 21 4.28e-01
GO:BP GO:0010460 positive regulation of heart rate 1 21 4.28e-01
GO:BP GO:0086012 membrane depolarization during cardiac muscle cell action potential 1 21 4.28e-01
GO:BP GO:0042770 signal transduction in response to DNA damage 3 178 4.28e-01
GO:BP GO:0034504 protein localization to nucleus 4 276 4.28e-01
GO:BP GO:0035640 exploration behavior 1 21 4.28e-01
GO:BP GO:1903076 regulation of protein localization to plasma membrane 2 90 4.28e-01
GO:BP GO:0090263 positive regulation of canonical Wnt signaling pathway 2 91 4.28e-01
GO:BP GO:0002269 leukocyte activation involved in inflammatory response 1 21 4.28e-01
GO:BP GO:0198738 cell-cell signaling by wnt 5 376 4.28e-01
GO:BP GO:1900048 positive regulation of hemostasis 1 21 4.28e-01
GO:BP GO:0060561 apoptotic process involved in morphogenesis 1 21 4.28e-01
GO:BP GO:0010667 negative regulation of cardiac muscle cell apoptotic process 1 21 4.28e-01
GO:BP GO:1902455 negative regulation of stem cell population maintenance 1 21 4.28e-01
GO:BP GO:0035268 protein mannosylation 1 21 4.28e-01
GO:BP GO:0016055 Wnt signaling pathway 5 375 4.28e-01
GO:BP GO:0050773 regulation of dendrite development 2 90 4.28e-01
GO:BP GO:0035020 regulation of Rac protein signal transduction 1 21 4.28e-01
GO:BP GO:0035136 forelimb morphogenesis 1 21 4.28e-01
GO:BP GO:0010959 regulation of metal ion transport 4 275 4.28e-01
GO:BP GO:0034620 cellular response to unfolded protein 2 91 4.28e-01
GO:BP GO:0006468 protein phosphorylation 12 1167 4.28e-01
GO:BP GO:0010604 positive regulation of macromolecule metabolic process 24 2646 4.28e-01
GO:BP GO:0046006 regulation of activated T cell proliferation 1 21 4.28e-01
GO:BP GO:0030194 positive regulation of blood coagulation 1 21 4.28e-01
GO:BP GO:0051291 protein heterooligomerization 1 21 4.28e-01
GO:BP GO:0046885 regulation of hormone biosynthetic process 1 21 4.28e-01
GO:BP GO:0071417 cellular response to organonitrogen compound 6 485 4.28e-01
GO:BP GO:0098754 detoxification 2 91 4.28e-01
GO:BP GO:0008637 apoptotic mitochondrial changes 2 90 4.28e-01
GO:BP GO:0031331 positive regulation of cellular catabolic process 4 277 4.31e-01
GO:BP GO:0048565 digestive tract development 2 92 4.34e-01
GO:BP GO:0046700 heterocycle catabolic process 5 381 4.35e-01
GO:BP GO:0032880 regulation of protein localization 8 710 4.36e-01
GO:BP GO:0055075 potassium ion homeostasis 1 22 4.36e-01
GO:BP GO:0060669 embryonic placenta morphogenesis 1 22 4.36e-01
GO:BP GO:0030900 forebrain development 4 281 4.36e-01
GO:BP GO:0039529 RIG-I signaling pathway 1 22 4.36e-01
GO:BP GO:2000352 negative regulation of endothelial cell apoptotic process 1 22 4.36e-01
GO:BP GO:0035493 SNARE complex assembly 1 22 4.36e-01
GO:BP GO:0060563 neuroepithelial cell differentiation 1 22 4.36e-01
GO:BP GO:0030182 neuron differentiation 11 1061 4.36e-01
GO:BP GO:0000966 RNA 5’-end processing 1 22 4.36e-01
GO:BP GO:0006403 RNA localization 3 182 4.36e-01
GO:BP GO:0086011 membrane repolarization during action potential 1 22 4.36e-01
GO:BP GO:0006760 folic acid-containing compound metabolic process 1 22 4.36e-01
GO:BP GO:0007039 protein catabolic process in the vacuole 1 22 4.36e-01
GO:BP GO:0043542 endothelial cell migration 3 182 4.36e-01
GO:BP GO:1904292 regulation of ERAD pathway 1 22 4.36e-01
GO:BP GO:0042634 regulation of hair cycle 1 22 4.36e-01
GO:BP GO:0006921 cellular component disassembly involved in execution phase of apoptosis 1 22 4.36e-01
GO:BP GO:0010595 positive regulation of endothelial cell migration 2 94 4.37e-01
GO:BP GO:0001824 blastocyst development 2 94 4.37e-01
GO:BP GO:0071900 regulation of protein serine/threonine kinase activity 4 282 4.38e-01
GO:BP GO:0051259 protein complex oligomerization 3 185 4.41e-01
GO:BP GO:1904752 regulation of vascular associated smooth muscle cell migration 1 23 4.41e-01
GO:BP GO:0036474 cell death in response to hydrogen peroxide 1 23 4.41e-01
GO:BP GO:0019080 viral gene expression 2 96 4.41e-01
GO:BP GO:0061900 glial cell activation 1 23 4.41e-01
GO:BP GO:0009888 tissue development 14 1425 4.41e-01
GO:BP GO:0010573 vascular endothelial growth factor production 1 23 4.41e-01
GO:BP GO:1904385 cellular response to angiotensin 1 23 4.41e-01
GO:BP GO:0032006 regulation of TOR signaling 2 96 4.41e-01
GO:BP GO:0071218 cellular response to misfolded protein 1 23 4.41e-01
GO:BP GO:0051220 cytoplasmic sequestering of protein 1 23 4.41e-01
GO:BP GO:0098703 calcium ion import across plasma membrane 1 23 4.41e-01
GO:BP GO:0033688 regulation of osteoblast proliferation 1 23 4.41e-01
GO:BP GO:0050820 positive regulation of coagulation 1 23 4.41e-01
GO:BP GO:0042417 dopamine metabolic process 1 23 4.41e-01
GO:BP GO:0099170 postsynaptic modulation of chemical synaptic transmission 1 23 4.41e-01
GO:BP GO:0061041 regulation of wound healing 2 95 4.41e-01
GO:BP GO:0097190 apoptotic signaling pathway 6 494 4.41e-01
GO:BP GO:0021952 central nervous system projection neuron axonogenesis 1 23 4.41e-01
GO:BP GO:0046822 regulation of nucleocytoplasmic transport 2 97 4.47e-01
GO:BP GO:0046777 protein autophosphorylation 3 188 4.48e-01
GO:BP GO:0055123 digestive system development 2 100 4.49e-01
GO:BP GO:0060055 angiogenesis involved in wound healing 1 25 4.49e-01
GO:BP GO:0033028 myeloid cell apoptotic process 1 25 4.49e-01
GO:BP GO:0050821 protein stabilization 3 191 4.49e-01
GO:BP GO:0071276 cellular response to cadmium ion 1 24 4.49e-01
GO:BP GO:0048261 negative regulation of receptor-mediated endocytosis 1 25 4.49e-01
GO:BP GO:0040008 regulation of growth 6 501 4.49e-01
GO:BP GO:0009057 macromolecule catabolic process 12 1199 4.49e-01
GO:BP GO:0050798 activated T cell proliferation 1 25 4.49e-01
GO:BP GO:0010962 regulation of glucan biosynthetic process 1 25 4.49e-01
GO:BP GO:0051788 response to misfolded protein 1 25 4.49e-01
GO:BP GO:1990776 response to angiotensin 1 24 4.49e-01
GO:BP GO:0021515 cell differentiation in spinal cord 1 24 4.49e-01
GO:BP GO:0048513 animal organ development 20 2189 4.49e-01
GO:BP GO:0021517 ventral spinal cord development 1 25 4.49e-01
GO:BP GO:0006541 glutamine metabolic process 1 24 4.49e-01
GO:BP GO:0042401 biogenic amine biosynthetic process 1 24 4.49e-01
GO:BP GO:0034470 ncRNA processing 5 400 4.49e-01
GO:BP GO:1905606 regulation of presynapse assembly 1 25 4.49e-01
GO:BP GO:0099174 regulation of presynapse organization 1 25 4.49e-01
GO:BP GO:1901796 regulation of signal transduction by p53 class mediator 2 101 4.49e-01
GO:BP GO:0014912 negative regulation of smooth muscle cell migration 1 25 4.49e-01
GO:BP GO:0090100 positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 2 100 4.49e-01
GO:BP GO:0001841 neural tube formation 2 101 4.49e-01
GO:BP GO:1902175 regulation of oxidative stress-induced intrinsic apoptotic signaling pathway 1 25 4.49e-01
GO:BP GO:0090279 regulation of calcium ion import 1 24 4.49e-01
GO:BP GO:0099558 maintenance of synapse structure 1 25 4.49e-01
GO:BP GO:0045732 positive regulation of protein catabolic process 3 192 4.49e-01
GO:BP GO:0009309 amine biosynthetic process 1 25 4.49e-01
GO:BP GO:1904738 vascular associated smooth muscle cell migration 1 25 4.49e-01
GO:BP GO:0036075 replacement ossification 1 25 4.49e-01
GO:BP GO:0003279 cardiac septum development 2 101 4.49e-01
GO:BP GO:0001958 endochondral ossification 1 25 4.49e-01
GO:BP GO:0010664 negative regulation of striated muscle cell apoptotic process 1 24 4.49e-01
GO:BP GO:0048729 tissue morphogenesis 6 504 4.49e-01
GO:BP GO:2000737 negative regulation of stem cell differentiation 1 24 4.49e-01
GO:BP GO:0061311 cell surface receptor signaling pathway involved in heart development 1 25 4.49e-01
GO:BP GO:0048713 regulation of oligodendrocyte differentiation 1 25 4.49e-01
GO:BP GO:0060964 regulation of miRNA-mediated gene silencing 1 25 4.49e-01
GO:BP GO:0003272 endocardial cushion formation 1 24 4.49e-01
GO:BP GO:0061036 positive regulation of cartilage development 1 25 4.49e-01
GO:BP GO:2000027 regulation of animal organ morphogenesis 2 101 4.49e-01
GO:BP GO:0080135 regulation of cellular response to stress 7 616 4.49e-01
GO:BP GO:1903203 regulation of oxidative stress-induced neuron death 1 25 4.49e-01
GO:BP GO:0050999 regulation of nitric-oxide synthase activity 1 25 4.49e-01
GO:BP GO:0010811 positive regulation of cell-substrate adhesion 2 100 4.49e-01
GO:BP GO:0005979 regulation of glycogen biosynthetic process 1 25 4.49e-01
GO:BP GO:1904019 epithelial cell apoptotic process 2 98 4.49e-01
GO:BP GO:0031123 RNA 3’-end processing 2 100 4.49e-01
GO:BP GO:0015931 nucleobase-containing compound transport 3 194 4.50e-01
GO:BP GO:0035909 aorta morphogenesis 1 26 4.54e-01
GO:BP GO:0030224 monocyte differentiation 1 26 4.54e-01
GO:BP GO:0034311 diol metabolic process 1 26 4.54e-01
GO:BP GO:0010092 specification of animal organ identity 1 26 4.54e-01
GO:BP GO:0010614 negative regulation of cardiac muscle hypertrophy 1 26 4.54e-01
GO:BP GO:0035994 response to muscle stretch 1 26 4.54e-01
GO:BP GO:0050931 pigment cell differentiation 1 26 4.54e-01
GO:BP GO:0031128 developmental induction 1 26 4.54e-01
GO:BP GO:0006914 autophagy 6 513 4.54e-01
GO:BP GO:0042542 response to hydrogen peroxide 2 103 4.54e-01
GO:BP GO:0060674 placenta blood vessel development 1 26 4.54e-01
GO:BP GO:0009887 animal organ morphogenesis 8 742 4.54e-01
GO:BP GO:0042398 cellular modified amino acid biosynthetic process 1 26 4.54e-01
GO:BP GO:0051223 regulation of protein transport 5 404 4.54e-01
GO:BP GO:0007431 salivary gland development 1 26 4.54e-01
GO:BP GO:0046326 positive regulation of glucose import 1 26 4.54e-01
GO:BP GO:0061919 process utilizing autophagic mechanism 6 513 4.54e-01
GO:BP GO:0110110 positive regulation of animal organ morphogenesis 1 26 4.54e-01
GO:BP GO:1901361 organic cyclic compound catabolic process 5 406 4.57e-01
GO:BP GO:0015698 inorganic anion transport 2 104 4.59e-01
GO:BP GO:0043153 entrainment of circadian clock by photoperiod 1 27 4.61e-01
GO:BP GO:1900368 regulation of post-transcriptional gene silencing by RNA 1 27 4.61e-01
GO:BP GO:0071466 cellular response to xenobiotic stimulus 2 105 4.61e-01
GO:BP GO:1904030 negative regulation of cyclin-dependent protein kinase activity 1 27 4.61e-01
GO:BP GO:0045736 negative regulation of cyclin-dependent protein serine/threonine kinase activity 1 27 4.61e-01
GO:BP GO:0033687 osteoblast proliferation 1 27 4.61e-01
GO:BP GO:0097484 dendrite extension 1 27 4.61e-01
GO:BP GO:1903532 positive regulation of secretion by cell 3 199 4.61e-01
GO:BP GO:0014741 negative regulation of muscle hypertrophy 1 27 4.61e-01
GO:BP GO:0062208 positive regulation of pattern recognition receptor signaling pathway 1 27 4.61e-01
GO:BP GO:0034067 protein localization to Golgi apparatus 1 27 4.61e-01
GO:BP GO:0010518 positive regulation of phospholipase activity 1 27 4.61e-01
GO:BP GO:1902105 regulation of leukocyte differentiation 3 199 4.61e-01
GO:BP GO:0061756 leukocyte adhesion to vascular endothelial cell 1 27 4.61e-01
GO:BP GO:0009048 dosage compensation by inactivation of X chromosome 1 27 4.61e-01
GO:BP GO:0042558 pteridine-containing compound metabolic process 1 28 4.63e-01
GO:BP GO:0034063 stress granule assembly 1 28 4.63e-01
GO:BP GO:0036475 neuron death in response to oxidative stress 1 28 4.63e-01
GO:BP GO:0050905 neuromuscular process 2 107 4.63e-01
GO:BP GO:0033522 histone H2A ubiquitination 1 28 4.63e-01
GO:BP GO:0086010 membrane depolarization during action potential 1 28 4.63e-01
GO:BP GO:1901798 positive regulation of signal transduction by p53 class mediator 1 28 4.63e-01
GO:BP GO:0048483 autonomic nervous system development 1 28 4.63e-01
GO:BP GO:0070098 chemokine-mediated signaling pathway 1 28 4.63e-01
GO:BP GO:0060306 regulation of membrane repolarization 1 28 4.63e-01
GO:BP GO:0060317 cardiac epithelial to mesenchymal transition 1 28 4.63e-01
GO:BP GO:0033146 regulation of intracellular estrogen receptor signaling pathway 1 28 4.63e-01
GO:BP GO:0000470 maturation of LSU-rRNA 1 28 4.63e-01
GO:BP GO:0046676 negative regulation of insulin secretion 1 28 4.63e-01
GO:BP GO:0009648 photoperiodism 1 28 4.63e-01
GO:BP GO:1900181 negative regulation of protein localization to nucleus 1 28 4.63e-01
GO:BP GO:0031365 N-terminal protein amino acid modification 1 28 4.63e-01
GO:BP GO:0046189 phenol-containing compound biosynthetic process 1 28 4.63e-01
GO:BP GO:0060325 face morphogenesis 1 28 4.63e-01
GO:BP GO:0060147 regulation of post-transcriptional gene silencing 1 28 4.63e-01
GO:BP GO:0030879 mammary gland development 2 106 4.63e-01
GO:BP GO:0016358 dendrite development 3 202 4.63e-01
GO:BP GO:0021537 telencephalon development 3 201 4.63e-01
GO:BP GO:0008207 C21-steroid hormone metabolic process 1 28 4.63e-01
GO:BP GO:0070873 regulation of glycogen metabolic process 1 28 4.63e-01
GO:BP GO:0045687 positive regulation of glial cell differentiation 1 28 4.63e-01
GO:BP GO:0006515 protein quality control for misfolded or incompletely synthesized proteins 1 28 4.63e-01
GO:BP GO:0009611 response to wounding 5 415 4.63e-01
GO:BP GO:0120178 steroid hormone biosynthetic process 1 29 4.63e-01
GO:BP GO:0044772 mitotic cell cycle phase transition 5 418 4.63e-01
GO:BP GO:0016049 cell growth 5 418 4.63e-01
GO:BP GO:0060047 heart contraction 3 205 4.63e-01
GO:BP GO:0045580 regulation of T cell differentiation 2 110 4.63e-01
GO:BP GO:0007549 dosage compensation 1 29 4.63e-01
GO:BP GO:0042743 hydrogen peroxide metabolic process 1 29 4.63e-01
GO:BP GO:0045926 negative regulation of growth 3 206 4.63e-01
GO:BP GO:0060966 regulation of gene silencing by RNA 1 29 4.63e-01
GO:BP GO:0048699 generation of neurons 11 1119 4.63e-01
GO:BP GO:0030833 regulation of actin filament polymerization 2 110 4.63e-01
GO:BP GO:0060914 heart formation 1 29 4.63e-01
GO:BP GO:0048762 mesenchymal cell differentiation 3 204 4.63e-01
GO:BP GO:0046165 alcohol biosynthetic process 2 110 4.63e-01
GO:BP GO:0042491 inner ear auditory receptor cell differentiation 1 29 4.63e-01
GO:BP GO:1903426 regulation of reactive oxygen species biosynthetic process 1 29 4.63e-01
GO:BP GO:0003206 cardiac chamber morphogenesis 2 109 4.63e-01
GO:BP GO:0001889 liver development 2 110 4.63e-01
GO:BP GO:0150117 positive regulation of cell-substrate junction organization 1 29 4.63e-01
GO:BP GO:0006730 one-carbon metabolic process 1 29 4.63e-01
GO:BP GO:0021953 central nervous system neuron differentiation 2 108 4.63e-01
GO:BP GO:0034260 negative regulation of GTPase activity 1 29 4.63e-01
GO:BP GO:0046688 response to copper ion 1 29 4.63e-01
GO:BP GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation 1 29 4.63e-01
GO:BP GO:0000902 cell morphogenesis 8 761 4.63e-01
GO:BP GO:0090075 relaxation of muscle 1 29 4.63e-01
GO:BP GO:0051174 regulation of phosphorus metabolic process 10 994 4.63e-01
GO:BP GO:0019220 regulation of phosphate metabolic process 10 993 4.63e-01
GO:BP GO:0007272 ensheathment of neurons 2 113 4.63e-01
GO:BP GO:0060828 regulation of canonical Wnt signaling pathway 3 213 4.63e-01
GO:BP GO:0008366 axon ensheathment 2 113 4.63e-01
GO:BP GO:0042110 T cell activation 4 313 4.63e-01
GO:BP GO:0099622 cardiac muscle cell membrane repolarization 1 31 4.63e-01
GO:BP GO:0048701 embryonic cranial skeleton morphogenesis 1 31 4.63e-01
GO:BP GO:0003009 skeletal muscle contraction 1 31 4.63e-01
GO:BP GO:1901701 cellular response to oxygen-containing compound 9 893 4.63e-01
GO:BP GO:0046825 regulation of protein export from nucleus 1 30 4.63e-01
GO:BP GO:1904375 regulation of protein localization to cell periphery 2 113 4.63e-01
GO:BP GO:0045910 negative regulation of DNA recombination 1 31 4.63e-01
GO:BP GO:0048546 digestive tract morphogenesis 1 31 4.63e-01
GO:BP GO:0070306 lens fiber cell differentiation 1 30 4.63e-01
GO:BP GO:0048568 embryonic organ development 4 316 4.63e-01
GO:BP GO:0070201 regulation of establishment of protein localization 5 428 4.63e-01
GO:BP GO:0051154 negative regulation of striated muscle cell differentiation 1 31 4.63e-01
GO:BP GO:2000026 regulation of multicellular organismal development 10 1014 4.63e-01
GO:BP GO:0061008 hepaticobiliary system development 2 112 4.63e-01
GO:BP GO:0061448 connective tissue development 3 208 4.63e-01
GO:BP GO:0030155 regulation of cell adhesion 6 539 4.63e-01
GO:BP GO:0023056 positive regulation of signaling 12 1256 4.63e-01
GO:BP GO:0002792 negative regulation of peptide secretion 1 31 4.63e-01
GO:BP GO:0042552 myelination 2 111 4.63e-01
GO:BP GO:0010647 positive regulation of cell communication 12 1255 4.63e-01
GO:BP GO:0021955 central nervous system neuron axonogenesis 1 31 4.63e-01
GO:BP GO:0061842 microtubule organizing center localization 1 31 4.63e-01
GO:BP GO:0090278 negative regulation of peptide hormone secretion 1 30 4.63e-01
GO:BP GO:0097106 postsynaptic density organization 1 30 4.63e-01
GO:BP GO:0032350 regulation of hormone metabolic process 1 30 4.63e-01
GO:BP GO:0035107 appendage morphogenesis 2 114 4.63e-01
GO:BP GO:0032885 regulation of polysaccharide biosynthetic process 1 31 4.63e-01
GO:BP GO:1901381 positive regulation of potassium ion transmembrane transport 1 30 4.63e-01
GO:BP GO:0060218 hematopoietic stem cell differentiation 1 30 4.63e-01
GO:BP GO:0009649 entrainment of circadian clock 1 31 4.63e-01
GO:BP GO:2000758 positive regulation of peptidyl-lysine acetylation 1 31 4.63e-01
GO:BP GO:0010390 histone monoubiquitination 1 31 4.63e-01
GO:BP GO:0003231 cardiac ventricle development 2 114 4.63e-01
GO:BP GO:0120161 regulation of cold-induced thermogenesis 2 112 4.63e-01
GO:BP GO:0009712 catechol-containing compound metabolic process 1 30 4.63e-01
GO:BP GO:0010828 positive regulation of glucose transmembrane transport 1 31 4.63e-01
GO:BP GO:0001775 cell activation 7 655 4.63e-01
GO:BP GO:0006359 regulation of transcription by RNA polymerase III 1 30 4.63e-01
GO:BP GO:0034405 response to fluid shear stress 1 31 4.63e-01
GO:BP GO:0090505 epiboly involved in wound healing 1 30 4.63e-01
GO:BP GO:0035108 limb morphogenesis 2 114 4.63e-01
GO:BP GO:0006584 catecholamine metabolic process 1 30 4.63e-01
GO:BP GO:0106106 cold-induced thermogenesis 2 113 4.63e-01
GO:BP GO:0051642 centrosome localization 1 31 4.63e-01
GO:BP GO:2000780 negative regulation of double-strand break repair 1 30 4.63e-01
GO:BP GO:0090504 epiboly 1 31 4.63e-01
GO:BP GO:0007006 mitochondrial membrane organization 2 114 4.63e-01
GO:BP GO:0033674 positive regulation of kinase activity 4 317 4.63e-01
GO:BP GO:1902742 apoptotic process involved in development 1 30 4.63e-01
GO:BP GO:0044319 wound healing, spreading of cells 1 30 4.63e-01
GO:BP GO:0051051 negative regulation of transport 4 318 4.63e-01
GO:BP GO:0031214 biomineral tissue development 2 111 4.63e-01
GO:BP GO:0016310 phosphorylation 13 1372 4.63e-01
GO:BP GO:1990573 potassium ion import across plasma membrane 1 31 4.63e-01
GO:BP GO:0010720 positive regulation of cell development 4 317 4.63e-01
GO:BP GO:0045766 positive regulation of angiogenesis 2 115 4.64e-01
GO:BP GO:1904018 positive regulation of vasculature development 2 115 4.64e-01
GO:BP GO:0031929 TOR signaling 2 115 4.64e-01
GO:BP GO:0008217 regulation of blood pressure 2 115 4.64e-01
GO:BP GO:0042060 wound healing 4 320 4.64e-01
GO:BP GO:0045785 positive regulation of cell adhesion 4 320 4.64e-01
GO:BP GO:0043066 negative regulation of apoptotic process 7 660 4.65e-01
GO:BP GO:0050796 regulation of insulin secretion 2 116 4.65e-01
GO:BP GO:0009913 epidermal cell differentiation 2 116 4.65e-01
GO:BP GO:0050853 B cell receptor signaling pathway 1 32 4.65e-01
GO:BP GO:1902253 regulation of intrinsic apoptotic signaling pathway by p53 class mediator 1 32 4.65e-01
GO:BP GO:0031018 endocrine pancreas development 1 32 4.65e-01
GO:BP GO:0045738 negative regulation of DNA repair 1 32 4.65e-01
GO:BP GO:0010543 regulation of platelet activation 1 32 4.65e-01
GO:BP GO:0003015 heart process 3 216 4.65e-01
GO:BP GO:0045823 positive regulation of heart contraction 1 32 4.65e-01
GO:BP GO:0097502 mannosylation 1 32 4.65e-01
GO:BP GO:1903524 positive regulation of blood circulation 1 32 4.65e-01
GO:BP GO:0050982 detection of mechanical stimulus 1 32 4.65e-01
GO:BP GO:0005975 carbohydrate metabolic process 5 433 4.65e-01
GO:BP GO:0001838 embryonic epithelial tube formation 2 116 4.65e-01
GO:BP GO:0051047 positive regulation of secretion 3 215 4.65e-01
GO:BP GO:0006402 mRNA catabolic process 3 216 4.65e-01
GO:BP GO:0016071 mRNA metabolic process 7 665 4.69e-01
GO:BP GO:1902107 positive regulation of leukocyte differentiation 2 118 4.72e-01
GO:BP GO:1903708 positive regulation of hemopoiesis 2 118 4.72e-01
GO:BP GO:1902930 regulation of alcohol biosynthetic process 1 33 4.74e-01
GO:BP GO:0003161 cardiac conduction system development 1 33 4.74e-01
GO:BP GO:0150076 neuroinflammatory response 1 33 4.74e-01
GO:BP GO:0010665 regulation of cardiac muscle cell apoptotic process 1 33 4.74e-01
GO:BP GO:0003180 aortic valve morphogenesis 1 33 4.74e-01
GO:BP GO:0060323 head morphogenesis 1 33 4.74e-01
GO:BP GO:0006040 amino sugar metabolic process 1 33 4.74e-01
GO:BP GO:0007399 nervous system development 17 1904 4.76e-01
GO:BP GO:1990845 adaptive thermogenesis 2 121 4.76e-01
GO:BP GO:0007283 spermatogenesis 4 330 4.76e-01
GO:BP GO:0048813 dendrite morphogenesis 2 120 4.76e-01
GO:BP GO:1901532 regulation of hematopoietic progenitor cell differentiation 1 34 4.76e-01
GO:BP GO:0009966 regulation of signal transduction 20 2285 4.76e-01
GO:BP GO:0043507 positive regulation of JUN kinase activity 1 34 4.76e-01
GO:BP GO:0045321 leukocyte activation 6 554 4.76e-01
GO:BP GO:0016242 negative regulation of macroautophagy 1 34 4.76e-01
GO:BP GO:0014037 Schwann cell differentiation 1 34 4.76e-01
GO:BP GO:0060193 positive regulation of lipase activity 1 34 4.76e-01
GO:BP GO:0019748 secondary metabolic process 1 34 4.76e-01
GO:BP GO:0032881 regulation of polysaccharide metabolic process 1 34 4.76e-01
GO:BP GO:0006364 rRNA processing 3 221 4.76e-01
GO:BP GO:0032768 regulation of monooxygenase activity 1 34 4.76e-01
GO:BP GO:0000956 nuclear-transcribed mRNA catabolic process 2 120 4.76e-01
GO:BP GO:1903034 regulation of response to wounding 2 121 4.76e-01
GO:BP GO:0051962 positive regulation of nervous system development 3 221 4.76e-01
GO:BP GO:0030177 positive regulation of Wnt signaling pathway 2 120 4.76e-01
GO:BP GO:0030501 positive regulation of bone mineralization 1 34 4.76e-01
GO:BP GO:0035315 hair cell differentiation 1 34 4.76e-01
GO:BP GO:1905898 positive regulation of response to endoplasmic reticulum stress 1 34 4.76e-01
GO:BP GO:0086004 regulation of cardiac muscle cell contraction 1 34 4.76e-01
GO:BP GO:0035272 exocrine system development 1 34 4.76e-01
GO:BP GO:0042176 regulation of protein catabolic process 4 331 4.78e-01
GO:BP GO:0001932 regulation of protein phosphorylation 8 796 4.81e-01
GO:BP GO:0030866 cortical actin cytoskeleton organization 1 35 4.82e-01
GO:BP GO:0060048 cardiac muscle contraction 2 123 4.82e-01
GO:BP GO:2000351 regulation of endothelial cell apoptotic process 1 35 4.82e-01
GO:BP GO:0010656 negative regulation of muscle cell apoptotic process 1 35 4.82e-01
GO:BP GO:0043069 negative regulation of programmed cell death 7 678 4.82e-01
GO:BP GO:0032501 multicellular organismal process 39 4794 4.82e-01
GO:BP GO:0034660 ncRNA metabolic process 6 561 4.82e-01
GO:BP GO:0010463 mesenchymal cell proliferation 1 35 4.82e-01
GO:BP GO:0060711 labyrinthine layer development 1 35 4.82e-01
GO:BP GO:0007095 mitotic G2 DNA damage checkpoint signaling 1 35 4.82e-01
GO:BP GO:0048538 thymus development 1 35 4.82e-01
GO:BP GO:0000209 protein polyubiquitination 3 226 4.85e-01
GO:BP GO:0090101 negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 2 124 4.86e-01
GO:BP GO:0000460 maturation of 5.8S rRNA 1 36 4.87e-01
GO:BP GO:0050775 positive regulation of dendrite morphogenesis 1 36 4.87e-01
GO:BP GO:0086091 regulation of heart rate by cardiac conduction 1 36 4.87e-01
GO:BP GO:0043268 positive regulation of potassium ion transport 1 36 4.87e-01
GO:BP GO:0050890 cognition 3 227 4.87e-01
GO:BP GO:0045668 negative regulation of osteoblast differentiation 1 36 4.87e-01
GO:BP GO:0023051 regulation of signaling 22 2565 4.87e-01
GO:BP GO:1903409 reactive oxygen species biosynthetic process 1 36 4.87e-01
GO:BP GO:0022008 neurogenesis 12 1294 4.87e-01
GO:BP GO:0048066 developmental pigmentation 1 36 4.87e-01
GO:BP GO:0099084 postsynaptic specialization organization 1 36 4.87e-01
GO:BP GO:0010659 cardiac muscle cell apoptotic process 1 36 4.87e-01
GO:BP GO:0006397 mRNA processing 5 450 4.87e-01
GO:BP GO:0010662 regulation of striated muscle cell apoptotic process 1 36 4.87e-01
GO:BP GO:0010769 regulation of cell morphogenesis involved in differentiation 1 37 4.89e-01
GO:BP GO:0010770 positive regulation of cell morphogenesis involved in differentiation 1 37 4.89e-01
GO:BP GO:0097178 ruffle assembly 1 37 4.89e-01
GO:BP GO:0008064 regulation of actin polymerization or depolymerization 2 126 4.89e-01
GO:BP GO:0001825 blastocyst formation 1 37 4.89e-01
GO:BP GO:1990868 response to chemokine 1 37 4.89e-01
GO:BP GO:1903146 regulation of autophagy of mitochondrion 1 37 4.89e-01
GO:BP GO:0008360 regulation of cell shape 2 126 4.89e-01
GO:BP GO:1990869 cellular response to chemokine 1 37 4.89e-01
GO:BP GO:0045663 positive regulation of myoblast differentiation 1 37 4.89e-01
GO:BP GO:0045727 positive regulation of translation 2 126 4.89e-01
GO:BP GO:0045747 positive regulation of Notch signaling pathway 1 37 4.89e-01
GO:BP GO:0000423 mitophagy 1 37 4.89e-01
GO:BP GO:0030832 regulation of actin filament length 2 127 4.89e-01
GO:BP GO:2000008 regulation of protein localization to cell surface 1 37 4.89e-01
GO:BP GO:0070509 calcium ion import 1 37 4.89e-01
GO:BP GO:0003176 aortic valve development 1 37 4.89e-01
GO:BP GO:0010517 regulation of phospholipase activity 1 37 4.89e-01
GO:BP GO:0072175 epithelial tube formation 2 127 4.89e-01
GO:BP GO:0042181 ketone biosynthetic process 1 37 4.89e-01
GO:BP GO:0043001 Golgi to plasma membrane protein transport 1 37 4.89e-01
GO:BP GO:0010646 regulation of cell communication 22 2573 4.89e-01
GO:BP GO:0008033 tRNA processing 2 128 4.92e-01
GO:BP GO:0006986 response to unfolded protein 2 128 4.92e-01
GO:BP GO:0048584 positive regulation of response to stimulus 14 1555 4.92e-01
GO:BP GO:0035556 intracellular signal transduction 18 2065 4.93e-01
GO:BP GO:0048232 male gamete generation 4 343 4.93e-01
GO:BP GO:0065009 regulation of molecular function 17 1939 4.95e-01
GO:BP GO:0071805 potassium ion transmembrane transport 2 129 4.95e-01
GO:BP GO:0051785 positive regulation of nuclear division 1 38 4.96e-01
GO:BP GO:0045454 cell redox homeostasis 1 38 4.96e-01
GO:BP GO:0007159 leukocyte cell-cell adhesion 3 234 4.96e-01
GO:BP GO:0006352 DNA-templated transcription initiation 2 130 4.99e-01
GO:BP GO:0042063 gliogenesis 3 235 4.99e-01
GO:BP GO:0042311 vasodilation 1 39 5.00e-01
GO:BP GO:0036294 cellular response to decreased oxygen levels 2 131 5.00e-01
GO:BP GO:1903115 regulation of actin filament-based movement 1 39 5.00e-01
GO:BP GO:0031952 regulation of protein autophosphorylation 1 39 5.00e-01
GO:BP GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 1 39 5.00e-01
GO:BP GO:0010658 striated muscle cell apoptotic process 1 39 5.00e-01
GO:BP GO:0010976 positive regulation of neuron projection development 2 131 5.00e-01
GO:BP GO:0043010 camera-type eye development 3 236 5.00e-01
GO:BP GO:0009066 aspartate family amino acid metabolic process 1 39 5.00e-01
GO:BP GO:0030838 positive regulation of actin filament polymerization 1 39 5.00e-01
GO:BP GO:0045604 regulation of epidermal cell differentiation 1 39 5.00e-01
GO:BP GO:0099054 presynapse assembly 1 39 5.00e-01
GO:BP GO:0006378 mRNA polyadenylation 1 39 5.00e-01
GO:BP GO:0050906 detection of stimulus involved in sensory perception 1 39 5.00e-01
GO:BP GO:0001659 temperature homeostasis 2 132 5.02e-01
GO:BP GO:0090276 regulation of peptide hormone secretion 2 132 5.02e-01
GO:BP GO:0048839 inner ear development 2 132 5.02e-01
GO:BP GO:0016331 morphogenesis of embryonic epithelium 2 132 5.02e-01
GO:BP GO:0060412 ventricular septum morphogenesis 1 40 5.02e-01
GO:BP GO:0045022 early endosome to late endosome transport 1 40 5.02e-01
