Last updated: 2023-05-26

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Rmd ac69e6e reneeisnowhere 2023-05-26 adding abs LFC of motifs
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Rmd c365253 reneeisnowhere 2023-03-22 updated code and plots
Rmd 3a26d52 reneeisnowhere 2023-03-22 Wed poster analysis changes
Rmd a150323 reneeisnowhere 2023-03-20 addingcormotif analysis and go on DEGs 
library(tidyverse)
library(gprofiler2)
library(readr)
library(BiocGenerics)
library(gridExtra)
library(VennDiagram)
library(kableExtra)
library(scales)
library(ggVennDiagram)
library(Cormotif)
library(RColorBrewer)
library(ggpubr)

Creation of the data set:

library(edgeR)
library(Cormotif)
library(RColorBrewer)

library(BiocParallel)
## read in count file##
design <- read.csv("data/data_outline.txt", row.names = 1)
mymatrix <- readRDS("data/filtermatrix_x.RDS")#should be 14084
x_counts <- mymatrix$counts

indv <- as.factor(rep(c(1,2,3,4,5,6), c(12,12,12,12,12,12)))
time <- rep((rep(c("3h", "24h"), c(6,6))), 6)
time <- ordered(time, levels =c("3h", "24h"))
group <- as.factor(rep((c("1","2","3","4","5","6","7","8","9","10","11","12")),6))
drug <- rep(c("Daunorubicin","Doxorubicin","Epirubicin","Mitoxantrone","Trastuzumab", "Vehicle"),12)
group1 <- interaction(drug,time)
label <- (interaction(substring(drug, 0, 2), indv, time))
colnames(x_counts) <- label
group_fac <- group1
groupid <- as.numeric(group_fac)

compid <- data.frame(c1= c(1,2,3,4,5,7,8,9,10,11), c2 = c( 6,6,6,6,6,12,12,12,12,12))

y_TMM_cpm <- cpm(x_counts, log = TRUE)

colnames(y_TMM_cpm) <- label
y_TMM_cpm
set.seed(12345)
cormotif_initial <- cormotiffit(exprs = y_TMM_cpm,
                             groupid = groupid,
                             compid = compid,
                             K=1:8, max.iter = 500,runtype="logCPM")
gene_prob_tran <- cormotif_initial$bestmotif$p.post
rownames(gene_prob_tran) <- rownames(y_TMM_cpm)
motif_prob <- cormotif_initial$bestmotif$clustlike
rownames(motif_prob) <- rownames(y_TMM_cpm)
write.csv(motif_prob,"cormotif_probability_genelist.csv")

cormotif_initial was created after calling corMotif, then running the corMotifcustom.R script. The extra R script enabled me to generate a table containing the likelihood of each gene that belongs to the specific cluster.

After generating the Motifs from 1 to 8, the number of motifs that best fit the data was 4 using the BIC and AIC results below.

cormotif_initial <- readRDS("data/cormotif_initialall.RDS")#
plotIC(cormotif_initial)

plotMotif(cormotif_initial)

Viewing the motifs, the following groups were named:

  • Motif 1: No Response (n=7409)

  • Motif 2: Top2\(\beta\) inhibitor response, Time-independent

    • (Time-independent response, n= 589)

  • Motif 3: Top2\(\beta\) inhibitor response, Early

    • (Early response, n= 487)

  • Motif 4: Top2\(\beta\) inhibitor response, Late

    • (Late response, n= 5596)
clust1 <- motif_prob %>%
  as.data.frame() %>%
  filter(V1>0.5) %>% 
  rownames
clust2 <- motif_prob %>%
  as.data.frame() %>%
  filter(V2>0.5) %>% 
  rownames
clust3 <- motif_prob %>%
  as.data.frame() %>%
  filter(V3>0.5) %>% 
  rownames
clust4 <- motif_prob %>%
  as.data.frame() %>%
  filter(V4>0.5) %>% 
  rownames
old_clust1  <- rownames(gene_prob_tran[(gene_prob_tran[,1] <0.45 &
                                          gene_prob_tran[,2] <0.45 &
                                          gene_prob_tran[,3] <0.45 &
                                          gene_prob_tran[,4] <0.45 &
                                          gene_prob_tran[,5] <0.45 &
                                          gene_prob_tran[,6] <0.45 &
                                          gene_prob_tran[,7] <0.45 &
                                          gene_prob_tran[,8] <0.45 &
                                          gene_prob_tran[,9] <0.45 &
                                         gene_prob_tran[,10] <0.45),])
length(intersect(old_clust1,clust1))##7358 out of 7362 oldclust1