GO:BP GO:0120163 negative regulation of cold-induced thermogenesis 1 40 5.02e-01
GO:BP GO:0042446 hormone biosynthetic process 1 40 5.02e-01
GO:BP GO:0039531 regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway 1 40 5.02e-01
GO:BP GO:0045778 positive regulation of ossification 1 40 5.02e-01
GO:BP GO:0010596 negative regulation of endothelial cell migration 1 40 5.02e-01
GO:BP GO:0014009 glial cell proliferation 1 40 5.02e-01
GO:BP GO:0098739 import across plasma membrane 2 133 5.02e-01
GO:BP GO:0007275 multicellular organism development 28 3386 5.02e-01
GO:BP GO:0034331 cell junction maintenance 1 40 5.02e-01
GO:BP GO:0072577 endothelial cell apoptotic process 1 40 5.02e-01
GO:BP GO:0009266 response to temperature stimulus 2 133 5.02e-01
GO:BP GO:0046649 lymphocyte activation 5 465 5.02e-01
GO:BP GO:0002376 immune system process 13 1447 5.02e-01
GO:BP GO:0098815 modulation of excitatory postsynaptic potential 1 40 5.02e-01
GO:BP GO:0006110 regulation of glycolytic process 1 40 5.02e-01
GO:BP GO:0030010 establishment of cell polarity 2 134 5.03e-01
GO:BP GO:0030041 actin filament polymerization 2 134 5.03e-01
GO:BP GO:0046890 regulation of lipid biosynthetic process 2 134 5.03e-01
GO:BP GO:0002791 regulation of peptide secretion 2 134 5.03e-01
GO:BP GO:0046686 response to cadmium ion 1 41 5.03e-01
GO:BP GO:1905314 semi-lunar valve development 1 41 5.03e-01
GO:BP GO:0050881 musculoskeletal movement 1 41 5.03e-01
GO:BP GO:0035196 miRNA processing 1 41 5.03e-01
GO:BP GO:0060612 adipose tissue development 1 41 5.03e-01
GO:BP GO:0086009 membrane repolarization 1 41 5.03e-01
GO:BP GO:0048013 ephrin receptor signaling pathway 1 41 5.03e-01
GO:BP GO:0043631 RNA polyadenylation 1 41 5.03e-01
GO:BP GO:0050879 multicellular organismal movement 1 41 5.03e-01
GO:BP GO:0030520 intracellular estrogen receptor signaling pathway 1 41 5.03e-01
GO:BP GO:0051222 positive regulation of protein transport 3 242 5.03e-01
GO:BP GO:0035329 hippo signaling 1 41 5.03e-01
GO:BP GO:0043525 positive regulation of neuron apoptotic process 1 41 5.03e-01
GO:BP GO:0008631 intrinsic apoptotic signaling pathway in response to oxidative stress 1 41 5.03e-01
GO:BP GO:0046324 regulation of glucose import 1 41 5.03e-01
GO:BP GO:0030307 positive regulation of cell growth 2 135 5.03e-01
GO:BP GO:1901985 positive regulation of protein acetylation 1 41 5.03e-01
GO:BP GO:0006749 glutathione metabolic process 1 41 5.03e-01
GO:BP GO:0051260 protein homooligomerization 2 136 5.05e-01
GO:BP GO:0051726 regulation of cell cycle 9 956 5.05e-01
GO:BP GO:0090087 regulation of peptide transport 2 136 5.05e-01
GO:BP GO:0051289 protein homotetramerization 1 42 5.10e-01
GO:BP GO:0099172 presynapse organization 1 42 5.10e-01
GO:BP GO:1902895 positive regulation of miRNA transcription 1 42 5.10e-01
GO:BP GO:0034655 nucleobase-containing compound catabolic process 4 358 5.10e-01
GO:BP GO:0031103 axon regeneration 1 42 5.10e-01
GO:BP GO:0098927 vesicle-mediated transport between endosomal compartments 1 42 5.10e-01
GO:BP GO:0016601 Rac protein signal transduction 1 42 5.10e-01
GO:BP GO:0001837 epithelial to mesenchymal transition 2 138 5.12e-01
GO:BP GO:0035148 tube formation 2 138 5.12e-01
GO:BP GO:0062012 regulation of small molecule metabolic process 3 246 5.12e-01
GO:BP GO:0048583 regulation of response to stimulus 24 2890 5.16e-01
GO:BP GO:1904036 negative regulation of epithelial cell apoptotic process 1 43 5.17e-01
GO:BP GO:0051353 positive regulation of oxidoreductase activity 1 43 5.17e-01
GO:BP GO:0032008 positive regulation of TOR signaling 1 43 5.17e-01
GO:BP GO:0098900 regulation of action potential 1 44 5.20e-01
GO:BP GO:0051489 regulation of filopodium assembly 1 44 5.20e-01
GO:BP GO:0001961 positive regulation of cytokine-mediated signaling pathway 1 44 5.20e-01
GO:BP GO:0072659 protein localization to plasma membrane 3 249 5.20e-01
GO:BP GO:0036293 response to decreased oxygen levels 3 249 5.20e-01
GO:BP GO:0036211 protein modification process 24 2901 5.20e-01
GO:BP GO:0045123 cellular extravasation 1 44 5.20e-01
GO:BP GO:1902459 positive regulation of stem cell population maintenance 1 44 5.20e-01
GO:BP GO:0043388 positive regulation of DNA binding 1 44 5.20e-01
GO:BP GO:0030073 insulin secretion 2 141 5.20e-01
GO:BP GO:0022029 telencephalon cell migration 1 44 5.20e-01
GO:BP GO:0001954 positive regulation of cell-matrix adhesion 1 44 5.20e-01
GO:BP GO:0060485 mesenchyme development 3 249 5.20e-01
GO:BP GO:0048731 system development 24 2901 5.20e-01
GO:BP GO:1902531 regulation of intracellular signal transduction 12 1345 5.20e-01
GO:BP GO:0051965 positive regulation of synapse assembly 1 44 5.20e-01
GO:BP GO:0050709 negative regulation of protein secretion 1 44 5.20e-01
GO:BP GO:0060173 limb development 2 142 5.22e-01
GO:BP GO:0048736 appendage development 2 142 5.22e-01
GO:BP GO:0031099 regeneration 2 142 5.22e-01
GO:BP GO:0009101 glycoprotein biosynthetic process 3 252 5.24e-01
GO:BP GO:0014015 positive regulation of gliogenesis 1 45 5.24e-01
GO:BP GO:0051445 regulation of meiotic cell cycle 1 45 5.24e-01
GO:BP GO:0031529 ruffle organization 1 45 5.24e-01
GO:BP GO:0010498 proteasomal protein catabolic process 5 486 5.24e-01
GO:BP GO:0086002 cardiac muscle cell action potential involved in contraction 1 45 5.24e-01
GO:BP GO:0048146 positive regulation of fibroblast proliferation 1 45 5.24e-01
GO:BP GO:0060324 face development 1 45 5.24e-01
GO:BP GO:0030514 negative regulation of BMP signaling pathway 1 45 5.24e-01
GO:BP GO:0010171 body morphogenesis 1 45 5.24e-01
GO:BP GO:0050870 positive regulation of T cell activation 2 144 5.26e-01
GO:BP GO:0044248 cellular catabolic process 11 1229 5.26e-01
GO:BP GO:0071453 cellular response to oxygen levels 2 144 5.26e-01
GO:BP GO:0006417 regulation of translation 4 370 5.28e-01
GO:BP GO:0098609 cell-cell adhesion 6 609 5.28e-01
GO:BP GO:0046888 negative regulation of hormone secretion 1 46 5.30e-01
GO:BP GO:0014823 response to activity 1 46 5.30e-01
GO:BP GO:0016574 histone ubiquitination 1 46 5.30e-01
GO:BP GO:0061462 protein localization to lysosome 1 46 5.30e-01
GO:BP GO:0021885 forebrain cell migration 1 46 5.30e-01
GO:BP GO:0006401 RNA catabolic process 3 256 5.30e-01
GO:BP GO:0016072 rRNA metabolic process 3 258 5.30e-01
GO:BP GO:0032007 negative regulation of TOR signaling 1 47 5.30e-01
GO:BP GO:0008015 blood circulation 4 374 5.30e-01
GO:BP GO:0060113 inner ear receptor cell differentiation 1 47 5.30e-01
GO:BP GO:0060350 endochondral bone morphogenesis 1 47 5.30e-01
GO:BP GO:0046173 polyol biosynthetic process 1 47 5.30e-01
GO:BP GO:0043470 regulation of carbohydrate catabolic process 1 47 5.30e-01
GO:BP GO:0033365 protein localization to organelle 8 859 5.30e-01
GO:BP GO:0006606 protein import into nucleus 2 147 5.30e-01
GO:BP GO:0031102 neuron projection regeneration 1 47 5.30e-01
GO:BP GO:0043536 positive regulation of blood vessel endothelial cell migration 1 47 5.30e-01
GO:BP GO:0010975 regulation of neuron projection development 4 372 5.30e-01
GO:BP GO:0045685 regulation of glial cell differentiation 1 47 5.30e-01
GO:BP GO:0021915 neural tube development 2 146 5.30e-01
GO:BP GO:1903351 cellular response to dopamine 1 47 5.30e-01
GO:BP GO:0070918 regulatory ncRNA processing 1 47 5.30e-01
GO:BP GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process 1 47 5.30e-01
GO:BP GO:0042102 positive regulation of T cell proliferation 1 47 5.30e-01
GO:BP GO:1904951 positive regulation of establishment of protein localization 3 258 5.30e-01
GO:BP GO:2001242 regulation of intrinsic apoptotic signaling pathway 2 147 5.30e-01
GO:BP GO:0060998 regulation of dendritic spine development 1 48 5.34e-01
GO:BP GO:1903350 response to dopamine 1 48 5.34e-01
GO:BP GO:0051235 maintenance of location 3 260 5.34e-01
GO:BP GO:0010611 regulation of cardiac muscle hypertrophy 1 48 5.34e-01
GO:BP GO:0048856 anatomical structure development 33 4128 5.34e-01
GO:BP GO:0045860 positive regulation of protein kinase activity 3 260 5.34e-01
GO:BP GO:2000630 positive regulation of miRNA metabolic process 1 48 5.34e-01
GO:BP GO:0003205 cardiac chamber development 2 149 5.34e-01
GO:BP GO:0019827 stem cell population maintenance 2 149 5.34e-01
GO:BP GO:0010718 positive regulation of epithelial to mesenchymal transition 1 48 5.34e-01
GO:BP GO:0040007 growth 7 742 5.34e-01
GO:BP GO:0050435 amyloid-beta metabolic process 1 48 5.34e-01
GO:BP GO:0019233 sensory perception of pain 1 48 5.34e-01
GO:BP GO:0034198 cellular response to amino acid starvation 1 48 5.34e-01
GO:BP GO:0044270 cellular nitrogen compound catabolic process 4 378 5.34e-01
GO:BP GO:0051247 positive regulation of protein metabolic process 10 1123 5.36e-01
GO:BP GO:0043506 regulation of JUN kinase activity 1 49 5.36e-01
GO:BP GO:0098727 maintenance of cell number 2 151 5.36e-01
GO:BP GO:0071300 cellular response to retinoic acid 1 49 5.36e-01
GO:BP GO:1905475 regulation of protein localization to membrane 2 150 5.36e-01
GO:BP GO:0006006 glucose metabolic process 2 151 5.36e-01
GO:BP GO:0001655 urogenital system development 1 49 5.36e-01
GO:BP GO:0014743 regulation of muscle hypertrophy 1 49 5.36e-01
GO:BP GO:0007005 mitochondrion organization 5 500 5.36e-01
GO:BP GO:0007596 blood coagulation 2 150 5.36e-01
GO:BP GO:0051099 positive regulation of binding 2 150 5.36e-01
GO:BP GO:0042490 mechanoreceptor differentiation 1 49 5.36e-01
GO:BP GO:1901605 alpha-amino acid metabolic process 2 151 5.36e-01
GO:BP GO:0051216 cartilage development 2 151 5.36e-01
GO:BP GO:0060760 positive regulation of response to cytokine stimulus 1 49 5.36e-01
GO:BP GO:0016241 regulation of macroautophagy 2 151 5.36e-01
GO:BP GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling 2 153 5.37e-01
GO:BP GO:0035019 somatic stem cell population maintenance 1 50 5.37e-01
GO:BP GO:1903530 regulation of secretion by cell 4 382 5.37e-01
GO:BP GO:0050790 regulation of catalytic activity 12 1380 5.37e-01
GO:BP GO:1903078 positive regulation of protein localization to plasma membrane 1 50 5.37e-01
GO:BP GO:0006941 striated muscle contraction 2 152 5.37e-01
GO:BP GO:1900046 regulation of hemostasis 1 50 5.37e-01
GO:BP GO:0009267 cellular response to starvation 2 152 5.37e-01
GO:BP GO:0050865 regulation of cell activation 4 384 5.37e-01
GO:BP GO:1903317 regulation of protein maturation 1 50 5.37e-01
GO:BP GO:0002067 glandular epithelial cell differentiation 1 50 5.37e-01
GO:BP GO:0010038 response to metal ion 3 264 5.37e-01
GO:BP GO:0044818 mitotic G2/M transition checkpoint 1 50 5.37e-01
GO:BP GO:0035904 aorta development 1 50 5.37e-01
GO:BP GO:0030193 regulation of blood coagulation 1 50 5.37e-01
GO:BP GO:0060997 dendritic spine morphogenesis 1 50 5.37e-01
GO:BP GO:0044770 cell cycle phase transition 5 504 5.37e-01
GO:BP GO:0007599 hemostasis 2 153 5.37e-01
GO:BP GO:0007416 synapse assembly 2 152 5.37e-01
GO:BP GO:0050817 coagulation 2 153 5.37e-01
GO:BP GO:0051170 import into nucleus 2 152 5.37e-01
GO:BP GO:0007507 heart development 5 506 5.40e-01
GO:BP GO:0045165 cell fate commitment 2 155 5.40e-01
GO:BP GO:1904888 cranial skeletal system development 1 51 5.40e-01
GO:BP GO:0019439 aromatic compound catabolic process 4 387 5.40e-01
GO:BP GO:0006809 nitric oxide biosynthetic process 1 51 5.40e-01
GO:BP GO:0099173 postsynapse organization 2 155 5.40e-01
GO:BP GO:1990928 response to amino acid starvation 1 51 5.40e-01
GO:BP GO:0048645 animal organ formation 1 51 5.40e-01
GO:BP GO:0042733 embryonic digit morphogenesis 1 51 5.40e-01
GO:BP GO:0043270 positive regulation of monoatomic ion transport 2 154 5.40e-01
GO:BP GO:1903829 positive regulation of protein localization 4 386 5.40e-01
GO:BP GO:0050810 regulation of steroid biosynthetic process 1 51 5.40e-01
GO:BP GO:1902476 chloride transmembrane transport 1 51 5.40e-01
GO:BP GO:0046605 regulation of centrosome cycle 1 51 5.40e-01
GO:BP GO:0071496 cellular response to external stimulus 3 270 5.44e-01
GO:BP GO:0002064 epithelial cell development 2 156 5.44e-01
GO:BP GO:0006081 cellular aldehyde metabolic process 1 52 5.44e-01
GO:BP GO:0051148 negative regulation of muscle cell differentiation 1 52 5.44e-01
GO:BP GO:0007062 sister chromatid cohesion 1 52 5.44e-01
GO:BP GO:0002011 morphogenesis of an epithelial sheet 1 52 5.44e-01
GO:BP GO:1902074 response to salt 3 271 5.44e-01
GO:BP GO:2001244 positive regulation of intrinsic apoptotic signaling pathway 1 52 5.44e-01
GO:BP GO:0050877 nervous system process 6 634 5.44e-01
GO:BP GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum 1 52 5.44e-01
GO:BP GO:0060191 regulation of lipase activity 1 52 5.44e-01
GO:BP GO:0007155 cell adhesion 9 1012 5.44e-01
GO:BP GO:1903039 positive regulation of leukocyte cell-cell adhesion 2 157 5.44e-01
GO:BP GO:0034762 regulation of transmembrane transport 4 391 5.45e-01
GO:BP GO:0070482 response to oxygen levels 3 272 5.45e-01
GO:BP GO:0001654 eye development 3 272 5.45e-01
GO:BP GO:0007167 enzyme-linked receptor protein signaling pathway 7 763 5.46e-01
GO:BP GO:0097194 execution phase of apoptosis 1 53 5.46e-01
GO:BP GO:1904705 regulation of vascular associated smooth muscle cell proliferation 1 53 5.46e-01
GO:BP GO:0030500 regulation of bone mineralization 1 53 5.46e-01
GO:BP GO:0031016 pancreas development 1 53 5.46e-01
GO:BP GO:0034764 positive regulation of transmembrane transport 2 158 5.46e-01
GO:BP GO:0150063 visual system development 3 273 5.46e-01
GO:BP GO:0010633 negative regulation of epithelial cell migration 1 53 5.46e-01
GO:BP GO:0046323 glucose import 1 53 5.46e-01
GO:BP GO:0030111 regulation of Wnt signaling pathway 3 273 5.46e-01
GO:BP GO:0046513 ceramide biosynthetic process 1 53 5.46e-01
GO:BP GO:0009615 response to virus 3 275 5.49e-01
GO:BP GO:0048880 sensory system development 3 275 5.49e-01
GO:BP GO:0042127 regulation of cell population proliferation 10 1147 5.49e-01
GO:BP GO:2000058 regulation of ubiquitin-dependent protein catabolic process 2 160 5.50e-01
GO:BP GO:0008154 actin polymerization or depolymerization 2 160 5.50e-01
GO:BP GO:0061035 regulation of cartilage development 1 54 5.50e-01
GO:BP GO:0051123 RNA polymerase II preinitiation complex assembly 1 54 5.50e-01
GO:BP GO:2000243 positive regulation of reproductive process 1 54 5.50e-01
GO:BP GO:0042246 tissue regeneration 1 54 5.50e-01
GO:BP GO:0006383 transcription by RNA polymerase III 1 54 5.50e-01
GO:BP GO:0072331 signal transduction by p53 class mediator 2 161 5.52e-01
GO:BP GO:0061013 regulation of mRNA catabolic process 2 161 5.52e-01
GO:BP GO:0035195 miRNA-mediated gene silencing 1 55 5.54e-01
GO:BP GO:0006611 protein export from nucleus 1 55 5.54e-01
GO:BP GO:0048704 embryonic skeletal system morphogenesis 1 55 5.54e-01
GO:BP GO:1990874 vascular associated smooth muscle cell proliferation 1 55 5.54e-01
GO:BP GO:0060562 epithelial tube morphogenesis 3 278 5.54e-01
GO:BP GO:0050818 regulation of coagulation 1 55 5.54e-01
GO:BP GO:0046209 nitric oxide metabolic process 1 55 5.54e-01
GO:BP GO:0030865 cortical cytoskeleton organization 1 55 5.54e-01
GO:BP GO:0042475 odontogenesis of dentin-containing tooth 1 55 5.54e-01
GO:BP GO:0010827 regulation of glucose transmembrane transport 1 55 5.54e-01
GO:BP GO:0009410 response to xenobiotic stimulus 3 279 5.54e-01
GO:BP GO:1903706 regulation of hemopoiesis 3 279 5.54e-01
GO:BP GO:0051347 positive regulation of transferase activity 4 400 5.55e-01
GO:BP GO:0009895 negative regulation of catabolic process 3 280 5.56e-01
GO:BP GO:0030163 protein catabolic process 8 901 5.56e-01
GO:BP GO:2001057 reactive nitrogen species metabolic process 1 56 5.57e-01
GO:BP GO:0045806 negative regulation of endocytosis 1 56 5.57e-01
GO:BP GO:0031589 cell-substrate adhesion 3 281 5.57e-01
GO:BP GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress 1 56 5.57e-01
GO:BP GO:0032024 positive regulation of insulin secretion 1 56 5.57e-01
GO:BP GO:1902893 regulation of miRNA transcription 1 56 5.57e-01
GO:BP GO:0033077 T cell differentiation in thymus 1 56 5.57e-01
GO:BP GO:0046847 filopodium assembly 1 56 5.57e-01
GO:BP GO:0033554 cellular response to stress 14 1681 5.60e-01
GO:BP GO:0007623 circadian rhythm 2 165 5.60e-01
GO:BP GO:0017148 negative regulation of translation 2 165 5.60e-01
GO:BP GO:0033555 multicellular organismal response to stress 1 57 5.60e-01
GO:BP GO:0098657 import into cell 2 166 5.60e-01
GO:BP GO:0044057 regulation of system process 4 405 5.60e-01
GO:BP GO:0061614 miRNA transcription 1 57 5.60e-01
GO:BP GO:1904377 positive regulation of protein localization to cell periphery 1 57 5.60e-01
GO:BP GO:0042116 macrophage activation 1 57 5.60e-01
GO:BP GO:2000756 regulation of peptidyl-lysine acetylation 1 57 5.60e-01
GO:BP GO:0030072 peptide hormone secretion 2 166 5.60e-01
GO:BP GO:0006576 biogenic amine metabolic process 1 57 5.60e-01
GO:BP GO:0002088 lens development in camera-type eye 1 57 5.60e-01
GO:BP GO:0043523 regulation of neuron apoptotic process 2 167 5.63e-01
GO:BP GO:1901215 negative regulation of neuron death 2 167 5.63e-01
GO:BP GO:0032271 regulation of protein polymerization 2 168 5.64e-01
GO:BP GO:0048844 artery morphogenesis 1 58 5.64e-01
GO:BP GO:0048814 regulation of dendrite morphogenesis 1 58 5.64e-01
GO:BP GO:0014910 regulation of smooth muscle cell migration 1 58 5.64e-01
GO:BP GO:1901888 regulation of cell junction assembly 2 168 5.64e-01
GO:BP GO:0032507 maintenance of protein location in cell 1 58 5.64e-01
GO:BP GO:0046883 regulation of hormone secretion 2 168 5.64e-01
GO:BP GO:0006821 chloride transport 1 58 5.64e-01
GO:BP GO:0033059 cellular pigmentation 1 58 5.64e-01
GO:BP GO:0071260 cellular response to mechanical stimulus 1 59 5.68e-01
GO:BP GO:0015980 energy derivation by oxidation of organic compounds 3 288 5.68e-01
GO:BP GO:0061951 establishment of protein localization to plasma membrane 1 59 5.68e-01
GO:BP GO:1901607 alpha-amino acid biosynthetic process 1 59 5.68e-01
GO:BP GO:0043954 cellular component maintenance 1 59 5.68e-01
GO:BP GO:0021510 spinal cord development 1 59 5.68e-01
GO:BP GO:0032502 developmental process 35 4494 5.68e-01
GO:BP GO:0051651 maintenance of location in cell 2 170 5.69e-01
GO:BP GO:0060348 bone development 2 170 5.69e-01
GO:BP GO:0002790 peptide secretion 2 170 5.69e-01
GO:BP GO:0031647 regulation of protein stability 3 290 5.71e-01
GO:BP GO:0071868 cellular response to monoamine stimulus 1 60 5.71e-01
GO:BP GO:0051899 membrane depolarization 1 60 5.71e-01
GO:BP GO:0035194 ncRNA-mediated post-transcriptional gene silencing 1 60 5.71e-01
GO:BP GO:0071870 cellular response to catecholamine stimulus 1 60 5.71e-01
GO:BP GO:0006893 Golgi to plasma membrane transport 1 60 5.71e-01
GO:BP GO:0009064 glutamine family amino acid metabolic process 1 60 5.71e-01
GO:BP GO:0010972 negative regulation of G2/M transition of mitotic cell cycle 1 60 5.71e-01
GO:BP GO:0034612 response to tumor necrosis factor 2 172 5.72e-01
GO:BP GO:1901617 organic hydroxy compound biosynthetic process 2 172 5.72e-01
GO:BP GO:0051924 regulation of calcium ion transport 2 172 5.72e-01
GO:BP GO:0010810 regulation of cell-substrate adhesion 2 172 5.72e-01
GO:BP GO:0008016 regulation of heart contraction 2 173 5.74e-01
GO:BP GO:0018958 phenol-containing compound metabolic process 1 61 5.74e-01
GO:BP GO:0034308 primary alcohol metabolic process 1 61 5.74e-01
GO:BP GO:0021954 central nervous system neuron development 1 61 5.74e-01
GO:BP GO:0030032 lamellipodium assembly 1 61 5.74e-01
GO:BP GO:0033143 regulation of intracellular steroid hormone receptor signaling pathway 1 61 5.74e-01
GO:BP GO:0042391 regulation of membrane potential 3 293 5.74e-01
GO:BP GO:0034394 protein localization to cell surface 1 61 5.74e-01
GO:BP GO:0045661 regulation of myoblast differentiation 1 61 5.74e-01
GO:BP GO:2000036 regulation of stem cell population maintenance 1 62 5.76e-01
GO:BP GO:0034765 regulation of monoatomic ion transmembrane transport 3 295 5.76e-01
GO:BP GO:0008380 RNA splicing 4 419 5.76e-01
GO:BP GO:1902750 negative regulation of cell cycle G2/M phase transition 1 62 5.76e-01
GO:BP GO:0002009 morphogenesis of an epithelium 4 418 5.76e-01
GO:BP GO:0051046 regulation of secretion 4 418 5.76e-01
GO:BP GO:0003208 cardiac ventricle morphogenesis 1 62 5.76e-01
GO:BP GO:0003073 regulation of systemic arterial blood pressure 1 62 5.76e-01
GO:BP GO:0022407 regulation of cell-cell adhesion 3 295 5.76e-01
GO:BP GO:0051246 regulation of protein metabolic process 16 1974 5.76e-01
GO:BP GO:0071869 response to catecholamine 1 62 5.76e-01
GO:BP GO:0043588 skin development 2 175 5.76e-01
GO:BP GO:0071867 response to monoamine 1 62 5.76e-01
GO:BP GO:0051249 regulation of lymphocyte activation 3 296 5.77e-01
GO:BP GO:0042327 positive regulation of phosphorylation 5 547 5.80e-01
GO:BP GO:0048488 synaptic vesicle endocytosis 1 63 5.81e-01
GO:BP GO:0046889 positive regulation of lipid biosynthetic process 1 63 5.81e-01
GO:BP GO:0048661 positive regulation of smooth muscle cell proliferation 1 63 5.81e-01
GO:BP GO:0032922 circadian regulation of gene expression 1 63 5.81e-01
GO:BP GO:0010569 regulation of double-strand break repair via homologous recombination 1 63 5.81e-01
GO:BP GO:0009605 response to external stimulus 14 1719 5.82e-01
GO:BP GO:0090596 sensory organ morphogenesis 2 178 5.84e-01
GO:BP GO:0150116 regulation of cell-substrate junction organization 1 64 5.84e-01
GO:BP GO:0051262 protein tetramerization 1 64 5.84e-01
GO:BP GO:0042326 negative regulation of phosphorylation 3 300 5.84e-01
GO:BP GO:0008652 amino acid biosynthetic process 1 64 5.84e-01
GO:BP GO:0042594 response to starvation 2 178 5.84e-01
GO:BP GO:0048678 response to axon injury 1 64 5.84e-01
GO:BP GO:1901379 regulation of potassium ion transmembrane transport 1 64 5.84e-01
GO:BP GO:1990778 protein localization to cell periphery 3 300 5.84e-01
GO:BP GO:0044283 small molecule biosynthetic process 4 425 5.84e-01
GO:BP GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process 4 427 5.85e-01
GO:BP GO:0014909 smooth muscle cell migration 1 65 5.85e-01
GO:BP GO:0060395 SMAD protein signal transduction 1 65 5.85e-01
GO:BP GO:0043087 regulation of GTPase activity 3 302 5.85e-01
GO:BP GO:0015833 peptide transport 2 179 5.85e-01
GO:BP GO:0022411 cellular component disassembly 4 427 5.85e-01
GO:BP GO:0042254 ribosome biogenesis 3 301 5.85e-01
GO:BP GO:0006414 translational elongation 1 65 5.85e-01
GO:BP GO:0006487 protein N-linked glycosylation 1 65 5.85e-01
GO:BP GO:2000144 positive regulation of DNA-templated transcription initiation 1 65 5.85e-01
GO:BP GO:0140238 presynaptic endocytosis 1 65 5.85e-01
GO:BP GO:0008306 associative learning 1 65 5.85e-01
GO:BP GO:0016441 post-transcriptional gene silencing 1 65 5.85e-01
GO:BP GO:0071230 cellular response to amino acid stimulus 1 65 5.85e-01
GO:BP GO:0065003 protein-containing complex assembly 11 1335 5.88e-01
GO:BP GO:0006954 inflammatory response 4 429 5.88e-01
GO:BP GO:0080134 regulation of response to stress 9 1075 5.90e-01
GO:BP GO:0098661 inorganic anion transmembrane transport 1 66 5.91e-01
GO:BP GO:0009582 detection of abiotic stimulus 1 68 5.91e-01
GO:BP GO:0050807 regulation of synapse organization 2 184 5.91e-01
GO:BP GO:0019318 hexose metabolic process 2 185 5.91e-01
GO:BP GO:0006094 gluconeogenesis 1 67 5.91e-01
GO:BP GO:0051851 modulation by host of symbiont process 1 68 5.91e-01
GO:BP GO:0062207 regulation of pattern recognition receptor signaling pathway 1 68 5.91e-01
GO:BP GO:0086003 cardiac muscle cell contraction 1 67 5.91e-01
GO:BP GO:0003151 outflow tract morphogenesis 1 68 5.91e-01
GO:BP GO:2000628 regulation of miRNA metabolic process 1 67 5.91e-01
GO:BP GO:0051707 response to other organism 7 820 5.91e-01
GO:BP GO:0009581 detection of external stimulus 1 67 5.91e-01
GO:BP GO:0001570 vasculogenesis 1 67 5.91e-01
GO:BP GO:0001942 hair follicle development 1 67 5.91e-01
GO:BP GO:0030001 metal ion transport 5 562 5.91e-01
GO:BP GO:0051153 regulation of striated muscle cell differentiation 1 67 5.91e-01
GO:BP GO:0065004 protein-DNA complex assembly 2 185 5.91e-01
GO:BP GO:0051341 regulation of oxidoreductase activity 1 68 5.91e-01
GO:BP GO:0048709 oligodendrocyte differentiation 1 68 5.91e-01
GO:BP GO:0097061 dendritic spine organization 1 67 5.91e-01
GO:BP GO:0070897 transcription preinitiation complex assembly 1 67 5.91e-01
GO:BP GO:0086001 cardiac muscle cell action potential 1 68 5.91e-01
GO:BP GO:0009308 amine metabolic process 1 68 5.91e-01
GO:BP GO:0071277 cellular response to calcium ion 1 67 5.91e-01
GO:BP GO:0007422 peripheral nervous system development 1 67 5.91e-01
GO:BP GO:0006839 mitochondrial transport 2 185 5.91e-01
GO:BP GO:0043207 response to external biotic stimulus 7 820 5.91e-01
GO:BP GO:0010822 positive regulation of mitochondrion organization 1 68 5.91e-01
GO:BP GO:0014013 regulation of gliogenesis 1 68 5.91e-01
GO:BP GO:2001233 regulation of apoptotic signaling pathway 3 307 5.91e-01
GO:BP GO:0043279 response to alkaloid 1 68 5.91e-01
GO:BP GO:0002753 cytosolic pattern recognition receptor signaling pathway 1 68 5.91e-01
GO:BP GO:0090257 regulation of muscle system process 2 184 5.91e-01
GO:BP GO:0070887 cellular response to chemical stimulus 15 1869 5.91e-01
GO:BP GO:0022402 cell cycle process 9 1086 5.92e-01
GO:BP GO:0120162 positive regulation of cold-induced thermogenesis 1 69 5.92e-01
GO:BP GO:0090277 positive regulation of peptide hormone secretion 1 69 5.92e-01
GO:BP GO:0006493 protein O-linked glycosylation 1 69 5.92e-01
GO:BP GO:0043502 regulation of muscle adaptation 1 69 5.92e-01
GO:BP GO:0022405 hair cycle process 1 69 5.92e-01
GO:BP GO:0006399 tRNA metabolic process 2 186 5.92e-01
GO:BP GO:0048562 embryonic organ morphogenesis 2 187 5.92e-01
GO:BP GO:1901983 regulation of protein acetylation 1 69 5.92e-01
GO:BP GO:0022404 molting cycle process 1 69 5.92e-01
GO:BP GO:0034249 negative regulation of amide metabolic process 2 186 5.92e-01
GO:BP GO:0050803 regulation of synapse structure or activity 2 187 5.92e-01
GO:BP GO:0043413 macromolecule glycosylation 2 187 5.92e-01
GO:BP GO:1901566 organonitrogen compound biosynthetic process 12 1484 5.92e-01
GO:BP GO:0006486 protein glycosylation 2 187 5.92e-01
GO:BP GO:0019218 regulation of steroid metabolic process 1 69 5.92e-01
GO:BP GO:0030901 midbrain development 1 69 5.92e-01
GO:BP GO:0030154 cell differentiation 23 2958 5.92e-01
GO:BP GO:0055117 regulation of cardiac muscle contraction 1 70 5.92e-01
GO:BP GO:0097306 cellular response to alcohol 1 70 5.92e-01
GO:BP GO:1901216 positive regulation of neuron death 1 70 5.92e-01
GO:BP GO:0002793 positive regulation of peptide secretion 1 70 5.92e-01
GO:BP GO:0043412 macromolecule modification 24 3090 5.92e-01
GO:BP GO:0033138 positive regulation of peptidyl-serine phosphorylation 1 70 5.92e-01
GO:BP GO:0060079 excitatory postsynaptic potential 1 70 5.92e-01
GO:BP GO:0022409 positive regulation of cell-cell adhesion 2 189 5.92e-01
GO:BP GO:0006096 glycolytic process 1 70 5.92e-01
GO:BP GO:0048534 hematopoietic or lymphoid organ development 1 70 5.92e-01
GO:BP GO:1901698 response to nitrogen compound 7 830 5.92e-01
GO:BP GO:0050769 positive regulation of neurogenesis 2 189 5.92e-01
GO:BP GO:0016239 positive regulation of macroautophagy 1 70 5.92e-01
GO:BP GO:0019319 hexose biosynthetic process 1 70 5.92e-01
GO:BP GO:1901700 response to oxygen-containing compound 10 1223 5.92e-01
GO:BP GO:2000736 regulation of stem cell differentiation 1 71 5.95e-01
GO:BP GO:0044419 biological process involved in interspecies interaction between organisms 8 963 5.95e-01
GO:BP GO:0098656 monoatomic anion transmembrane transport 1 71 5.95e-01
GO:BP GO:0071229 cellular response to acid chemical 1 71 5.95e-01
GO:BP GO:1904035 regulation of epithelial cell apoptotic process 1 71 5.95e-01
GO:BP GO:0062014 negative regulation of small molecule metabolic process 1 71 5.95e-01
GO:BP GO:0046620 regulation of organ growth 1 71 5.95e-01
GO:BP GO:0001892 embryonic placenta development 1 71 5.95e-01
GO:BP GO:0009100 glycoprotein metabolic process 3 316 5.95e-01
GO:BP GO:0006473 protein acetylation 2 190 5.95e-01
GO:BP GO:0031396 regulation of protein ubiquitination 2 191 5.95e-01
GO:BP GO:0070372 regulation of ERK1 and ERK2 cascade 2 191 5.95e-01
GO:BP GO:0043933 protein-containing complex organization 12 1496 5.97e-01
GO:BP GO:0010639 negative regulation of organelle organization 3 318 5.97e-01
GO:BP GO:0051603 proteolysis involved in protein catabolic process 6 706 5.97e-01
GO:BP GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic 1 72 5.97e-01
GO:BP GO:0003300 cardiac muscle hypertrophy 1 72 5.97e-01
GO:BP GO:0072665 protein localization to vacuole 1 72 5.97e-01
GO:BP GO:0007166 cell surface receptor signaling pathway 15 1898 5.97e-01
GO:BP GO:0050671 positive regulation of lymphocyte proliferation 1 72 5.97e-01
GO:BP GO:0003013 circulatory system process 4 447 5.99e-01
GO:BP GO:0006446 regulation of translational initiation 1 73 6.00e-01
GO:BP GO:0042471 ear morphogenesis 1 73 6.00e-01
GO:BP GO:0031669 cellular response to nutrient levels 2 194 6.00e-01
GO:BP GO:0042273 ribosomal large subunit biogenesis 1 73 6.00e-01
GO:BP GO:0014897 striated muscle hypertrophy 1 73 6.00e-01
GO:BP GO:2001234 negative regulation of apoptotic signaling pathway 2 194 6.00e-01
GO:BP GO:0060993 kidney morphogenesis 1 73 6.00e-01
GO:BP GO:0036465 synaptic vesicle recycling 1 73 6.00e-01
GO:BP GO:0009987 cellular process 84 11336 6.01e-01
GO:BP GO:0014896 muscle hypertrophy 1 74 6.05e-01
GO:BP GO:0001938 positive regulation of endothelial cell proliferation 1 74 6.05e-01
GO:BP GO:0010507 negative regulation of autophagy 1 74 6.05e-01
GO:BP GO:0048869 cellular developmental process 23 2984 6.05e-01
GO:BP GO:0022613 ribonucleoprotein complex biogenesis 4 453 6.08e-01
GO:BP GO:0099565 chemical synaptic transmission, postsynaptic 1 75 6.08e-01
GO:BP GO:0051865 protein autoubiquitination 1 75 6.08e-01
GO:BP GO:0043535 regulation of blood vessel endothelial cell migration 1 75 6.08e-01
GO:BP GO:0033673 negative regulation of kinase activity 2 197 6.08e-01
GO:BP GO:0032946 positive regulation of mononuclear cell proliferation 1 75 6.08e-01
GO:BP GO:0048863 stem cell differentiation 2 197 6.08e-01
GO:BP GO:0030216 keratinocyte differentiation 1 75 6.08e-01
GO:BP GO:2000142 regulation of DNA-templated transcription initiation 1 76 6.08e-01
GO:BP GO:0031397 negative regulation of protein ubiquitination 1 76 6.08e-01
GO:BP GO:0031401 positive regulation of protein modification process 6 719 6.08e-01
GO:BP GO:0009607 response to biotic stimulus 7 850 6.08e-01
GO:BP GO:0106027 neuron projection organization 1 76 6.08e-01
GO:BP GO:0048738 cardiac muscle tissue development 2 198 6.08e-01
GO:BP GO:0045927 positive regulation of growth 2 199 6.08e-01
GO:BP GO:0014812 muscle cell migration 1 76 6.08e-01
GO:BP GO:0032273 positive regulation of protein polymerization 1 76 6.08e-01
GO:BP GO:0006900 vesicle budding from membrane 1 76 6.08e-01
GO:BP GO:0051251 positive regulation of lymphocyte activation 2 199 6.08e-01
GO:BP GO:1905897 regulation of response to endoplasmic reticulum stress 1 76 6.08e-01
GO:BP GO:0006282 regulation of DNA repair 2 198 6.08e-01
GO:BP GO:1903522 regulation of blood circulation 2 198 6.08e-01
GO:BP GO:0051402 neuron apoptotic process 2 200 6.11e-01
GO:BP GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator 1 77 6.13e-01
GO:BP GO:0048145 regulation of fibroblast proliferation 1 77 6.13e-01
GO:BP GO:0043255 regulation of carbohydrate biosynthetic process 1 77 6.13e-01
GO:BP GO:0007420 brain development 5 591 6.14e-01
GO:BP GO:0032092 positive regulation of protein binding 1 78 6.16e-01
GO:BP GO:0007276 gamete generation 4 461 6.16e-01
GO:BP GO:0048706 embryonic skeletal system development 1 78 6.16e-01
GO:BP GO:0097581 lamellipodium organization 1 78 6.16e-01
GO:BP GO:0070085 glycosylation 2 202 6.16e-01
GO:BP GO:0008593 regulation of Notch signaling pathway 1 78 6.16e-01
GO:BP GO:0051702 biological process involved in interaction with symbiont 1 78 6.16e-01
GO:BP GO:1902533 positive regulation of intracellular signal transduction 6 726 6.16e-01
GO:BP GO:0043122 regulation of I-kappaB kinase/NF-kappaB signaling 2 203 6.17e-01
GO:BP GO:0045765 regulation of angiogenesis 2 203 6.17e-01
GO:BP GO:0007049 cell cycle 12 1529 6.18e-01
GO:BP GO:0071824 protein-DNA complex subunit organization 2 204 6.19e-01
GO:BP GO:0006289 nucleotide-excision repair 1 79 6.19e-01
GO:BP GO:0046364 monosaccharide biosynthetic process 1 79 6.19e-01
GO:BP GO:0045937 positive regulation of phosphate metabolic process 5 597 6.20e-01
GO:BP GO:0003012 muscle system process 3 334 6.20e-01
GO:BP GO:0010562 positive regulation of phosphorus metabolic process 5 597 6.20e-01
GO:BP GO:0003006 developmental process involved in reproduction 5 598 6.21e-01
GO:BP GO:0071310 cellular response to organic substance 11 1399 6.21e-01
GO:BP GO:1901342 regulation of vasculature development 2 206 6.21e-01
GO:BP GO:0006334 nucleosome assembly 1 80 6.21e-01
GO:BP GO:0045995 regulation of embryonic development 1 80 6.21e-01
GO:BP GO:0006513 protein monoubiquitination 1 80 6.21e-01
GO:BP GO:0007163 establishment or maintenance of cell polarity 2 206 6.21e-01
GO:BP GO:0006672 ceramide metabolic process 1 80 6.21e-01
GO:BP GO:0010817 regulation of hormone levels 3 336 6.21e-01
GO:BP GO:0010608 post-transcriptional regulation of gene expression 4 468 6.22e-01
GO:BP GO:0044773 mitotic DNA damage checkpoint signaling 1 81 6.23e-01
GO:BP GO:0000082 G1/S transition of mitotic cell cycle 2 207 6.23e-01
GO:BP GO:0090288 negative regulation of cellular response to growth factor stimulus 1 81 6.23e-01
GO:BP GO:0009628 response to abiotic stimulus 7 868 6.23e-01
GO:BP GO:0010586 miRNA metabolic process 1 81 6.23e-01
GO:BP GO:1904659 glucose transmembrane transport 1 81 6.23e-01
GO:BP GO:0007267 cell-cell signaling 9 1138 6.26e-01
GO:BP GO:1901890 positive regulation of cell junction assembly 1 82 6.26e-01
GO:BP GO:0051928 positive regulation of calcium ion transport 1 82 6.26e-01
GO:BP GO:0043406 positive regulation of MAP kinase activity 1 82 6.26e-01
GO:BP GO:0019751 polyol metabolic process 1 82 6.26e-01
GO:BP GO:0060284 regulation of cell development 5 605 6.26e-01
GO:BP GO:0050900 leukocyte migration 2 209 6.26e-01
GO:BP GO:0060078 regulation of postsynaptic membrane potential 1 82 6.26e-01
GO:BP GO:0005996 monosaccharide metabolic process 2 209 6.26e-01
GO:BP GO:0032970 regulation of actin filament-based process 3 340 6.26e-01
GO:BP GO:0014706 striated muscle tissue development 2 210 6.27e-01
GO:BP GO:0046879 hormone secretion 2 210 6.27e-01
GO:BP GO:0034341 response to type II interferon 1 83 6.28e-01
GO:BP GO:0030433 ubiquitin-dependent ERAD pathway 1 83 6.28e-01
GO:BP GO:0006820 monoatomic anion transport 1 83 6.28e-01
GO:BP GO:0009056 catabolic process 16 2088 6.28e-01
GO:BP GO:0060840 artery development 1 83 6.28e-01
GO:BP GO:0070665 positive regulation of leukocyte proliferation 1 83 6.28e-01
GO:BP GO:0070371 ERK1 and ERK2 cascade 2 211 6.28e-01
GO:BP GO:1903037 regulation of leukocyte cell-cell adhesion 2 211 6.28e-01
GO:BP GO:0043408 regulation of MAPK cascade 4 475 6.28e-01
GO:BP GO:0045936 negative regulation of phosphate metabolic process 3 344 6.28e-01
GO:BP GO:0008645 hexose transmembrane transport 1 84 6.28e-01
GO:BP GO:0030278 regulation of ossification 1 84 6.28e-01
GO:BP GO:0009408 response to heat 1 84 6.28e-01
GO:BP GO:0016032 viral process 3 344 6.28e-01
GO:BP GO:1905477 positive regulation of protein localization to membrane 1 84 6.28e-01
GO:BP GO:0120254 olefinic compound metabolic process 1 84 6.28e-01
GO:BP GO:0050852 T cell receptor signaling pathway 1 84 6.28e-01
GO:BP GO:0021782 glial cell development 1 84 6.28e-01
GO:BP GO:1990830 cellular response to leukemia inhibitory factor 1 84 6.28e-01
GO:BP GO:0015749 monosaccharide transmembrane transport 1 85 6.30e-01
GO:BP GO:0044774 mitotic DNA integrity checkpoint signaling 1 85 6.30e-01
GO:BP GO:0006942 regulation of striated muscle contraction 1 85 6.30e-01
GO:BP GO:0010563 negative regulation of phosphorus metabolic process 3 345 6.30e-01
GO:BP GO:0051716 cellular response to stimulus 37 4953 6.30e-01
GO:BP GO:0032526 response to retinoic acid 1 85 6.30e-01
GO:BP GO:1903050 regulation of proteolysis involved in protein catabolic process 2 214 6.30e-01
GO:BP GO:0050921 positive regulation of chemotaxis 1 85 6.30e-01
GO:BP GO:1990823 response to leukemia inhibitory factor 1 85 6.30e-01
GO:BP GO:0034644 cellular response to UV 1 86 6.32e-01
GO:BP GO:0035270 endocrine system development 1 86 6.32e-01
GO:BP GO:0006511 ubiquitin-dependent protein catabolic process 5 615 6.32e-01
GO:BP GO:0009914 hormone transport 2 215 6.32e-01
GO:BP GO:0043254 regulation of protein-containing complex assembly 3 348 6.32e-01
GO:BP GO:0010717 regulation of epithelial to mesenchymal transition 1 86 6.32e-01
GO:BP GO:0010906 regulation of glucose metabolic process 1 86 6.32e-01
GO:BP GO:1901655 cellular response to ketone 1 86 6.32e-01
GO:BP GO:0042476 odontogenesis 1 86 6.32e-01
GO:BP GO:1903321 negative regulation of protein modification by small protein conjugation or removal 1 86 6.32e-01
GO:BP GO:0002694 regulation of leukocyte activation 3 348 6.32e-01
GO:BP GO:0050863 regulation of T cell activation 2 216 6.32e-01
GO:BP GO:0048259 regulation of receptor-mediated endocytosis 1 87 6.35e-01
GO:BP GO:0098773 skin epidermis development 1 87 6.35e-01
GO:BP GO:0050728 negative regulation of inflammatory response 1 87 6.35e-01
GO:BP GO:0044092 negative regulation of molecular function 6 755 6.38e-01
GO:BP GO:0061337 cardiac conduction 1 88 6.40e-01
GO:BP GO:0030148 sphingolipid biosynthetic process 1 88 6.40e-01
GO:BP GO:0031668 cellular response to extracellular stimulus 2 219 6.40e-01
GO:BP GO:0033043 regulation of organelle organization 8 1028 6.41e-01
GO:BP GO:0007229 integrin-mediated signaling pathway 1 89 6.41e-01
GO:BP GO:0045445 myoblast differentiation 1 90 6.41e-01
GO:BP GO:0043467 regulation of generation of precursor metabolites and energy 1 89 6.41e-01
GO:BP GO:0006400 tRNA modification 1 90 6.41e-01
GO:BP GO:0001843 neural tube closure 1 90 6.41e-01
GO:BP GO:0043271 negative regulation of monoatomic ion transport 1 90 6.41e-01
GO:BP GO:0043500 muscle adaptation 1 90 6.41e-01
GO:BP GO:0007204 positive regulation of cytosolic calcium ion concentration 1 90 6.41e-01
GO:BP GO:0002696 positive regulation of leukocyte activation 2 222 6.41e-01
GO:BP GO:1901575 organic substance catabolic process 13 1712 6.41e-01
GO:BP GO:0045446 endothelial cell differentiation 1 90 6.41e-01
GO:BP GO:0019941 modification-dependent protein catabolic process 5 625 6.41e-01
GO:BP GO:2001243 negative regulation of intrinsic apoptotic signaling pathway 1 89 6.41e-01
GO:BP GO:0030326 embryonic limb morphogenesis 1 89 6.41e-01
GO:BP GO:0031644 regulation of nervous system process 1 90 6.41e-01
GO:BP GO:0046887 positive regulation of hormone secretion 1 90 6.41e-01
GO:BP GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process 1 89 6.41e-01
GO:BP GO:0006520 amino acid metabolic process 2 222 6.41e-01
GO:BP GO:0070252 actin-mediated cell contraction 1 89 6.41e-01
GO:BP GO:0061912 selective autophagy 1 90 6.41e-01
GO:BP GO:0035113 embryonic appendage morphogenesis 1 89 6.41e-01
GO:BP GO:0051960 regulation of nervous system development 3 357 6.42e-01
GO:BP GO:0044403 biological process involved in symbiotic interaction 2 223 6.43e-01
GO:BP GO:0060606 tube closure 1 91 6.44e-01
GO:BP GO:0031399 regulation of protein modification process 9 1173 6.44e-01
GO:BP GO:0048593 camera-type eye morphogenesis 1 91 6.44e-01
GO:BP GO:0051224 negative regulation of protein transport 1 91 6.44e-01
GO:BP GO:0030168 platelet activation 1 91 6.44e-01
GO:BP GO:0000422 autophagy of mitochondrion 1 92 6.45e-01
GO:BP GO:0061726 mitochondrion disassembly 1 92 6.45e-01
GO:BP GO:0001934 positive regulation of protein phosphorylation 4 496 6.45e-01
GO:BP GO:0048144 fibroblast proliferation 1 92 6.45e-01
GO:BP GO:0034219 carbohydrate transmembrane transport 1 92 6.45e-01
GO:BP GO:0008284 positive regulation of cell population proliferation 5 631 6.45e-01
GO:BP GO:0043473 pigmentation 1 92 6.45e-01
GO:BP GO:0019953 sexual reproduction 5 631 6.45e-01
GO:BP GO:0010389 regulation of G2/M transition of mitotic cell cycle 1 92 6.45e-01
GO:BP GO:0060322 head development 5 633 6.47e-01
GO:BP GO:0007249 I-kappaB kinase/NF-kappaB signaling 2 227 6.48e-01
GO:BP GO:0006090 pyruvate metabolic process 1 93 6.48e-01
GO:BP GO:0006518 peptide metabolic process 6 771 6.48e-01
GO:BP GO:0071333 cellular response to glucose stimulus 1 93 6.48e-01
GO:BP GO:0006367 transcription initiation at RNA polymerase II promoter 1 93 6.48e-01
GO:BP GO:0030522 intracellular receptor signaling pathway 2 227 6.48e-01
GO:BP GO:0110053 regulation of actin filament organization 2 228 6.50e-01
GO:BP GO:0043543 protein acylation 2 228 6.50e-01
GO:BP GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage 1 94 6.50e-01
GO:BP GO:0014020 primary neural tube formation 1 94 6.50e-01
GO:BP GO:0043632 modification-dependent macromolecule catabolic process 5 637 6.50e-01
GO:BP GO:0071331 cellular response to hexose stimulus 1 94 6.50e-01
GO:BP GO:0050867 positive regulation of cell activation 2 229 6.51e-01
GO:BP GO:0006811 monoatomic ion transport 6 775 6.51e-01
GO:BP GO:0043604 amide biosynthetic process 6 775 6.51e-01
GO:BP GO:0044843 cell cycle G1/S phase transition 2 229 6.51e-01
GO:BP GO:0014070 response to organic cyclic compound 5 640 6.51e-01
GO:BP GO:0002757 immune response-activating signaling pathway 2 230 6.51e-01
GO:BP GO:0042129 regulation of T cell proliferation 1 95 6.51e-01
GO:BP GO:1904950 negative regulation of establishment of protein localization 1 95 6.51e-01
GO:BP GO:0030518 intracellular steroid hormone receptor signaling pathway 1 95 6.51e-01
GO:BP GO:0043200 response to amino acid 1 95 6.51e-01
GO:BP GO:0071326 cellular response to monosaccharide stimulus 1 95 6.51e-01
GO:BP GO:0016197 endosomal transport 2 231 6.53e-01
GO:BP GO:0051128 regulation of cellular component organization 15 2011 6.53e-01
GO:BP GO:1903320 regulation of protein modification by small protein conjugation or removal 2 232 6.54e-01
GO:BP GO:0006091 generation of precursor metabolites and energy 3 369 6.54e-01
GO:BP GO:0006575 cellular modified amino acid metabolic process 1 96 6.54e-01
GO:BP GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process 1 96 6.54e-01
GO:BP GO:0045088 regulation of innate immune response 2 232 6.54e-01
GO:BP GO:0007059 chromosome segregation 3 369 6.54e-01
GO:BP GO:0031175 neuron projection development 6 780 6.54e-01
GO:BP GO:0034446 substrate adhesion-dependent cell spreading 1 97 6.55e-01
GO:BP GO:0043534 blood vessel endothelial cell migration 1 97 6.55e-01
GO:BP GO:0010243 response to organonitrogen compound 6 782 6.55e-01
GO:BP GO:0001952 regulation of cell-matrix adhesion 1 97 6.55e-01
GO:BP GO:0042752 regulation of circadian rhythm 1 97 6.55e-01
GO:BP GO:0051348 negative regulation of transferase activity 2 234 6.57e-01
GO:BP GO:0034728 nucleosome organization 1 98 6.59e-01
GO:BP GO:0150115 cell-substrate junction organization 1 98 6.59e-01
GO:BP GO:0010565 regulation of cellular ketone metabolic process 1 98 6.59e-01
GO:BP GO:0042886 amide transport 2 235 6.59e-01
GO:BP GO:0008584 male gonad development 1 99 6.59e-01
GO:BP GO:0097746 blood vessel diameter maintenance 1 99 6.59e-01
GO:BP GO:1903531 negative regulation of secretion by cell 1 99 6.59e-01
GO:BP GO:0071482 cellular response to light stimulus 1 99 6.59e-01
GO:BP GO:0035296 regulation of tube diameter 1 99 6.59e-01
GO:BP GO:1904064 positive regulation of cation transmembrane transport 1 99 6.59e-01
GO:BP GO:0090630 activation of GTPase activity 1 99 6.59e-01
GO:BP GO:0035150 regulation of tube size 1 99 6.59e-01
GO:BP GO:0050878 regulation of body fluid levels 2 236 6.59e-01
GO:BP GO:0048511 rhythmic process 2 237 6.60e-01
GO:BP GO:0001666 response to hypoxia 2 237 6.60e-01
GO:BP GO:0042177 negative regulation of protein catabolic process 1 100 6.62e-01
GO:BP GO:0033135 regulation of peptidyl-serine phosphorylation 1 100 6.62e-01
GO:BP GO:0046546 development of primary male sexual characteristics 1 100 6.62e-01
GO:BP GO:0007417 central nervous system development 6 792 6.63e-01
GO:BP GO:0000904 cell morphogenesis involved in differentiation 4 516 6.64e-01
GO:BP GO:0071901 negative regulation of protein serine/threonine kinase activity 1 101 6.64e-01
GO:BP GO:0021987 cerebral cortex development 1 101 6.64e-01
GO:BP GO:0030856 regulation of epithelial cell differentiation 1 101 6.64e-01
GO:BP GO:0000018 regulation of DNA recombination 1 101 6.64e-01
GO:BP GO:0051258 protein polymerization 2 241 6.68e-01
GO:BP GO:0071674 mononuclear cell migration 1 102 6.68e-01
GO:BP GO:0001936 regulation of endothelial cell proliferation 1 102 6.68e-01
GO:BP GO:0002764 immune response-regulating signaling pathway 2 242 6.70e-01
GO:BP GO:1902749 regulation of cell cycle G2/M phase transition 1 103 6.70e-01
GO:BP GO:0031047 RNA-mediated gene silencing 1 103 6.70e-01
GO:BP GO:0006892 post-Golgi vesicle-mediated transport 1 103 6.70e-01
GO:BP GO:2000060 positive regulation of ubiquitin-dependent protein catabolic process 1 103 6.70e-01
GO:BP GO:0022904 respiratory electron transport chain 1 104 6.74e-01
GO:BP GO:0003158 endothelium development 1 104 6.74e-01
GO:BP GO:0006906 vesicle fusion 1 104 6.74e-01
GO:BP GO:0043043 peptide biosynthetic process 5 666 6.76e-01
GO:BP GO:0001101 response to acid chemical 1 105 6.76e-01
GO:BP GO:1901214 regulation of neuron death 2 246 6.76e-01
GO:BP GO:0006952 defense response 7 944 6.76e-01
GO:BP GO:0001508 action potential 1 105 6.76e-01
GO:BP GO:0009416 response to light stimulus 2 246 6.76e-01
GO:BP GO:0051093 negative regulation of developmental process 5 665 6.76e-01
GO:BP GO:0071322 cellular response to carbohydrate stimulus 1 105 6.76e-01
GO:BP GO:0050851 antigen receptor-mediated signaling pathway 1 106 6.78e-01
GO:BP GO:0090174 organelle membrane fusion 1 106 6.78e-01
GO:BP GO:0048660 regulation of smooth muscle cell proliferation 1 106 6.78e-01
GO:BP GO:0036503 ERAD pathway 1 106 6.78e-01
GO:BP GO:0120035 regulation of plasma membrane bounded cell projection organization 4 529 6.78e-01
GO:BP GO:0006935 chemotaxis 3 389 6.78e-01
GO:BP GO:0006812 monoatomic cation transport 5 669 6.78e-01
GO:BP GO:0042330 taxis 3 389 6.78e-01
GO:BP GO:2001056 positive regulation of cysteine-type endopeptidase activity 1 107 6.80e-01
GO:BP GO:0046718 viral entry into host cell 1 107 6.80e-01
GO:BP GO:0061024 membrane organization 5 671 6.80e-01
GO:BP GO:0031398 positive regulation of protein ubiquitination 1 108 6.82e-01
GO:BP GO:0045834 positive regulation of lipid metabolic process 1 108 6.82e-01
GO:BP GO:0019216 regulation of lipid metabolic process 2 250 6.82e-01
GO:BP GO:2001235 positive regulation of apoptotic signaling pathway 1 108 6.82e-01
GO:BP GO:0051248 negative regulation of protein metabolic process 6 816 6.86e-01
GO:BP GO:0060041 retina development in camera-type eye 1 109 6.86e-01
GO:BP GO:0090066 regulation of anatomical structure size 3 395 6.88e-01
GO:BP GO:0051606 detection of stimulus 1 110 6.88e-01
GO:BP GO:0001678 intracellular glucose homeostasis 1 110 6.88e-01
GO:BP GO:0048659 smooth muscle cell proliferation 1 110 6.88e-01
GO:BP GO:0008283 cell population proliferation 10 1378 6.88e-01
GO:BP GO:0048609 multicellular organismal reproductive process 4 538 6.89e-01
GO:BP GO:0051048 negative regulation of secretion 1 111 6.90e-01
GO:BP GO:1901800 positive regulation of proteasomal protein catabolic process 1 111 6.90e-01
GO:BP GO:0008643 carbohydrate transport 1 111 6.90e-01
GO:BP GO:0030048 actin filament-based movement 1 112 6.92e-01
GO:BP GO:0050954 sensory perception of mechanical stimulus 1 112 6.92e-01
GO:BP GO:0043401 steroid hormone mediated signaling pathway 1 112 6.92e-01
GO:BP GO:0018108 peptidyl-tyrosine phosphorylation 2 256 6.92e-01
GO:BP GO:0031344 regulation of cell projection organization 4 541 6.92e-01
GO:BP GO:0051053 negative regulation of DNA metabolic process 1 112 6.92e-01
GO:BP GO:0048592 eye morphogenesis 1 113 6.94e-01
GO:BP GO:0051592 response to calcium ion 1 113 6.94e-01
GO:BP GO:0018212 peptidyl-tyrosine modification 2 258 6.94e-01
GO:BP GO:0044409 entry into host 1 113 6.94e-01
GO:BP GO:0048638 regulation of developmental growth 2 258 6.94e-01
GO:BP GO:0006950 response to stress 20 2780 6.96e-01
GO:BP GO:0090090 negative regulation of canonical Wnt signaling pathway 1 114 6.97e-01
GO:BP GO:0046661 male sex differentiation 1 114 6.97e-01
GO:BP GO:0034767 positive regulation of monoatomic ion transmembrane transport 1 114 6.97e-01
GO:BP GO:0002221 pattern recognition receptor signaling pathway 1 115 6.99e-01
GO:BP GO:0030595 leukocyte chemotaxis 1 115 6.99e-01
GO:BP GO:0007612 learning 1 115 6.99e-01
GO:BP GO:0007568 aging 1 115 6.99e-01
GO:BP GO:0097553 calcium ion transmembrane import into cytosol 1 115 6.99e-01
GO:BP GO:0043085 positive regulation of catalytic activity 6 834 7.01e-01
GO:BP GO:0001935 endothelial cell proliferation 1 116 7.01e-01
GO:BP GO:0051783 regulation of nuclear division 1 116 7.01e-01
GO:BP GO:0010033 response to organic substance 14 1957 7.01e-01
GO:BP GO:0006413 translational initiation 1 116 7.01e-01
GO:BP GO:0007009 plasma membrane organization 1 116 7.01e-01
GO:BP GO:1903047 mitotic cell cycle process 5 694 7.02e-01
GO:BP GO:1900180 regulation of protein localization to nucleus 1 117 7.02e-01
GO:BP GO:0001959 regulation of cytokine-mediated signaling pathway 1 117 7.02e-01
GO:BP GO:0001890 placenta development 1 117 7.02e-01
GO:BP GO:0010977 negative regulation of neuron projection development 1 117 7.02e-01
GO:BP GO:0048468 cell development 14 1963 7.04e-01
GO:BP GO:0006066 alcohol metabolic process 2 265 7.04e-01
GO:BP GO:0051147 regulation of muscle cell differentiation 1 118 7.05e-01
GO:BP GO:0000165 MAPK cascade 4 556 7.07e-01
GO:BP GO:0032504 multicellular organism reproduction 4 556 7.07e-01
GO:BP GO:1903311 regulation of mRNA metabolic process 2 267 7.07e-01
GO:BP GO:0006936 muscle contraction 2 267 7.07e-01
GO:BP GO:0042098 T cell proliferation 1 120 7.08e-01
GO:BP GO:0043524 negative regulation of neuron apoptotic process 1 120 7.08e-01
GO:BP GO:0104004 cellular response to environmental stimulus 2 268 7.08e-01
GO:BP GO:0071214 cellular response to abiotic stimulus 2 268 7.08e-01
GO:BP GO:0071407 cellular response to organic cyclic compound 3 414 7.08e-01
GO:BP GO:0051225 spindle assembly 1 120 7.08e-01
GO:BP GO:0140013 meiotic nuclear division 1 120 7.08e-01
GO:BP GO:0016052 carbohydrate catabolic process 1 120 7.08e-01
GO:BP GO:0006816 calcium ion transport 2 269 7.09e-01
GO:BP GO:0070374 positive regulation of ERK1 and ERK2 cascade 1 121 7.10e-01
GO:BP GO:2000779 regulation of double-strand break repair 1 121 7.10e-01
GO:BP GO:0051983 regulation of chromosome segregation 1 121 7.10e-01
GO:BP GO:0000077 DNA damage checkpoint signaling 1 121 7.10e-01
GO:BP GO:0006694 steroid biosynthetic process 1 121 7.10e-01
GO:BP GO:0098660 inorganic ion transmembrane transport 4 563 7.11e-01
GO:BP GO:0031400 negative regulation of protein modification process 3 418 7.11e-01
GO:BP GO:0019722 calcium-mediated signaling 1 122 7.11e-01
GO:BP GO:0050792 regulation of viral process 1 122 7.11e-01
GO:BP GO:0002758 innate immune response-activating signaling pathway 1 122 7.11e-01
GO:BP GO:0044272 sulfur compound biosynthetic process 1 122 7.11e-01
GO:BP GO:0043603 amide metabolic process 7 993 7.11e-01
GO:BP GO:0002253 activation of immune response 2 272 7.11e-01
GO:BP GO:0071456 cellular response to hypoxia 1 123 7.12e-01
GO:BP GO:0003002 regionalization 2 273 7.12e-01
GO:BP GO:0051896 regulation of protein kinase B signaling 1 123 7.12e-01
GO:BP GO:0002274 myeloid leukocyte activation 1 123 7.12e-01
GO:BP GO:0046467 membrane lipid biosynthetic process 1 124 7.15e-01
GO:BP GO:0048639 positive regulation of developmental growth 1 124 7.15e-01
GO:BP GO:0032940 secretion by cell 4 569 7.17e-01
GO:BP GO:0019725 cellular homeostasis 4 569 7.17e-01
GO:BP GO:0010950 positive regulation of endopeptidase activity 1 126 7.19e-01
GO:BP GO:1903322 positive regulation of protein modification by small protein conjugation or removal 1 126 7.19e-01
GO:BP GO:0050670 regulation of lymphocyte proliferation 1 126 7.19e-01
GO:BP GO:0060759 regulation of response to cytokine stimulus 1 126 7.19e-01
GO:BP GO:0001933 negative regulation of protein phosphorylation 2 277 7.19e-01
GO:BP GO:1901565 organonitrogen compound catabolic process 8 1145 7.19e-01
GO:BP GO:1903052 positive regulation of proteolysis involved in protein catabolic process 1 127 7.21e-01
GO:BP GO:0007098 centrosome cycle 1 127 7.21e-01
GO:BP GO:0009952 anterior/posterior pattern specification 1 127 7.21e-01
GO:BP GO:0044093 positive regulation of molecular function 8 1149 7.21e-01
GO:BP GO:0006796 phosphate-containing compound metabolic process 15 2139 7.21e-01
GO:BP GO:2000241 regulation of reproductive process 1 128 7.24e-01
GO:BP GO:0007165 signal transduction 27 3818 7.25e-01
GO:BP GO:0031570 DNA integrity checkpoint signaling 1 129 7.26e-01
GO:BP GO:0032944 regulation of mononuclear cell proliferation 1 129 7.26e-01
GO:BP GO:0031333 negative regulation of protein-containing complex assembly 1 130 7.29e-01
GO:BP GO:0002684 positive regulation of immune system process 4 581 7.30e-01
GO:BP GO:0035265 organ growth 1 131 7.31e-01
GO:BP GO:0006665 sphingolipid metabolic process 1 131 7.31e-01
GO:BP GO:0070997 neuron death 2 286 7.34e-01
GO:BP GO:0048666 neuron development 6 877 7.35e-01
GO:BP GO:0032434 regulation of proteasomal ubiquitin-dependent protein catabolic process 1 133 7.35e-01
GO:BP GO:0006793 phosphorus metabolic process 15 2161 7.35e-01
GO:BP GO:0006937 regulation of muscle contraction 1 133 7.35e-01
GO:BP GO:0042445 hormone metabolic process 1 133 7.35e-01
GO:BP GO:0001764 neuron migration 1 133 7.35e-01
GO:BP GO:0002682 regulation of immune system process 6 877 7.35e-01
GO:BP GO:0046907 intracellular transport 10 1453 7.35e-01
GO:BP GO:0010638 positive regulation of organelle organization 3 439 7.36e-01
GO:BP GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 2 289 7.36e-01
GO:BP GO:0000398 mRNA splicing, via spliceosome 2 289 7.36e-01
GO:BP GO:0010952 positive regulation of peptidase activity 1 135 7.38e-01
GO:BP GO:0071902 positive regulation of protein serine/threonine kinase activity 1 135 7.38e-01
GO:BP GO:0048284 organelle fusion 1 135 7.38e-01
GO:BP GO:0006955 immune response 6 882 7.38e-01
GO:BP GO:1903046 meiotic cell cycle process 1 135 7.38e-01
GO:BP GO:0032386 regulation of intracellular transport 2 292 7.41e-01
GO:BP GO:0090501 RNA phosphodiester bond hydrolysis 1 136 7.41e-01
GO:BP GO:1903008 organelle disassembly 1 137 7.41e-01
GO:BP GO:0000375 RNA splicing, via transesterification reactions 2 293 7.41e-01
GO:BP GO:0009749 response to glucose 1 137 7.41e-01
GO:BP GO:0031023 microtubule organizing center organization 1 137 7.41e-01
GO:BP GO:0061025 membrane fusion 1 137 7.41e-01
GO:BP GO:0002831 regulation of response to biotic stimulus 2 293 7.41e-01
GO:BP GO:0045664 regulation of neuron differentiation 1 137 7.41e-01
GO:BP GO:0007030 Golgi organization 1 137 7.41e-01
GO:BP GO:0044000 movement in host 1 138 7.43e-01
GO:BP GO:0009746 response to hexose 1 138 7.43e-01
GO:BP GO:0045862 positive regulation of proteolysis 2 295 7.43e-01
GO:BP GO:0031347 regulation of defense response 3 448 7.44e-01
GO:BP GO:0009755 hormone-mediated signaling pathway 1 139 7.44e-01
GO:BP GO:0050770 regulation of axonogenesis 1 139 7.44e-01
GO:BP GO:0021543 pallium development 1 139 7.44e-01
GO:BP GO:0007093 mitotic cell cycle checkpoint signaling 1 139 7.44e-01
GO:BP GO:0051241 negative regulation of multicellular organismal process 5 748 7.46e-01
GO:BP GO:0030178 negative regulation of Wnt signaling pathway 1 140 7.46e-01
GO:BP GO:0051052 regulation of DNA metabolic process 3 452 7.47e-01
GO:BP GO:0043405 regulation of MAP kinase activity 1 141 7.47e-01
GO:BP GO:0032956 regulation of actin cytoskeleton organization 2 299 7.47e-01
GO:BP GO:0009411 response to UV 1 141 7.47e-01
GO:BP GO:0048167 regulation of synaptic plasticity 1 141 7.47e-01
GO:BP GO:0070663 regulation of leukocyte proliferation 1 141 7.47e-01
GO:BP GO:0003008 system process 8 1189 7.47e-01
GO:BP GO:0050920 regulation of chemotaxis 1 142 7.47e-01
GO:BP GO:0022900 electron transport chain 1 142 7.47e-01
GO:BP GO:0034284 response to monosaccharide 1 142 7.47e-01
GO:BP GO:0002218 activation of innate immune response 1 142 7.47e-01
GO:BP GO:1902075 cellular response to salt 1 142 7.47e-01
GO:BP GO:0051129 negative regulation of cellular component organization 4 604 7.47e-01
GO:BP GO:0050767 regulation of neurogenesis 2 301 7.47e-01
GO:BP GO:0051668 localization within membrane 4 605 7.47e-01
GO:BP GO:0034097 response to cytokine 4 607 7.50e-01
GO:BP GO:0031346 positive regulation of cell projection organization 2 303 7.50e-01
GO:BP GO:0098542 defense response to other organism 4 608 7.51e-01
GO:BP GO:0002520 immune system development 1 144 7.51e-01
GO:BP GO:0051130 positive regulation of cellular component organization 6 906 7.52e-01
GO:BP GO:0032535 regulation of cellular component size 2 305 7.53e-01
GO:BP GO:0140352 export from cell 4 611 7.54e-01
GO:BP GO:0007389 pattern specification process 2 306 7.54e-01
GO:BP GO:0043491 protein kinase B signaling 1 146 7.55e-01
GO:BP GO:0007219 Notch signaling pathway 1 146 7.55e-01
GO:BP GO:0030324 lung development 1 146 7.55e-01
GO:BP GO:0043488 regulation of mRNA stability 1 147 7.56e-01
GO:BP GO:1901654 response to ketone 1 147 7.56e-01
GO:BP GO:0016236 macroautophagy 2 308 7.56e-01
GO:BP GO:1990138 neuron projection extension 1 148 7.59e-01
GO:BP GO:0030099 myeloid cell differentiation 2 310 7.59e-01
GO:BP GO:0000724 double-strand break repair via homologous recombination 1 149 7.61e-01
GO:BP GO:0030323 respiratory tube development 1 150 7.63e-01
GO:BP GO:0002429 immune response-activating cell surface receptor signaling pathway 1 151 7.65e-01
GO:BP GO:0015031 protein transport 9 1361 7.65e-01
GO:BP GO:0002573 myeloid leukocyte differentiation 1 151 7.65e-01
GO:BP GO:1902905 positive regulation of supramolecular fiber organization 1 151 7.65e-01
GO:BP GO:0045637 regulation of myeloid cell differentiation 1 152 7.67e-01
GO:BP GO:0010648 negative regulation of cell communication 7 1074 7.68e-01
GO:BP GO:0010564 regulation of cell cycle process 4 626 7.68e-01
GO:BP GO:0040029 epigenetic regulation of gene expression 1 153 7.68e-01
GO:BP GO:0000725 recombinational repair 1 153 7.68e-01
GO:BP GO:0043410 positive regulation of MAPK cascade 2 317 7.68e-01
GO:BP GO:0022414 reproductive process 6 927 7.68e-01
GO:BP GO:0023057 negative regulation of signaling 7 1076 7.69e-01
GO:BP GO:0051701 biological process involved in interaction with host 1 154 7.69e-01
GO:BP GO:0071356 cellular response to tumor necrosis factor 1 155 7.71e-01
GO:BP GO:0071478 cellular response to radiation 1 156 7.71e-01
GO:BP GO:0051641 cellular localization 19 2810 7.71e-01
GO:BP GO:0016050 vesicle organization 2 320 7.71e-01
GO:BP GO:0031345 negative regulation of cell projection organization 1 156 7.71e-01
GO:BP GO:0043281 regulation of cysteine-type endopeptidase activity involved in apoptotic process 1 155 7.71e-01
GO:BP GO:0043086 negative regulation of catalytic activity 3 478 7.71e-01
GO:BP GO:0010628 positive regulation of gene expression 5 783 7.71e-01
GO:BP GO:0034220 monoatomic ion transmembrane transport 4 632 7.71e-01
GO:BP GO:0050679 positive regulation of epithelial cell proliferation 1 155 7.71e-01
GO:BP GO:0023061 signal release 2 321 7.71e-01
GO:BP GO:0000003 reproduction 6 934 7.71e-01
GO:BP GO:0010629 negative regulation of gene expression 5 785 7.71e-01
GO:BP GO:0006974 DNA damage response 5 785 7.71e-01
GO:BP GO:0033002 muscle cell proliferation 1 157 7.72e-01
GO:BP GO:0045596 negative regulation of cell differentiation 3 482 7.73e-01
GO:BP GO:0008406 gonad development 1 158 7.73e-01
GO:BP GO:0042180 cellular ketone metabolic process 1 158 7.73e-01
GO:BP GO:0031348 negative regulation of defense response 1 159 7.75e-01
GO:BP GO:0097305 response to alcohol 1 159 7.75e-01
GO:BP GO:0043487 regulation of RNA stability 1 159 7.75e-01
GO:BP GO:0050776 regulation of immune response 3 484 7.75e-01
GO:BP GO:1902903 regulation of supramolecular fiber organization 2 326 7.76e-01
GO:BP GO:0018394 peptidyl-lysine acetylation 1 160 7.76e-01
GO:BP GO:0002768 immune response-regulating cell surface receptor signaling pathway 1 162 7.76e-01
GO:BP GO:0071702 organic substance transport 14 2116 7.76e-01
GO:BP GO:0019538 protein metabolic process 29 4241 7.76e-01
GO:BP GO:0071705 nitrogen compound transport 11 1684 7.76e-01
GO:BP GO:0009743 response to carbohydrate 1 161 7.76e-01
GO:BP GO:0045087 innate immune response 3 488 7.76e-01
GO:BP GO:0031334 positive regulation of protein-containing complex assembly 1 161 7.76e-01
GO:BP GO:0046651 lymphocyte proliferation 1 162 7.76e-01
GO:BP GO:0055082 intracellular chemical homeostasis 3 486 7.76e-01
GO:BP GO:0045137 development of primary sexual characteristics 1 161 7.76e-01
GO:BP GO:0060326 cell chemotaxis 1 162 7.76e-01
GO:BP GO:0009451 RNA modification 1 162 7.76e-01
GO:BP GO:0016482 cytosolic transport 1 161 7.76e-01
GO:BP GO:0050896 response to stimulus 40 5770 7.77e-01
GO:BP GO:0046903 secretion 4 645 7.77e-01
GO:BP GO:0060541 respiratory system development 1 163 7.77e-01
GO:BP GO:0099504 synaptic vesicle cycle 1 163 7.77e-01
GO:BP GO:0006412 translation 4 646 7.77e-01
GO:BP GO:0043484 regulation of RNA splicing 1 164 7.79e-01
GO:BP GO:0051179 localization 27 3969 7.79e-01
GO:BP GO:0051495 positive regulation of cytoskeleton organization 1 165 7.80e-01
GO:BP GO:0120032 regulation of plasma membrane bounded cell projection assembly 1 165 7.80e-01
GO:BP GO:0031330 negative regulation of cellular catabolic process 1 165 7.80e-01
GO:BP GO:0042221 response to chemical 17 2559 7.80e-01
GO:BP GO:0008104 protein localization 14 2129 7.81e-01
GO:BP GO:1901991 negative regulation of mitotic cell cycle phase transition 1 166 7.81e-01
GO:BP GO:0071383 cellular response to steroid hormone stimulus 1 166 7.81e-01
GO:BP GO:0046578 regulation of Ras protein signal transduction 1 166 7.81e-01
GO:BP GO:0060491 regulation of cell projection assembly 1 167 7.83e-01
GO:BP GO:0044087 regulation of cellular component biogenesis 5 809 7.83e-01
GO:BP GO:0032103 positive regulation of response to external stimulus 2 337 7.83e-01
GO:BP GO:0032943 mononuclear cell proliferation 1 168 7.83e-01
GO:BP GO:0098742 cell-cell adhesion via plasma-membrane adhesion molecules 1 168 7.83e-01
GO:BP GO:0045786 negative regulation of cell cycle 2 338 7.83e-01
GO:BP GO:0042593 glucose homeostasis 1 168 7.83e-01
GO:BP GO:0070727 cellular macromolecule localization 14 2138 7.83e-01
GO:BP GO:2000116 regulation of cysteine-type endopeptidase activity 1 169 7.84e-01
GO:BP GO:0033500 carbohydrate homeostasis 1 169 7.84e-01
GO:BP GO:0050804 modulation of chemical synaptic transmission 2 341 7.87e-01
GO:BP GO:0099177 regulation of trans-synaptic signaling 2 342 7.88e-01
GO:BP GO:0060537 muscle tissue development 2 343 7.88e-01
GO:BP GO:0044085 cellular component biogenesis 18 2724 7.88e-01
GO:BP GO:0043393 regulation of protein binding 1 172 7.88e-01
GO:BP GO:0032101 regulation of response to external stimulus 4 662 7.88e-01
GO:BP GO:0023052 signaling 28 4141 7.88e-01
GO:BP GO:0034329 cell junction assembly 2 344 7.89e-01
GO:BP GO:0006643 membrane lipid metabolic process 1 173 7.89e-01
GO:BP GO:0006810 transport 22 3298 7.89e-01
GO:BP GO:0033036 macromolecule localization 16 2450 7.95e-01
GO:BP GO:0048812 neuron projection morphogenesis 3 512 7.96e-01
GO:BP GO:0000278 mitotic cell cycle 5 827 7.97e-01
GO:BP GO:0098771 inorganic ion homeostasis 2 351 7.98e-01
GO:BP GO:0032496 response to lipopolysaccharide 1 178 7.99e-01
GO:BP GO:0009314 response to radiation 2 352 7.99e-01
GO:BP GO:0006469 negative regulation of protein kinase activity 1 179 7.99e-01
GO:BP GO:0007160 cell-matrix adhesion 1 179 7.99e-01
GO:BP GO:0098662 inorganic cation transmembrane transport 3 517 7.99e-01
GO:BP GO:0097191 extrinsic apoptotic signaling pathway 1 179 7.99e-01
GO:BP GO:0031667 response to nutrient levels 2 353 7.99e-01
GO:BP GO:0099003 vesicle-mediated transport in synapse 1 180 8.00e-01
GO:BP GO:0030003 intracellular monoatomic cation homeostasis 2 357 8.03e-01
GO:BP GO:0045089 positive regulation of innate immune response 1 182 8.03e-01
GO:BP GO:0048589 developmental growth 3 522 8.03e-01
GO:BP GO:0140694 non-membrane-bounded organelle assembly 2 357 8.03e-01
GO:BP GO:0061136 regulation of proteasomal protein catabolic process 1 183 8.04e-01
GO:BP GO:0072657 protein localization to membrane 3 523 8.04e-01
GO:BP GO:0000075 cell cycle checkpoint signaling 1 183 8.04e-01
GO:BP GO:0006897 endocytosis 3 527 8.08e-01
GO:BP GO:0007411 axon guidance 1 185 8.08e-01
GO:BP GO:0120039 plasma membrane bounded cell projection morphogenesis 3 527 8.08e-01
GO:BP GO:0006873 intracellular monoatomic ion homeostasis 2 362 8.08e-01
GO:BP GO:0097485 neuron projection guidance 1 186 8.08e-01
GO:BP GO:0045444 fat cell differentiation 1 187 8.10e-01
GO:BP GO:0002237 response to molecule of bacterial origin 1 187 8.10e-01
GO:BP GO:0051321 meiotic cell cycle 1 188 8.10e-01
GO:BP GO:0070661 leukocyte proliferation 1 188 8.10e-01
GO:BP GO:0048858 cell projection morphogenesis 3 531 8.10e-01
GO:BP GO:0050808 synapse organization 2 365 8.10e-01
GO:BP GO:0007051 spindle organization 1 188 8.10e-01
GO:BP GO:0048871 multicellular organismal-level homeostasis 3 532 8.10e-01
GO:BP GO:0009968 negative regulation of signal transduction 6 1006 8.10e-01
GO:BP GO:0045184 establishment of protein localization 9 1462 8.11e-01
GO:BP GO:0006281 DNA repair 3 534 8.11e-01
GO:BP GO:0030162 regulation of proteolysis 3 535 8.12e-01
GO:BP GO:0019932 second-messenger-mediated signaling 1 191 8.13e-01
GO:BP GO:0007548 sex differentiation 1 191 8.13e-01
GO:BP GO:0050778 positive regulation of immune response 2 369 8.13e-01
GO:BP GO:0006457 protein folding 1 192 8.14e-01
GO:BP GO:0002833 positive regulation of response to biotic stimulus 1 192 8.14e-01
GO:BP GO:0048588 developmental cell growth 1 192 8.14e-01
GO:BP GO:0051336 regulation of hydrolase activity 4 701 8.15e-01
GO:BP GO:0071345 cellular response to cytokine stimulus 3 540 8.15e-01
GO:BP GO:0098655 monoatomic cation transmembrane transport 3 540 8.15e-01
GO:BP GO:0007015 actin filament organization 2 373 8.15e-01
GO:BP GO:0007154 cell communication 28 4226 8.17e-01
GO:BP GO:0051276 chromosome organization 3 543 8.17e-01
GO:BP GO:0006898 receptor-mediated endocytosis 1 196 8.18e-01
GO:BP GO:1901137 carbohydrate derivative biosynthetic process 3 544 8.18e-01
GO:BP GO:1901615 organic hydroxy compound metabolic process 2 376 8.18e-01
GO:BP GO:0009991 response to extracellular stimulus 2 377 8.19e-01
GO:BP GO:0033157 regulation of intracellular protein transport 1 197 8.19e-01
GO:BP GO:0006338 chromatin remodeling 2 378 8.19e-01
GO:BP GO:0003018 vascular process in circulatory system 1 198 8.20e-01
GO:BP GO:0006874 intracellular calcium ion homeostasis 1 200 8.23e-01
GO:BP GO:0032990 cell part morphogenesis 3 551 8.23e-01
GO:BP GO:0006325 chromatin organization 3 551 8.23e-01
GO:BP GO:0140546 defense response to symbiont 1 202 8.25e-01
GO:BP GO:0007611 learning or memory 1 202 8.25e-01
GO:BP GO:0051607 defense response to virus 1 202 8.25e-01
GO:BP GO:0022618 ribonucleoprotein complex assembly 1 203 8.26e-01
GO:BP GO:0060560 developmental growth involved in morphogenesis 1 204 8.27e-01
GO:BP GO:0008202 steroid metabolic process 1 204 8.27e-01
GO:BP GO:0007186 G protein-coupled receptor signaling pathway 2 389 8.30e-01
GO:BP GO:0120036 plasma membrane bounded cell projection organization 7 1201 8.33e-01
GO:BP GO:0090068 positive regulation of cell cycle process 1 209 8.35e-01
GO:BP GO:0090305 nucleic acid phosphodiester bond hydrolysis 1 211 8.36e-01
GO:BP GO:0045930 negative regulation of mitotic cell cycle 1 211 8.36e-01
GO:BP GO:0045333 cellular respiration 1 211 8.36e-01
GO:BP GO:0030100 regulation of endocytosis 1 211 8.36e-01
GO:BP GO:0021700 developmental maturation 1 211 8.36e-01
GO:BP GO:0071826 ribonucleoprotein complex subunit organization 1 211 8.36e-01
GO:BP GO:0008150 biological_process 86 12070 8.36e-01
GO:BP GO:0061564 axon development 2 398 8.36e-01
GO:BP GO:0048608 reproductive structure development 1 212 8.36e-01
GO:BP GO:0050727 regulation of inflammatory response 1 212 8.36e-01
GO:BP GO:0051234 establishment of localization 22 3433 8.36e-01
GO:BP GO:0071396 cellular response to lipid 2 398 8.36e-01
GO:BP GO:0070588 calcium ion transmembrane transport 1 213 8.37e-01
GO:BP GO:0055074 calcium ion homeostasis 1 214 8.38e-01
GO:BP GO:0055080 monoatomic cation homeostasis 2 401 8.38e-01
GO:BP GO:0061458 reproductive system development 1 215 8.39e-01
GO:BP GO:0060627 regulation of vesicle-mediated transport 2 403 8.40e-01
GO:BP GO:0032886 regulation of microtubule-based process 1 217 8.41e-01
GO:BP GO:0000819 sister chromatid segregation 1 217 8.41e-01
GO:BP GO:0002250 adaptive immune response 1 218 8.42e-01
GO:BP GO:0050801 monoatomic ion homeostasis 2 408 8.44e-01
GO:BP GO:0051346 negative regulation of hydrolase activity 1 220 8.44e-01
GO:BP GO:0032984 protein-containing complex disassembly 1 222 8.46e-01
GO:BP GO:0043547 positive regulation of GTPase activity 1 222 8.46e-01
GO:BP GO:0030030 cell projection organization 7 1233 8.46e-01
GO:BP GO:0046394 carboxylic acid biosynthetic process 1 223 8.47e-01
GO:BP GO:0016053 organic acid biosynthetic process 1 224 8.48e-01
GO:BP GO:0016042 lipid catabolic process 1 225 8.49e-01
GO:BP GO:0033993 response to lipid 3 592 8.51e-01
GO:BP GO:0048872 homeostasis of number of cells 1 228 8.53e-01
GO:BP GO:0044089 positive regulation of cellular component biogenesis 2 420 8.54e-01
GO:BP GO:0048585 negative regulation of response to stimulus 7 1248 8.54e-01
GO:BP GO:0007264 small GTPase mediated signal transduction 2 421 8.54e-01
GO:BP GO:1904062 regulation of monoatomic cation transmembrane transport 1 230 8.54e-01
GO:BP GO:0051345 positive regulation of hydrolase activity 2 422 8.54e-01
GO:BP GO:0072594 establishment of protein localization to organelle 2 422 8.54e-01
GO:BP GO:0052548 regulation of endopeptidase activity 1 232 8.56e-01
GO:BP GO:0030198 extracellular matrix organization 1 233 8.57e-01
GO:BP GO:0051146 striated muscle cell differentiation 1 233 8.57e-01
GO:BP GO:0043062 extracellular structure organization 1 234 8.57e-01
GO:BP GO:0045229 external encapsulating structure organization 1 234 8.57e-01
GO:BP GO:1901988 negative regulation of cell cycle phase transition 1 235 8.58e-01
GO:BP GO:0016570 histone modification 2 433 8.63e-01
GO:BP GO:0071375 cellular response to peptide hormone stimulus 1 241 8.66e-01
GO:BP GO:1902532 negative regulation of intracellular signal transduction 2 438 8.68e-01
GO:BP GO:0001822 kidney development 1 244 8.68e-01
GO:BP GO:0019058 viral life cycle 1 244 8.68e-01
GO:BP GO:0007346 regulation of mitotic cell cycle 2 441 8.69e-01
GO:BP GO:0048545 response to steroid hormone 1 245 8.69e-01
GO:BP GO:0018105 peptidyl-serine phosphorylation 1 247 8.71e-01
GO:BP GO:0006790 sulfur compound metabolic process 1 248 8.72e-01
GO:BP GO:0090150 establishment of protein localization to membrane 1 250 8.74e-01
GO:BP GO:0072001 renal system development 1 251 8.74e-01
GO:BP GO:0031349 positive regulation of defense response 1 251 8.74e-01
GO:BP GO:0006886 intracellular protein transport 4 803 8.75e-01
GO:BP GO:0032989 cellular component morphogenesis 3 639 8.80e-01
GO:BP GO:0006310 DNA recombination 1 257 8.80e-01
GO:BP GO:0051056 regulation of small GTPase mediated signal transduction 1 257 8.80e-01
GO:BP GO:0032870 cellular response to hormone stimulus 2 457 8.80e-01
GO:BP GO:0051604 protein maturation 1 259 8.81e-01
GO:BP GO:0051493 regulation of cytoskeleton organization 2 459 8.81e-01
GO:BP GO:0018209 peptidyl-serine modification 1 259 8.81e-01
GO:BP GO:0120031 plasma membrane bounded cell projection assembly 2 461 8.82e-01
GO:BP GO:0048667 cell morphogenesis involved in neuron differentiation 2 463 8.83e-01
GO:BP GO:0006508 proteolysis 7 1318 8.84e-01
GO:BP GO:0051054 positive regulation of DNA metabolic process 1 265 8.86e-01
GO:BP GO:0030031 cell projection assembly 2 469 8.87e-01
GO:BP GO:0055085 transmembrane transport 5 998 8.87e-01
GO:BP GO:0007600 sensory perception 1 269 8.88e-01
GO:BP GO:0032102 negative regulation of response to external stimulus 1 269 8.88e-01
GO:BP GO:0006302 double-strand break repair 1 271 8.90e-01
GO:BP GO:0052547 regulation of peptidase activity 1 271 8.90e-01
GO:BP GO:0098813 nuclear chromosome segregation 1 273 8.91e-01
GO:BP GO:0010948 negative regulation of cell cycle process 1 273 8.91e-01
GO:BP GO:0019221 cytokine-mediated signaling pathway 1 274 8.91e-01
GO:BP GO:0045787 positive regulation of cell cycle 1 274 8.91e-01
GO:BP GO:0050678 regulation of epithelial cell proliferation 1 276 8.92e-01
GO:BP GO:0001819 positive regulation of cytokine production 1 276 8.92e-01
GO:BP GO:0007517 muscle organ development 1 277 8.93e-01
GO:BP GO:0048878 chemical homeostasis 3 676 8.98e-01
GO:BP GO:0098916 anterograde trans-synaptic signaling 2 490 8.98e-01
GO:BP GO:0007268 chemical synaptic transmission 2 490 8.98e-01
GO:BP GO:0051649 establishment of localization in cell 10 1836 8.98e-01
GO:BP GO:0048193 Golgi vesicle transport 1 285 8.99e-01
GO:BP GO:0019752 carboxylic acid metabolic process 3 681 8.99e-01
GO:BP GO:0010256 endomembrane system organization 2 496 8.99e-01
GO:BP GO:1901653 cellular response to peptide 1 287 8.99e-01
GO:BP GO:1901564 organonitrogen compound metabolic process 31 4955 8.99e-01
GO:BP GO:0022607 cellular component assembly 14 2466 8.99e-01
GO:BP GO:0099537 trans-synaptic signaling 2 495 8.99e-01
GO:BP GO:0030029 actin filament-based process 3 687 9.01e-01
GO:BP GO:0007265 Ras protein signal transduction 1 294 9.03e-01
GO:BP GO:0090407 organophosphate biosynthetic process 2 506 9.05e-01
GO:BP GO:0043436 oxoacid metabolic process 3 696 9.05e-01
GO:BP GO:0044281 small molecule metabolic process 7 1389 9.07e-01
GO:BP GO:0099536 synaptic signaling 2 511 9.07e-01
GO:BP GO:0006082 organic acid metabolic process 3 700 9.07e-01
GO:BP GO:0006259 DNA metabolic process 4 884 9.08e-01
GO:BP GO:1901990 regulation of mitotic cell cycle phase transition 1 308 9.12e-01
GO:BP GO:0009617 response to bacterium 1 321 9.21e-01
GO:BP GO:0043434 response to peptide hormone 1 321 9.21e-01
GO:BP GO:0050673 epithelial cell proliferation 1 323 9.22e-01
GO:BP GO:0042692 muscle cell differentiation 1 324 9.22e-01
GO:BP GO:0061061 muscle structure development 2 546 9.25e-01
GO:BP GO:0000226 microtubule cytoskeleton organization 2 552 9.28e-01
GO:BP GO:0018205 peptidyl-lysine modification 1 336 9.29e-01
GO:BP GO:0008610 lipid biosynthetic process 2 560 9.31e-01
GO:BP GO:0000280 nuclear division 1 344 9.33e-01
GO:BP GO:0051301 cell division 2 570 9.35e-01
GO:BP GO:0071840 cellular component organization or biogenesis 32 5274 9.36e-01
GO:BP GO:0034330 cell junction organization 2 575 9.37e-01
GO:BP GO:0018193 peptidyl-amino acid modification 4 963 9.37e-01
GO:BP GO:0007409 axonogenesis 1 359 9.39e-01
GO:BP GO:0042592 homeostatic process 5 1159 9.42e-01
GO:BP GO:1901652 response to peptide 1 377 9.48e-01
GO:BP GO:0030036 actin cytoskeleton organization 2 612 9.50e-01
GO:BP GO:0048285 organelle fission 1 388 9.52e-01
GO:BP GO:1901987 regulation of cell cycle phase transition 1 391 9.52e-01
GO:BP GO:1901135 carbohydrate derivative metabolic process 3 843 9.57e-01
GO:BP GO:0009725 response to hormone 2 642 9.58e-01
GO:BP GO:0016192 vesicle-mediated transport 5 1238 9.60e-01
GO:BP GO:0097435 supramolecular fiber organization 2 665 9.64e-01
GO:BP GO:0032787 monocarboxylic acid metabolic process 1 433 9.65e-01
GO:BP GO:0007610 behavior 1 436 9.66e-01
GO:BP GO:0016043 cellular component organization 29 5076 9.68e-01
GO:BP GO:0001817 regulation of cytokine production 1 447 9.68e-01
GO:BP GO:0001816 cytokine production 1 451 9.69e-01
GO:BP GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway 1 484 9.76e-01
GO:BP GO:0051640 organelle localization 1 503 9.79e-01
GO:BP GO:0007017 microtubule-based process 2 760 9.80e-01
GO:BP GO:0006629 lipid metabolic process 3 994 9.81e-01
GO:BP GO:0019637 organophosphate metabolic process 2 784 9.82e-01
GO:BP GO:0007010 cytoskeleton organization 4 1226 9.83e-01
GO:BP GO:0070925 organelle assembly 2 817 9.85e-01
GO:BP GO:0044255 cellular lipid metabolic process 1 740 9.97e-01
GO:BP GO:0006996 organelle organization 11 3000 9.99e-01
KEGG KEGG:05168 Herpes simplex virus 1 infection 11 415 2.84e-02
KEGG KEGG:03260 Virion - Human immunodeficiency virus 1 1 4.85e-01
KEGG KEGG:04660 T cell receptor signaling pathway 2 70 6.29e-01
KEGG KEGG:05226 Gastric cancer 2 117 6.29e-01
KEGG KEGG:04668 TNF signaling pathway 2 87 6.29e-01
KEGG KEGG:03013 Nucleocytoplasmic transport 2 99 6.29e-01
KEGG KEGG:03040 Spliceosome 3 132 6.29e-01
KEGG KEGG:04658 Th1 and Th2 cell differentiation 1 53 6.29e-01
KEGG KEGG:03015 mRNA surveillance pathway 3 86 6.29e-01
KEGG KEGG:04659 Th17 cell differentiation 1 64 6.29e-01
KEGG KEGG:05225 Hepatocellular carcinoma 3 145 6.29e-01
KEGG KEGG:05224 Breast cancer 3 117 6.29e-01
KEGG KEGG:05231 Choline metabolism in cancer 1 84 6.29e-01
KEGG KEGG:01240 Biosynthesis of cofactors 2 115 6.29e-01
KEGG KEGG:03018 RNA degradation 1 74 6.29e-01
KEGG KEGG:04666 Fc gamma R-mediated phagocytosis 1 75 6.29e-01
KEGG KEGG:05235 PD-L1 expression and PD-1 checkpoint pathway in cancer 1 69 6.29e-01
KEGG KEGG:05321 Inflammatory bowel disease 1 22 6.29e-01
KEGG KEGG:03022 Basal transcription factors 1 40 6.29e-01
KEGG KEGG:04662 B cell receptor signaling pathway 1 56 6.29e-01
KEGG KEGG:05323 Rheumatoid arthritis 1 43 6.29e-01
KEGG KEGG:01522 Endocrine resistance 1 85 6.29e-01
KEGG KEGG:05221 Acute myeloid leukemia 1 56 6.29e-01
KEGG KEGG:03008 Ribosome biogenesis in eukaryotes 2 75 6.29e-01
KEGG KEGG:04750 Inflammatory mediator regulation of TRP channels 1 72 6.29e-01
KEGG KEGG:01230 Biosynthesis of amino acids 1 60 6.29e-01
KEGG KEGG:04310 Wnt signaling pathway 4 138 6.29e-01
KEGG KEGG:04934 Cushing syndrome 3 121 6.29e-01
KEGG KEGG:04932 Non-alcoholic fatty liver disease 2 131 6.29e-01
KEGG KEGG:04928 Parathyroid hormone synthesis, secretion and action 1 82 6.29e-01
KEGG KEGG:05142 Chagas disease 1 75 6.29e-01
KEGG KEGG:05161 Hepatitis B 2 136 6.29e-01
KEGG KEGG:05140 Leishmaniasis 1 42 6.29e-01
KEGG KEGG:04350 TGF-beta signaling pathway 1 84 6.29e-01
KEGG KEGG:04926 Relaxin signaling pathway 2 104 6.29e-01
KEGG KEGG:04925 Aldosterone synthesis and secretion 1 77 6.29e-01
KEGG KEGG:04924 Renin secretion 1 50 6.29e-01
KEGG KEGG:04922 Glucagon signaling pathway 1 84 6.29e-01
KEGG KEGG:04921 Oxytocin signaling pathway 2 115 6.29e-01
KEGG KEGG:04918 Thyroid hormone synthesis 1 55 6.29e-01
KEGG KEGG:04927 Cortisol synthesis and secretion 2 48 6.29e-01
KEGG KEGG:05163 Human cytomegalovirus infection 2 176 6.29e-01
KEGG KEGG:04971 Gastric acid secretion 1 52 6.29e-01
KEGG KEGG:04978 Mineral absorption 1 42 6.29e-01
KEGG KEGG:05132 Salmonella infection 2 214 6.29e-01
KEGG KEGG:04210 Apoptosis 2 118 6.29e-01
KEGG KEGG:05133 Pertussis 1 45 6.29e-01
KEGG KEGG:05131 Shigellosis 2 210 6.29e-01
KEGG KEGG:05130 Pathogenic Escherichia coli infection 2 150 6.29e-01
KEGG KEGG:04211 Longevity regulating pathway 1 78 6.29e-01
KEGG KEGG:05135 Yersinia infection 2 112 6.29e-01
KEGG KEGG:05120 Epithelial cell signaling in Helicobacter pylori infection 1 58 6.29e-01
KEGG KEGG:05030 Cocaine addiction 2 35 6.29e-01
KEGG KEGG:05017 Spinocerebellar ataxia 2 124 6.29e-01
KEGG KEGG:04144 Endocytosis 3 232 6.29e-01
KEGG KEGG:04141 Protein processing in endoplasmic reticulum 2 161 6.29e-01
KEGG KEGG:04137 Mitophagy - animal 2 70 6.29e-01
KEGG KEGG:05010 Alzheimer disease 3 315 6.29e-01
KEGG KEGG:05031 Amphetamine addiction 2 49 6.29e-01
KEGG KEGG:04360 Axon guidance 2 162 6.29e-01
KEGG KEGG:04380 Osteoclast differentiation 2 87 6.29e-01
KEGG KEGG:04916 Melanogenesis 1 77 6.29e-01
KEGG KEGG:05208 Chemical carcinogenesis - reactive oxygen species 2 186 6.29e-01
KEGG KEGG:05210 Colorectal cancer 1 84 6.29e-01
KEGG KEGG:04550 Signaling pathways regulating pluripotency of stem cells 2 104 6.29e-01
KEGG KEGG:00000 KEGG root term 47 5558 6.29e-01
KEGG KEGG:04620 Toll-like receptor signaling pathway 1 60 6.29e-01
KEGG KEGG:04625 C-type lectin receptor signaling pathway 1 76 6.29e-01
KEGG KEGG:05207 Chemical carcinogenesis - receptor activation 2 142 6.29e-01
KEGG KEGG:00270 Cysteine and methionine metabolism 1 38 6.29e-01
KEGG KEGG:05215 Prostate cancer 1 86 6.29e-01
KEGG KEGG:00510 N-Glycan biosynthesis 1 48 6.29e-01
KEGG KEGG:04657 IL-17 signaling pathway 1 56 6.29e-01
KEGG KEGG:00515 Mannose type O-glycan biosynthesis 1 19 6.29e-01
KEGG KEGG:00565 Ether lipid metabolism 1 28 6.29e-01
KEGG KEGG:00790 Folate biosynthesis 1 18 6.29e-01
KEGG KEGG:05211 Renal cell carcinoma 1 65 6.29e-01
KEGG KEGG:04392 Hippo signaling pathway - multiple species 1 25 6.29e-01
KEGG KEGG:05203 Viral carcinogenesis 3 172 6.29e-01
KEGG KEGG:05200 Pathways in cancer 6 409 6.29e-01
KEGG KEGG:04915 Estrogen signaling pathway 2 97 6.29e-01
KEGG KEGG:05166 Human T-cell leukemia virus 1 infection 3 180 6.29e-01
KEGG KEGG:04122 Sulfur relay system 1 8 6.29e-01
KEGG KEGG:04061 Viral protein interaction with cytokine and cytokine receptor 1 20 6.29e-01
KEGG KEGG:04390 Hippo signaling pathway 2 134 6.29e-01
KEGG KEGG:04060 Cytokine-cytokine receptor interaction 2 98 6.29e-01
KEGG KEGG:04912 GnRH signaling pathway 2 76 6.29e-01
KEGG KEGG:04911 Insulin secretion 1 64 6.29e-01
KEGG KEGG:04725 Cholinergic synapse 2 83 6.29e-01
KEGG KEGG:04722 Neurotrophin signaling pathway 2 110 6.29e-01
KEGG KEGG:04720 Long-term potentiation 1 55 6.29e-01
KEGG KEGG:04672 Intestinal immune network for IgA production 1 12 6.29e-01
KEGG KEGG:04012 ErbB signaling pathway 1 78 6.29e-01
KEGG KEGG:05170 Human immunodeficiency virus 1 infection 2 165 6.29e-01
KEGG KEGG:04670 Leukocyte transendothelial migration 1 79 6.29e-01
KEGG KEGG:05217 Basal cell carcinoma 1 49 6.29e-01
KEGG KEGG:03250 Viral life cycle - HIV-1 1 56 6.29e-01
KEGG KEGG:05418 Fluid shear stress and atherosclerosis 2 114 6.29e-01
KEGG KEGG:05417 Lipid and atherosclerosis 3 153 6.29e-01
KEGG KEGG:04933 AGE-RAGE signaling pathway in diabetic complications 1 91 6.48e-01
KEGG KEGG:05012 Parkinson disease 2 226 6.49e-01
KEGG KEGG:04931 Insulin resistance 1 95 6.55e-01
KEGG KEGG:04935 Growth hormone synthesis, secretion and action 1 98 6.56e-01
KEGG KEGG:05162 Measles 1 98 6.56e-01
KEGG KEGG:05164 Influenza A 1 103 6.59e-01
KEGG KEGG:04728 Dopaminergic synapse 1 103 6.59e-01
KEGG KEGG:04010 MAPK signaling pathway 2 240 6.59e-01
KEGG KEGG:05022 Pathways of neurodegeneration - multiple diseases 3 385 6.59e-01
KEGG KEGG:04072 Phospholipase D signaling pathway 1 110 6.76e-01
KEGG KEGG:04062 Chemokine signaling pathway 1 113 6.82e-01
KEGG KEGG:04621 NOD-like receptor signaling pathway 1 117 6.91e-01
KEGG KEGG:04910 Insulin signaling pathway 1 121 6.97e-01
KEGG KEGG:05034 Alcoholism 1 122 6.97e-01
KEGG KEGG:04261 Adrenergic signaling in cardiomyocytes 1 128 7.11e-01
KEGG KEGG:04150 mTOR signaling pathway 1 135 7.15e-01
KEGG KEGG:04022 cGMP-PKG signaling pathway 1 133 7.15e-01
KEGG KEGG:04120 Ubiquitin mediated proteolysis 1 134 7.15e-01
KEGG KEGG:04530 Tight junction 1 137 7.15e-01
KEGG KEGG:05014 Amyotrophic lateral sclerosis 2 303 7.27e-01
KEGG KEGG:05167 Kaposi sarcoma-associated herpesvirus infection 1 145 7.27e-01
KEGG KEGG:05169 Epstein-Barr virus infection 1 153 7.30e-01
KEGG KEGG:04024 cAMP signaling pathway 1 151 7.30e-01
KEGG KEGG:05206 MicroRNAs in cancer 1 149 7.30e-01
KEGG KEGG:04020 Calcium signaling pathway 1 157 7.35e-01
KEGG KEGG:05171 Coronavirus disease - COVID-19 1 162 7.41e-01
KEGG KEGG:05205 Proteoglycans in cancer 1 170 7.50e-01
KEGG KEGG:04014 Ras signaling pathway 1 171 7.50e-01
KEGG KEGG:04510 Focal adhesion 1 177 7.55e-01
KEGG KEGG:04810 Regulation of actin cytoskeleton 1 179 7.55e-01
KEGG KEGG:05020 Prion disease 1 220 8.21e-01
KEGG KEGG:04151 PI3K-Akt signaling pathway 1 254 8.60e-01
KEGG KEGG:05165 Human papillomavirus infection 1 272 8.73e-01
KEGG KEGG:01100 Metabolic pathways 5 1146 9.28e-01 
Dnr3_sp_DEGtable  %>% 
    dplyr::filter(source=="KEGG") %>% 
  # dplyr::filter(p_value<0.05) %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=2 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) %>%
  
    # slice_max(., n=10,order_by = p_value) %>%
   ggplot(., aes(x = log_val, y =reorder(term_name,p_value), col= intersection_size)) +
    geom_point(aes(size = intersection_size)) +
  geom_vline(xintercept = (-log10(0.05)))+
    scale_y_discrete(labels = wrap_format(30))+
  scale_linetype(3)+
    guides(col="none", size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('DNR 3 hour specific(stringent)\n gene set KEGG terms') +
    xlab(expression(" -"~log[10]~("adj. p-value")))+
    ylab("KEGG pathway")+
    theme_bw()+
    theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, color = "black", angle = 0),
        strip.text.x = element_text(size = 12, color = "black", face = "bold"))

Mtx3_sp_DEGtable  %>% 
    dplyr::filter(source=="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) %>%
   # slice_max(., n=10,order_by = p_value) %>%
   ggplot(., aes(x = log_val, y =reorder(term_name,p_value), col= intersection_size)) +
    geom_point(aes(size = intersection_size)) +
    scale_y_discrete(labels = wrap_format(30))+
  geom_vline(xintercept = (-log10(0.05)))+
    guides(col="none", size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('MTX 3 hour specific(stringent)\n gene set GO:BP terms') +
    xlab(expression(" -"~log[10]~("adj. p-value")))+
    ylab("GO: BP term")+
    theme_bw()+
    theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, color = "black", angle = 0),
        strip.text.x = element_text(size = 12, color = "black", face = "bold"))

Mtx3_sp_DEGtable  %>% 
  mutate_at(.vars = 6, .funs= scientific_format()) %>%
  kable(., caption= "Stringent (adj. P value of <0.01) MTX 3 hour specific genes (n = 4)  enriched GO  and KEGG terms") %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped","hover")) %>% 
  scroll_box(width = "100%", height = "400px")
Stringent (adj. P value of <0.01) MTX 3 hour specific genes (n = 4) enriched GO and KEGG terms
source term_id term_name intersection_size term_size p_value
GO:BP GO:0006367 transcription initiation at RNA polymerase II promoter 2 93 2.93e-02
GO:BP GO:0060260 regulation of transcription initiation by RNA polymerase II 2 69 2.93e-02
GO:BP GO:2000142 regulation of DNA-templated transcription initiation 2 76 2.93e-02
GO:BP GO:0006352 DNA-templated transcription initiation 2 130 4.29e-02
GO:BP GO:0070427 nucleotide-binding oligomerization domain containing 1 signaling pathway 1 5 7.82e-02
GO:BP GO:0006470 protein dephosphorylation 2 214 7.82e-02
GO:BP GO:0016311 dephosphorylation 2 284 8.60e-02
GO:BP GO:0009617 response to bacterium 2 321 8.60e-02
GO:BP GO:0070417 cellular response to cold 1 8 8.60e-02
GO:BP GO:0010745 negative regulation of macrophage derived foam cell differentiation 1 10 8.60e-02
GO:BP GO:0070431 nucleotide-binding oligomerization domain containing 2 signaling pathway 1 11 8.60e-02
GO:BP GO:0007253 cytoplasmic sequestering of NF-kappaB 1 7 8.60e-02
GO:BP GO:0032495 response to muramyl dipeptide 1 15 8.81e-02
GO:BP GO:0045746 negative regulation of Notch signaling pathway 1 31 8.81e-02
GO:BP GO:0043330 response to exogenous dsRNA 1 27 8.81e-02
GO:BP GO:0032373 positive regulation of sterol transport 1 30 8.81e-02
GO:BP GO:0042994 cytoplasmic sequestering of transcription factor 1 15 8.81e-02
GO:BP GO:0035970 peptidyl-threonine dephosphorylation 1 17 8.81e-02
GO:BP GO:0035872 nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway 1 19 8.81e-02
GO:BP GO:0034142 toll-like receptor 4 signaling pathway 1 24 8.81e-02
GO:BP GO:0010742 macrophage derived foam cell differentiation 1 22 8.81e-02
GO:BP GO:0010743 regulation of macrophage derived foam cell differentiation 1 18 8.81e-02
GO:BP GO:0032376 positive regulation of cholesterol transport 1 30 8.81e-02
GO:BP GO:0050853 B cell receptor signaling pathway 1 32 8.81e-02
GO:BP GO:0010888 negative regulation of lipid storage 1 16 8.81e-02
GO:BP GO:0010875 positive regulation of cholesterol efflux 1 23 8.81e-02
GO:BP GO:0035994 response to muscle stretch 1 26 8.81e-02
GO:BP GO:0010874 regulation of cholesterol efflux 1 31 8.81e-02
GO:BP GO:0051220 cytoplasmic sequestering of protein 1 23 8.81e-02
GO:BP GO:0140895 cell surface toll-like receptor signaling pathway 1 27 8.81e-02
GO:BP GO:0002752 cell surface pattern recognition receptor signaling pathway 1 27 8.81e-02
GO:BP GO:0070423 nucleotide-binding oligomerization domain containing signaling pathway 1 18 8.81e-02
GO:BP GO:0090077 foam cell differentiation 1 22 8.81e-02
GO:BP GO:1905953 negative regulation of lipid localization 1 32 8.81e-02
GO:BP GO:0043331 response to dsRNA 1 33 8.82e-02
GO:BP GO:0006357 regulation of transcription by RNA polymerase II 3 1914 8.85e-02
GO:BP GO:0031663 lipopolysaccharide-mediated signaling pathway 1 36 9.10e-02
GO:BP GO:0002220 innate immune response activating cell surface receptor signaling pathway 1 37 9.11e-02
GO:BP GO:0006366 transcription by RNA polymerase II 3 1995 9.12e-02
GO:BP GO:0010883 regulation of lipid storage 1 39 9.12e-02
GO:BP GO:0033344 cholesterol efflux 1 40 9.12e-02
GO:BP GO:0009409 response to cold 1 41 9.13e-02
GO:BP GO:0006306 DNA methylation 1 46 9.15e-02
GO:BP GO:0032374 regulation of cholesterol transport 1 45 9.15e-02
GO:BP GO:0006305 DNA alkylation 1 46 9.15e-02
GO:BP GO:0043392 negative regulation of DNA binding 1 46 9.15e-02
GO:BP GO:0032371 regulation of sterol transport 1 45 9.15e-02
GO:BP GO:0032370 positive regulation of lipid transport 1 58 1.07e-01
GO:BP GO:0032088 negative regulation of NF-kappaB transcription factor activity 1 66 1.07e-01
GO:BP GO:0031507 heterochromatin formation 1 69 1.07e-01
GO:BP GO:0030330 DNA damage response, signal transduction by p53 class mediator 1 69 1.07e-01
GO:BP GO:0050729 positive regulation of inflammatory response 1 75 1.07e-01
GO:BP GO:1905954 positive regulation of lipid localization 1 75 1.07e-01
GO:BP GO:2000144 positive regulation of DNA-templated transcription initiation 1 65 1.07e-01
GO:BP GO:0051707 response to other organism 2 820 1.07e-01
GO:BP GO:1903506 regulation of nucleic acid-templated transcription 3 2576 1.07e-01
GO:BP GO:0033209 tumor necrosis factor-mediated signaling pathway 1 76 1.07e-01
GO:BP GO:1901222 regulation of NIK/NF-kappaB signaling 1 65 1.07e-01
GO:BP GO:0070828 heterochromatin organization 1 77 1.07e-01
GO:BP GO:0045638 negative regulation of myeloid cell differentiation 1 69 1.07e-01
GO:BP GO:0060261 positive regulation of transcription initiation by RNA polymerase II 1 59 1.07e-01
GO:BP GO:0045814 negative regulation of gene expression, epigenetic 1 79 1.07e-01
GO:BP GO:0030301 cholesterol transport 1 80 1.07e-01
GO:BP GO:0019915 lipid storage 1 66 1.07e-01
GO:BP GO:0043207 response to external biotic stimulus 2 820 1.07e-01
GO:BP GO:0008593 regulation of Notch signaling pathway 1 78 1.07e-01
GO:BP GO:0009607 response to biotic stimulus 2 850 1.07e-01
GO:BP GO:0009628 response to abiotic stimulus 2 868 1.07e-01
GO:BP GO:0006355 regulation of DNA-templated transcription 3 2574 1.07e-01
GO:BP GO:0002753 cytosolic pattern recognition receptor signaling pathway 1 68 1.07e-01
GO:BP GO:2001141 regulation of RNA biosynthetic process 3 2593 1.07e-01
GO:BP GO:0045185 maintenance of protein location 1 83 1.07e-01
GO:BP GO:0006304 DNA modification 1 89 1.09e-01
GO:BP GO:0097659 nucleic acid-templated transcription 3 2684 1.09e-01
GO:BP GO:0015918 sterol transport 1 92 1.09e-01
GO:BP GO:0032774 RNA biosynthetic process 3 2714 1.09e-01
GO:BP GO:0038061 NIK/NF-kappaB signaling 1 86 1.09e-01
GO:BP GO:0032368 regulation of lipid transport 1 92 1.09e-01
GO:BP GO:0044419 biological process involved in interspecies interaction between organisms 2 963 1.09e-01
GO:BP GO:0006351 DNA-templated transcription 3 2683 1.09e-01
GO:BP GO:0051101 regulation of DNA binding 1 104 1.19e-01
GO:BP GO:0051252 regulation of RNA metabolic process 3 2845 1.19e-01
GO:BP GO:0050851 antigen receptor-mediated signaling pathway 1 106 1.19e-01
GO:BP GO:0071222 cellular response to lipopolysaccharide 1 110 1.22e-01
GO:BP GO:1905952 regulation of lipid localization 1 112 1.22e-01
GO:BP GO:0071219 cellular response to molecule of bacterial origin 1 114 1.23e-01
GO:BP GO:0002221 pattern recognition receptor signaling pathway 1 115 1.23e-01
GO:BP GO:0044839 cell cycle G2/M phase transition 1 149 1.28e-01
GO:BP GO:0043433 negative regulation of DNA-binding transcription factor activity 1 138 1.28e-01
GO:BP GO:0010556 regulation of macromolecule biosynthetic process 3 3012 1.28e-01
GO:BP GO:0045637 regulation of myeloid cell differentiation 1 152 1.28e-01
GO:BP GO:0042127 regulation of cell population proliferation 2 1147 1.28e-01
GO:BP GO:0040029 epigenetic regulation of gene expression 1 153 1.28e-01
GO:BP GO:0019438 aromatic compound biosynthetic process 3 3133 1.28e-01
GO:BP GO:0009267 cellular response to starvation 1 152 1.28e-01
GO:BP GO:0051170 import into nucleus 1 152 1.28e-01
GO:BP GO:0009889 regulation of biosynthetic process 3 3169 1.28e-01
GO:BP GO:0071216 cellular response to biotic stimulus 1 138 1.28e-01
GO:BP GO:0009266 response to temperature stimulus 1 133 1.28e-01
GO:BP GO:1901362 organic cyclic compound biosynthetic process 3 3237 1.28e-01
GO:BP GO:0007219 Notch signaling pathway 1 146 1.28e-01
GO:BP GO:0006606 protein import into nucleus 1 147 1.28e-01
GO:BP GO:0002758 innate immune response-activating signaling pathway 1 122 1.28e-01
GO:BP GO:0002429 immune response-activating cell surface receptor signaling pathway 1 151 1.28e-01
GO:BP GO:0002218 activation of innate immune response 1 142 1.28e-01
GO:BP GO:0051100 negative regulation of binding 1 135 1.28e-01
GO:BP GO:0034654 nucleobase-containing compound biosynthetic process 3 3070 1.28e-01
GO:BP GO:0000086 G2/M transition of mitotic cell cycle 1 134 1.28e-01
GO:BP GO:0018130 heterocycle biosynthetic process 3 3132 1.28e-01
GO:BP GO:0031326 regulation of cellular biosynthetic process 3 3080 1.28e-01
GO:BP GO:0019219 regulation of nucleobase-containing compound metabolic process 3 3080 1.28e-01
GO:BP GO:0071356 cellular response to tumor necrosis factor 1 155 1.28e-01
GO:BP GO:0009612 response to mechanical stimulus 1 158 1.29e-01
GO:BP GO:0072331 signal transduction by p53 class mediator 1 161 1.30e-01
GO:BP GO:0002768 immune response-regulating cell surface receptor signaling pathway 1 162 1.30e-01
GO:BP GO:0032496 response to lipopolysaccharide 1 178 1.37e-01
GO:BP GO:0042594 response to starvation 1 178 1.37e-01
GO:BP GO:0042770 signal transduction in response to DNA damage 1 178 1.37e-01
GO:BP GO:0034612 response to tumor necrosis factor 1 172 1.37e-01
GO:BP GO:0015850 organic hydroxy compound transport 1 174 1.37e-01
GO:BP GO:0045089 positive regulation of innate immune response 1 182 1.38e-01
GO:BP GO:0002237 response to molecule of bacterial origin 1 187 1.40e-01
GO:BP GO:0008283 cell population proliferation 2 1378 1.40e-01
GO:BP GO:0002833 positive regulation of response to biotic stimulus 1 192 1.42e-01
GO:BP GO:0031669 cellular response to nutrient levels 1 194 1.43e-01
GO:BP GO:0010468 regulation of gene expression 3 3580 1.49e-01
GO:BP GO:0016070 RNA metabolic process 3 3600 1.50e-01
GO:BP GO:0050727 regulation of inflammatory response 1 212 1.52e-01
GO:BP GO:0031668 cellular response to extracellular stimulus 1 219 1.56e-01
GO:BP GO:0044271 cellular nitrogen compound biosynthetic process 3 3750 1.56e-01
GO:BP GO:0009059 macromolecule biosynthetic process 3 3730 1.56e-01
GO:BP GO:0045088 regulation of innate immune response 1 232 1.56e-01
GO:BP GO:0030522 intracellular receptor signaling pathway 1 227 1.56e-01
GO:BP GO:0007249 I-kappaB kinase/NF-kappaB signaling 1 227 1.56e-01
GO:BP GO:0007049 cell cycle 2 1529 1.56e-01
GO:BP GO:0002757 immune response-activating signaling pathway 1 230 1.56e-01
GO:BP GO:0002764 immune response-regulating signaling pathway 1 242 1.62e-01
GO:BP GO:0044237 cellular metabolic process 4 6996 1.62e-01
GO:BP GO:0031349 positive regulation of defense response 1 251 1.65e-01
GO:BP GO:0043170 macromolecule metabolic process 4 7069 1.67e-01
GO:BP GO:0051235 maintenance of location 1 260 1.68e-01
GO:BP GO:0006869 lipid transport 1 272 1.70e-01
GO:BP GO:0033554 cellular response to stress 2 1681 1.70e-01
GO:BP GO:0071496 cellular response to external stimulus 1 270 1.70e-01
GO:BP GO:0002253 activation of immune response 1 272 1.70e-01
GO:BP GO:0043414 macromolecule methylation 1 272 1.70e-01
GO:BP GO:0019221 cytokine-mediated signaling pathway 1 274 1.70e-01
GO:BP GO:0034504 protein localization to nucleus 1 276 1.70e-01
GO:BP GO:1903706 regulation of hemopoiesis 1 279 1.71e-01
GO:BP GO:0009605 response to external stimulus 2 1719 1.71e-01
GO:BP GO:0090304 nucleic acid metabolic process 3 4048 1.74e-01
GO:BP GO:0006913 nucleocytoplasmic transport 1 295 1.74e-01
GO:BP GO:0051169 nuclear transport 1 295 1.74e-01
GO:BP GO:0002831 regulation of response to biotic stimulus 1 293 1.74e-01
GO:BP GO:0010876 lipid localization 1 310 1.80e-01
GO:BP GO:0032259 methylation 1 313 1.80e-01
GO:BP GO:0051098 regulation of binding 1 317 1.80e-01
GO:BP GO:0030099 myeloid cell differentiation 1 310 1.80e-01
GO:BP GO:0006807 nitrogen compound metabolic process 4 7441 1.80e-01
GO:BP GO:0031323 regulation of cellular metabolic process 3 4174 1.80e-01
GO:BP GO:0019538 protein metabolic process 3 4241 1.84e-01
GO:BP GO:0044249 cellular biosynthetic process 3 4245 1.84e-01
GO:BP GO:0032103 positive regulation of response to external stimulus 1 337 1.85e-01
GO:BP GO:0051090 regulation of DNA-binding transcription factor activity 1 335 1.85e-01
GO:BP GO:0050794 regulation of cellular process 4 7552 1.85e-01
GO:BP GO:0051171 regulation of nitrogen compound metabolic process 3 4292 1.85e-01
GO:BP GO:0009314 response to radiation 1 352 1.90e-01
GO:BP GO:0031667 response to nutrient levels 1 353 1.90e-01
GO:BP GO:1901652 response to peptide 1 377 1.96e-01
GO:BP GO:0006338 chromatin remodeling 1 378 1.96e-01
GO:BP GO:0006139 nucleobase-containing compound metabolic process 3 4455 1.96e-01
GO:BP GO:0009991 response to extracellular stimulus 1 377 1.96e-01
GO:BP GO:0080090 regulation of primary metabolic process 3 4417 1.96e-01
GO:BP GO:0050778 positive regulation of immune response 1 369 1.96e-01
GO:BP GO:0044238 primary metabolic process 4 7806 1.99e-01
GO:BP GO:1901576 organic substance biosynthetic process 3 4539 2.01e-01
GO:BP GO:0071396 cellular response to lipid 1 398 2.01e-01
GO:BP GO:0035556 intracellular signal transduction 2 2065 2.01e-01
GO:BP GO:0030335 positive regulation of cell migration 1 407 2.01e-01
GO:BP GO:0006725 cellular aromatic compound metabolic process 3 4596 2.01e-01
GO:BP GO:0046483 heterocycle metabolic process 3 4570 2.01e-01
GO:BP GO:0010467 gene expression 3 4587 2.01e-01
GO:BP GO:0009058 biosynthetic process 3 4590 2.01e-01
GO:BP GO:0060255 regulation of macromolecule metabolic process 3 4617 2.02e-01
GO:BP GO:0006954 inflammatory response 1 429 2.02e-01
GO:BP GO:0006796 phosphate-containing compound metabolic process 2 2139 2.02e-01
GO:BP GO:0072594 establishment of protein localization to organelle 1 422 2.02e-01
GO:BP GO:0040017 positive regulation of locomotion 1 429 2.02e-01
GO:BP GO:2000147 positive regulation of cell motility 1 421 2.02e-01
GO:BP GO:0044772 mitotic cell cycle phase transition 1 418 2.02e-01
GO:BP GO:0006793 phosphorus metabolic process 2 2161 2.03e-01
GO:BP GO:0050789 regulation of biological process 4 8061 2.06e-01
GO:BP GO:0031347 regulation of defense response 1 448 2.07e-01
GO:BP GO:1901360 organic cyclic compound metabolic process 3 4747 2.07e-01
GO:BP GO:0071704 organic substance metabolic process 4 8169 2.14e-01
GO:BP GO:0045596 negative regulation of cell differentiation 1 482 2.19e-01
GO:BP GO:0050776 regulation of immune response 1 484 2.19e-01
GO:BP GO:0045087 innate immune response 1 488 2.19e-01
GO:BP GO:1901564 organonitrogen compound metabolic process 3 4955 2.23e-01
GO:BP GO:0044770 cell cycle phase transition 1 504 2.23e-01
GO:BP GO:0034641 cellular nitrogen compound metabolic process 3 4946 2.23e-01
GO:BP GO:0065007 biological regulation 4 8320 2.23e-01
GO:BP GO:0008285 negative regulation of cell population proliferation 1 513 2.24e-01
GO:BP GO:0019222 regulation of metabolic process 3 5017 2.28e-01
GO:BP GO:0071345 cellular response to cytokine stimulus 1 540 2.33e-01
GO:BP GO:0006325 chromatin organization 1 551 2.36e-01
GO:BP GO:0008152 metabolic process 4 8518 2.38e-01
GO:BP GO:0002684 positive regulation of immune system process 1 581 2.46e-01
GO:BP GO:0033993 response to lipid 1 592 2.49e-01
GO:BP GO:0098542 defense response to other organism 1 608 2.52e-01
GO:BP GO:0060284 regulation of cell development 1 605 2.52e-01
GO:BP GO:0034097 response to cytokine 1 607 2.52e-01
GO:BP GO:0014070 response to organic cyclic compound 1 640 2.63e-01
GO:BP GO:0030097 hemopoiesis 1 656 2.68e-01
GO:BP GO:0051050 positive regulation of transport 1 667 2.68e-01
GO:BP GO:0051093 negative regulation of developmental process 1 665 2.68e-01
GO:BP GO:0032101 regulation of response to external stimulus 1 662 2.68e-01
GO:BP GO:0006950 response to stress 2 2780 2.75e-01
GO:BP GO:1903047 mitotic cell cycle process 1 694 2.76e-01
GO:BP GO:0030334 regulation of cell migration 1 706 2.79e-01
GO:BP GO:2000145 regulation of cell motility 1 742 2.90e-01
GO:BP GO:0036211 protein modification process 2 2901 2.90e-01
GO:BP GO:0044092 negative regulation of molecular function 1 755 2.92e-01
GO:BP GO:0040012 regulation of locomotion 1 763 2.94e-01
GO:BP GO:0010243 response to organonitrogen compound 1 782 2.98e-01
GO:BP GO:0010629 negative regulation of gene expression 1 785 2.98e-01
GO:BP GO:0006974 DNA damage response 1 785 2.98e-01
GO:BP GO:0006886 intracellular protein transport 1 803 3.03e-01
GO:BP GO:1901698 response to nitrogen compound 1 830 3.09e-01
GO:BP GO:0000278 mitotic cell cycle 1 827 3.09e-01
GO:BP GO:0043412 macromolecule modification 2 3090 3.10e-01
GO:BP GO:0033365 protein localization to organelle 1 859 3.16e-01
GO:BP GO:0002682 regulation of immune system process 1 877 3.20e-01
GO:BP GO:0006259 DNA metabolic process 1 884 3.20e-01
GO:BP GO:0006955 immune response 1 882 3.20e-01
GO:BP GO:1901701 cellular response to oxygen-containing compound 1 893 3.22e-01
GO:BP GO:0045944 positive regulation of transcription by RNA polymerase II 1 937 3.35e-01
GO:BP GO:0006952 defense response 1 944 3.35e-01
GO:BP GO:0040011 locomotion 1 954 3.37e-01
GO:BP GO:0009968 negative regulation of signal transduction 1 1006 3.52e-01
GO:BP GO:2000026 regulation of multicellular organismal development 1 1014 3.53e-01
GO:BP GO:0010648 negative regulation of cell communication 1 1074 3.68e-01
GO:BP GO:0080134 regulation of response to stress 1 1075 3.68e-01
GO:BP GO:0023057 negative regulation of signaling 1 1076 3.68e-01
GO:BP GO:0022402 cell cycle process 1 1086 3.68e-01
GO:BP GO:0016477 cell migration 1 1081 3.68e-01
GO:BP GO:0048523 negative regulation of cellular process 2 3625 3.75e-01
GO:BP GO:0051247 positive regulation of protein metabolic process 1 1123 3.75e-01
GO:BP GO:0045595 regulation of cell differentiation 1 1137 3.78e-01
GO:BP GO:0048870 cell motility 1 1182 3.89e-01
GO:BP GO:1901700 response to oxygen-containing compound 1 1223 3.99e-01
GO:BP GO:0007165 signal transduction 2 3818 3.99e-01
GO:BP GO:0048585 negative regulation of response to stimulus 1 1248 4.03e-01
GO:BP GO:0051049 regulation of transport 1 1267 4.07e-01
GO:BP GO:0045893 positive regulation of DNA-templated transcription 1 1315 4.17e-01
GO:BP GO:1903508 positive regulation of nucleic acid-templated transcription 1 1315 4.17e-01
GO:BP GO:1902680 positive regulation of RNA biosynthetic process 1 1322 4.17e-01
GO:BP GO:1902531 regulation of intracellular signal transduction 1 1345 4.22e-01
GO:BP GO:0048519 negative regulation of biological process 2 4045 4.23e-01
GO:BP GO:0015031 protein transport 1 1361 4.23e-01
GO:BP GO:0048522 positive regulation of cellular process 2 4099 4.29e-01
GO:BP GO:0071310 cellular response to organic substance 1 1399 4.29e-01
GO:BP GO:0023052 signaling 2 4141 4.33e-01
GO:BP GO:0051254 positive regulation of RNA metabolic process 1 1441 4.35e-01
GO:BP GO:0006915 apoptotic process 1 1443 4.35e-01
GO:BP GO:0046907 intracellular transport 1 1453 4.35e-01
GO:BP GO:0002376 immune system process 1 1447 4.35e-01
GO:BP GO:0045184 establishment of protein localization 1 1462 4.35e-01
GO:BP GO:0007154 cell communication 2 4226 4.36e-01
GO:BP GO:0012501 programmed cell death 1 1479 4.36e-01
GO:BP GO:0010557 positive regulation of macromolecule biosynthetic process 1 1507 4.42e-01
GO:BP GO:0032879 regulation of localization 1 1555 4.50e-01
GO:BP GO:0048584 positive regulation of response to stimulus 1 1555 4.50e-01
GO:BP GO:0031328 positive regulation of cellular biosynthetic process 1 1564 4.50e-01
GO:BP GO:0045935 positive regulation of nucleobase-containing compound metabolic process 1 1602 4.55e-01
GO:BP GO:0008219 cell death 1 1596 4.55e-01
GO:BP GO:0009891 positive regulation of biosynthetic process 1 1604 4.55e-01
GO:BP GO:0071705 nitrogen compound transport 1 1684 4.72e-01
GO:BP GO:0048518 positive regulation of biological process 2 4579 4.73e-01
GO:BP GO:0050793 regulation of developmental process 1 1835 5.00e-01
GO:BP GO:0051649 establishment of localization in cell 1 1836 5.00e-01
GO:BP GO:0070887 cellular response to chemical stimulus 1 1869 5.05e-01
GO:BP GO:0007166 cell surface receptor signaling pathway 1 1898 5.10e-01
GO:BP GO:0065009 regulation of molecular function 1 1939 5.16e-01
GO:BP GO:0048468 cell development 1 1963 5.16e-01
GO:BP GO:0010033 response to organic substance 1 1957 5.16e-01
GO:BP GO:0051716 cellular response to stimulus 2 4953 5.16e-01
GO:BP GO:0051246 regulation of protein metabolic process 1 1974 5.17e-01
GO:BP GO:0051239 regulation of multicellular organismal process 1 2035 5.27e-01
GO:BP GO:0009987 cellular process 4 11336 5.33e-01
GO:BP GO:0070727 cellular macromolecule localization 1 2138 5.38e-01
GO:BP GO:0008104 protein localization 1 2129 5.38e-01
GO:BP GO:0010605 negative regulation of macromolecule metabolic process 1 2135 5.38e-01
GO:BP GO:0071702 organic substance transport 1 2116 5.38e-01
GO:BP GO:0031325 positive regulation of cellular metabolic process 1 2270 5.61e-01
GO:BP GO:0009892 negative regulation of metabolic process 1 2293 5.61e-01
GO:BP GO:0009966 regulation of signal transduction 1 2285 5.61e-01
GO:BP GO:0051173 positive regulation of nitrogen compound metabolic process 1 2412 5.81e-01
GO:BP GO:0033036 macromolecule localization 1 2450 5.85e-01
GO:BP GO:0042221 response to chemical 1 2559 5.98e-01
GO:BP GO:0023051 regulation of signaling 1 2565 5.98e-01
GO:BP GO:0050896 response to stimulus 2 5770 5.98e-01
GO:BP GO:0010646 regulation of cell communication 1 2573 5.98e-01
GO:BP GO:0010604 positive regulation of macromolecule metabolic process 1 2646 6.08e-01
GO:BP GO:0051641 cellular localization 1 2810 6.32e-01
GO:BP GO:0009893 positive regulation of metabolic process 1 2880 6.40e-01
GO:BP GO:0048583 regulation of response to stimulus 1 2890 6.40e-01
GO:BP GO:0008150 biological_process 4 12070 6.45e-01
GO:BP GO:0030154 cell differentiation 1 2958 6.46e-01
GO:BP GO:0048869 cellular developmental process 1 2984 6.47e-01
GO:BP GO:0006810 transport 1 3298 6.88e-01
GO:BP GO:0007275 multicellular organism development 1 3386 6.98e-01
GO:BP GO:0051234 establishment of localization 1 3433 7.01e-01
GO:BP GO:0051179 localization 1 3969 7.61e-01
GO:BP GO:0048856 anatomical structure development 1 4128 7.75e-01
GO:BP GO:0032502 developmental process 1 4494 8.07e-01
GO:BP GO:0032501 multicellular organismal process 1 4794 8.30e-01
GO:BP GO:0016043 cellular component organization 1 5076 8.49e-01
GO:BP GO:0071840 cellular component organization or biogenesis 1 5274 8.60e-01
KEGG KEGG:04625 C-type lectin receptor signaling pathway 1 76 5.00e-02
KEGG KEGG:05135 Yersinia infection 1 112 5.00e-02
KEGG KEGG:05134 Legionellosis 1 39 5.00e-02
KEGG KEGG:04657 IL-17 signaling pathway 1 56 5.00e-02
KEGG KEGG:04658 Th1 and Th2 cell differentiation 1 53 5.00e-02
KEGG KEGG:04659 Th17 cell differentiation 1 64 5.00e-02
KEGG KEGG:04062 Chemokine signaling pathway 1 113 5.00e-02
KEGG KEGG:04623 Cytosolic DNA-sensing pathway 1 42 5.00e-02
KEGG KEGG:04662 B cell receptor signaling pathway 1 56 5.00e-02
KEGG KEGG:04668 TNF signaling pathway 1 87 5.00e-02
KEGG KEGG:05120 Epithelial cell signaling in Helicobacter pylori infection 1 58 5.00e-02
KEGG KEGG:04936 Alcoholic liver disease 1 97 5.00e-02
KEGG KEGG:04931 Insulin resistance 1 95 5.00e-02
KEGG KEGG:04926 Relaxin signaling pathway 1 104 5.00e-02
KEGG KEGG:04660 T cell receptor signaling pathway 1 70 5.00e-02
KEGG KEGG:05140 Leishmaniasis 1 42 5.00e-02
KEGG KEGG:05145 Toxoplasmosis 1 82 5.00e-02
KEGG KEGG:04920 Adipocytokine signaling pathway 1 51 5.00e-02
KEGG KEGG:05222 Small cell lung cancer 1 87 5.00e-02
KEGG KEGG:05220 Chronic myeloid leukemia 1 75 5.00e-02
KEGG KEGG:05235 PD-L1 expression and PD-1 checkpoint pathway in cancer 1 69 5.00e-02
KEGG KEGG:05215 Prostate cancer 1 86 5.00e-02
KEGG KEGG:04064 NF-kappa B signaling pathway 1 71 5.00e-02
KEGG KEGG:04115 p53 signaling pathway 1 65 5.00e-02
KEGG KEGG:05142 Chagas disease 1 75 5.00e-02
KEGG KEGG:05168 Herpes simplex virus 1 infection 2 415 5.00e-02
KEGG KEGG:04380 Osteoclast differentiation 1 87 5.00e-02
KEGG KEGG:04620 Toll-like receptor signaling pathway 1 60 5.00e-02
KEGG KEGG:05164 Influenza A 1 103 5.00e-02
KEGG KEGG:04621 NOD-like receptor signaling pathway 1 117 5.00e-02
KEGG KEGG:05162 Measles 1 98 5.00e-02
KEGG KEGG:04622 RIG-I-like receptor signaling pathway 1 49 5.00e-02
KEGG KEGG:05160 Hepatitis C 1 115 5.00e-02
KEGG KEGG:04210 Apoptosis 1 118 5.00e-02
KEGG KEGG:04722 Neurotrophin signaling pathway 1 110 5.00e-02
KEGG KEGG:04024 cAMP signaling pathway 1 151 5.51e-02
KEGG KEGG:05417 Lipid and atherosclerosis 1 153 5.51e-02
KEGG KEGG:05130 Pathogenic Escherichia coli infection 1 150 5.51e-02
KEGG KEGG:05161 Hepatitis B 1 136 5.51e-02
KEGG KEGG:05167 Kaposi sarcoma-associated herpesvirus infection 1 145 5.51e-02
KEGG KEGG:05169 Epstein-Barr virus infection 1 153 5.51e-02
KEGG KEGG:05171 Coronavirus disease - COVID-19 1 162 5.66e-02
KEGG KEGG:05170 Human immunodeficiency virus 1 infection 1 165 5.66e-02
KEGG KEGG:05203 Viral carcinogenesis 1 172 5.76e-02
KEGG KEGG:05163 Human cytomegalovirus infection 1 176 5.76e-02
KEGG KEGG:05166 Human T-cell leukemia virus 1 infection 1 180 5.76e-02
KEGG KEGG:05208 Chemical carcinogenesis - reactive oxygen species 1 186 5.82e-02
KEGG KEGG:05131 Shigellosis 1 210 6.41e-02
KEGG KEGG:05132 Salmonella infection 1 214 6.41e-02
KEGG KEGG:05200 Pathways in cancer 1 409 1.17e-01
KEGG KEGG:00000 KEGG root term 3 5558 1.90e-01 
Mtx3_sp_DEGtable  %>% 
    dplyr::filter(source=="KEGG") %>% 
  # dplyr::filter(p_value<0.05) %>%
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) %>%
  
    # slice_max(., n=10,order_by = p_value) %>%
   ggplot(., aes(x = log_val, y =reorder(term_name,p_value), col= intersection_size)) +
    geom_point(aes(size = intersection_size)) +
  geom_vline(xintercept = (-log10(0.05)))+
    scale_y_discrete(labels = wrap_format(30))+
      guides(col="none", size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('MTX 3 hour specific(stringent)\n gene set KEGG terms') +
    xlab(expression(" -"~log[10]~("adj. p-value")))+
    ylab("KEGG pathway")+
    theme_bw()+
    theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, color = "black", angle = 0),
        strip.text.x = element_text(size = 12, color = "black", face = "bold"))

toplist3hr <- toplistall %>% 
  mutate(id =case_match(id, "Da"~"DNR",
                            "Do"~"DOX",
                            "Ep"~"EPI",
                            "Mi"~"MTX",
                            "Tr"~"TRZ",
                            "Ve"~"VEH", .default = id)) %>% 
      mutate(id=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  filter(time=="3_hours")
  

densityDOX3sp <-
  toplist3hr %>% 
  filter(ENTREZID %in% Dox3onlyDEG) %>% 
    # filter(adj.P.Val<0.5) %>% 
  ggplot(., aes(x=adj.P.Val))+
   geom_density(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()+
  ylab("DOX\n n = 0")+
  guides(fill=FALSE,alpha=FALSE)+
  theme(
      axis.title = element_text(size = 14, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
    

densityDNR3sp <-
  toplist3hr %>% 
  filter(ENTREZID %in% Dnr3onlyDEG) %>% 
    # filter(adj.P.Val<0.5) %>% 
  ggplot(., aes(x=adj.P.Val))+
   geom_density(aes(fill=id, alpha= 0.8))+
  # geom_histogram(aes(y = ..density.., fill = id, alpha = 0.8), bins = 120)+
  fill_palette(palette = drug_palc)+
  theme_bw()+
  ylab("DNR-only 3 hour DEGs\n n = 322")+
  guides(fill=FALSE,alpha=FALSE)+
  theme(
      axis.title = element_text(size = 14, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
    

densityEPI3sp <-
 
  toplist3hr %>% 
  filter(ENTREZID %in% Epi3onlyDEG) %>% 
    # filter(adj.P.Val<0.5) %>% 
  ggplot(., aes(x=adj.P.Val))+
   geom_density(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()+
  ylab("EPI-only DEGs\n n = 18")+
  ylim(0,50)+
  guides(fill=FALSE,alpha=FALSE)+
  theme(axis.title = element_text(size = 14, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
    


densityMTX3sp <-
  toplist3hr %>% 
  filter(ENTREZID %in% Mtx3onlyDEG) %>% 
    # filter(adj.P.Val<0.5) %>% 
  ggplot(., aes(x=adj.P.Val))+
   geom_density(aes(fill=id, alpha= 0.8))+
  fill_palette(palette = drug_palc)+
  theme_bw()+
  ylab("MTX-only DEGs\n n = 16")+
    # ylim(0,0.5)+
  guides(fill=FALSE,alpha=FALSE)+
  theme(axis.title = element_text(size = 14, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
Dox3Bplot <- toplist3hr %>% 
  group_by(time,id) %>% 
  dplyr::filter(ENTREZID %in% DOX3deg_sp$ENTREZID) %>%
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment" = id) %>%
  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  ylab("DOX n = 0")+
  theme_classic()+
  fill_palette(palette = drug_palc)+
 guides(fill= "none")+
  theme(
      axis.title = element_text(size = 10, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))

    



Dnr3Bplot <-
  toplist3hr %>% 
  group_by(time,id) %>% 
  dplyr::filter(ENTREZID %in% DNR3deg_sp$ENTREZID) %>% 
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment" = id) %>%
  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  ylab("DNR-spec. adj.P.V <0.01\n n = 100")+
  theme_classic()+
  guides(fill= "none")+
  fill_palette(palette = drug_palc)+
 theme(
      axis.title = element_text(size = 10, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
    
Epi3Bplot <-
  toplist3hr %>% 
  group_by(time,id) %>% 
  filter(ENTREZID %in% EPI3deg_sp$ENTREZID) %>% 
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment" = id) %>%
  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  ylab("EPI-spec.adj.P.V <0.01\n n = 0")+
  theme_classic()+
  guides(fill= "none")+
  fill_palette(palette = drug_palc)+
   theme(axis.title = element_text(size = 10, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
    

Mtx3Bplot <-
  toplist3hr %>% 
  group_by(time,id) %>% 
    filter(time=="3_hours") %>% 
  filter(ENTREZID %in% MTX3deg_sp$ENTREZID) %>% 
  mutate(logFC=logFC*(-1)) %>% 
  mutate("treatment" = id) %>%
  ggplot(., aes(x= treatment, y=logFC))+
  geom_boxplot(aes(fill=id))+
  xlab(" ")+
  ylab("MTX-spec. adj.P.V <0.01\n n = 4")+
  guides(fill= "none")+
  theme_classic()+
  fill_palette(palette = drug_palc)+
  theme(axis.title = element_text(size = 10, color = "black"), 
      axis.ticks = element_line(size = 1.5),    
      axis.text = element_text(size = 10, color = "black", angle = 0))
Dox3genesp_example <- "none"#cpm_boxplot(cpmcounts,GOI=101927720,"Dark2",drug_palc,
  #               ylab=bquote(~italic("ZNF793-AS1 ")~log[2]~"cpm "))+ 
  # theme(axis.title = element_text(size = 10, color = "black"), axis.text = element_text(size = 10, color = "black", angle = 0))

Dnr3genesp_example <- cpm_boxplot_time(cpmcounts,"3h",7975 ,"Dark2",drug_palc,
                ylab=bquote(~italic("MAFK")~log[2]~"cpm "))+ 
   theme(axis.title = element_text(size = 10, color = "black"), axis.text = element_text(size = 10, color = "black", angle = 0))

Epi3genesp_example <- "none"#cpm_boxplot(cpmcounts,GOI=79169,"Dark2",drug_palc,
   #              ylab=bquote(~italic("C1orf35")~log[2]~"cpm "))+ 
   # theme(axis.title = element_text(size = 10, color = "black"), axis.text = element_text(size = 10, color = "black", angle = 0))


Mtx3genesp_example <- cpm_boxplot_time(cpmcounts, "3h",GOI=284306,"Dark2",drug_palc,
                ylab=bquote(~italic("ZNF547")~log[2]~"cpm "))+ 
   theme(axis.title = element_text(size = 10, color = "black"), axis.text = element_text(size = 10, color = "black", angle = 0))

grid 3 hour


sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] gprofiler2_0.2.2      paletteer_1.5.0       ggVennDiagram_1.2.2  
 [4] ComplexHeatmap_2.16.0 broom_1.0.5           kableExtra_1.3.4     
 [7] sjmisc_2.8.9          scales_1.2.1          ggpubr_0.6.0         
[10] cowplot_1.1.1         ggsignif_0.6.4        lubridate_1.9.2      
[13] forcats_1.0.0         stringr_1.5.0         dplyr_1.1.2          
[16] purrr_1.0.1           readr_2.1.4           tidyr_1.3.0          
[19] tibble_3.2.1          ggplot2_3.4.2         tidyverse_2.0.0      
[22] RColorBrewer_1.1-3    limma_3.56.2          workflowr_1.7.0      

loaded via a namespace (and not attached):
  [1] rstudioapi_0.15.0    jsonlite_1.8.7       shape_1.4.6         
  [4] magrittr_2.0.3       farver_2.1.1         rmarkdown_2.23      
  [7] GlobalOptions_0.1.2  fs_1.6.3             vctrs_0.6.3         
 [10] rstatix_0.7.2        webshot_0.5.5        htmltools_0.5.5     
 [13] lambda.r_1.2.4       sass_0.4.7           KernSmooth_2.23-22  
 [16] bslib_0.5.0          htmlwidgets_1.6.2    futile.options_1.0.1
 [19] plotly_4.10.2        cachem_1.0.8         whisker_0.4.1       
 [22] mime_0.12            lifecycle_1.0.3      iterators_1.0.14    
 [25] pkgconfig_2.0.3      sjlabelled_1.2.0     R6_2.5.1            
 [28] fastmap_1.1.1        shiny_1.7.4.1        clue_0.3-64         
 [31] digest_0.6.33        colorspace_2.1-0     rematch2_2.1.2      
 [34] S4Vectors_0.38.1     ps_1.7.5             rprojroot_2.0.3     
 [37] prismatic_1.1.1      crosstalk_1.2.0      labeling_0.4.2      
 [40] fansi_1.0.4          timechange_0.2.0     httr_1.4.6          
 [43] abind_1.4-5          compiler_4.3.1       proxy_0.4-27        
 [46] withr_2.5.0          doParallel_1.0.17    backports_1.4.1     
 [49] carData_3.0-5        DBI_1.1.3            highr_0.10          
 [52] rjson_0.2.21         classInt_0.4-9       tools_4.3.1         
 [55] units_0.8-2          httpuv_1.6.11        glue_1.6.2          
 [58] VennDiagram_1.7.3    callr_3.7.3          promises_1.2.0.1    
 [61] sf_1.0-14            getPass_0.2-2        cluster_2.1.4       
 [64] generics_0.1.3       gtable_0.3.3         tzdb_0.4.0          
 [67] class_7.3-22         data.table_1.14.8    hms_1.1.3           
 [70] xml2_1.3.5           car_3.1-2            utf8_1.2.3          
 [73] BiocGenerics_0.46.0  foreach_1.5.2        pillar_1.9.0        
 [76] later_1.3.1          circlize_0.4.15      tidyselect_1.2.0    
 [79] knitr_1.43           git2r_0.32.0         IRanges_2.34.1      
 [82] svglite_2.1.1        stats4_4.3.1         futile.logger_1.4.3 
 [85] xfun_0.39            matrixStats_1.0.0    stringi_1.7.12      
 [88] lazyeval_0.2.2       yaml_2.3.7           evaluate_0.21       
 [91] codetools_0.2-19     RVenn_1.1.0          cli_3.6.1           
 [94] xtable_1.8-4         systemfonts_1.0.4    munsell_0.5.0       
 [97] processx_3.8.2       jquerylib_0.1.4      Rcpp_1.0.11         
[100] png_0.1-8            parallel_4.3.1       ellipsis_0.3.2      
[103] viridisLite_0.4.2    e1071_1.7-13         insight_0.19.3      
[106] crayon_1.5.2         GetoptLong_1.0.5     rlang_1.1.1         
[109] rvest_1.0.3          formatR_1.14