old_clust2  <- rownames(gene_prob_tran[(gene_prob_tran[,1]> 0.10 &
                                         gene_prob_tran[,2] > 0.10 &
                                         gene_prob_tran[,3] > 0.10 &
                                         gene_prob_tran[,4] > 0.10 &
                                         # gene_prob_tran[,5] < 0.10 &
                                           gene_prob_tran[,6] > 0.10&
                                           gene_prob_tran[,7]> 0.10 &
                                           gene_prob_tran[,8]> 0.10 &
                                           gene_prob_tran[,9]> 0.10),])
# &                                      # gene_prob_tran[,10]< 0.10),])
                                                   
length(intersect(old_clust2,clust2))##251 out of 432 oldclust2

old_clust3 <- rownames(gene_prob_tran[(gene_prob_tran[,1]>0.55 &
                                           gene_prob_tran[,2] >0.55 &
                                           gene_prob_tran[,3] >0.55 &
                                           gene_prob_tran[,4] >0.25&
                                           gene_prob_tran[,5] <0.90 &
                                           gene_prob_tran[,6] <0.9 &
                                           gene_prob_tran[,7]<0.9&
                                           gene_prob_tran[,8]<0.9 &
                                          gene_prob_tran[,9]<0.9 &
                                           gene_prob_tran[,10]<0.90),])
length(intersect(old_clust3,clust3)) ##414 out of 481 oldclust3

old_clust4 <- rownames(gene_prob_tran[(gene_prob_tran[,1] <0.970 &
                                            gene_prob_tran[,2] <0.97 &
                                            gene_prob_tran[,3] <0.97 &
                                            gene_prob_tran[,4] <0.97 &
                                            gene_prob_tran[,5] <0.9&
                                            gene_prob_tran[,6] >0.55 &
                                            gene_prob_tran[,7] >0.55 &
                                            gene_prob_tran[,8] >0.55 &
                                            gene_prob_tran[,9] >0.05 &
                                            gene_prob_tran[,10] <0.9),])
length(intersect(old_clust4,clust4))##4675 out of 4850 oldclust4
backGL <- read.csv("data/backGL.txt")  ##14084
length(setdiff(backGL$ENTREZID,(union(clust1,union(clust2,union(clust3,clust4))))))
##63 genes not used overall  same as (14084-7504-528-444-5545)

Pie Chart of overall numbers

#make data frame
Set <- c("Early Response", "Time-Independent Response","Late Response", "No Response")
gene_num <- c(487,589,5596,7409)
fills <- c("#F8766D",  "#00BFC4","#7CAE00", "#C77CFF")

pie_chartdata <- data.frame(Set, gene_num, fills)
 
    pie(gene_num,labels =Set )       

#library(stringr)

##label computation
pie_chartdata <- pie_chartdata %>% 
   mutate(prop = gene_num / sum(pie_chartdata$gene_num) *100) %>%
  mutate(ypos = (prop)+ 0.5*prop )
#data=pie_chartdata[,c(1,2)]

pie_chartdata %>% 
  ggplot(.,aes(x="",y=gene_num, fill=Set))+
  geom_col(width =1) +
  coord_polar("y", pi/2)+
  theme_void()+
  ggtitle("Distribution of genes for each set")+
  geom_text(aes(label = paste0(Set," (",gene_num,")")),
                position = position_stack(vjust =.55)) +
  theme(legend.position="none") +
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5))

The genes belonging to each set were identified by the following:

motif 1- No Response set: 7504 (gene list made by filtering likelihood of gene belonging to cluster 1 <0.5)

motif 2- Time-independent Top2\(\beta\)i response cluster: 528 (gene list made by filtering likelihood of gene belonging to cluster 2 <0.5)

motif 3- Early Top2\(\beta\)i response cluster: 444 (gene list made by filtering likelihood of gene belonging to cluster 3 <0.5)

motif 4- Late Top2\(\beta\)i response cluster: 5545 (gene list made by filtering likelihood of gene belonging to cluster 4 <0.5)

There was overlap between the previous sets and the new sets, so I moved on expecting similar responses in the GO analysis. I did subset out the genes not used overall from the background gene list (rowmeans>0 from log(cpm(count matrix)))

DEG_cormotif <- readRDS("data/DEG_cormotif.RDS")
motif_NR <- DEG_cormotif$motif_NR
motif_TI <- DEG_cormotif$motif_TI
motif_LR <- DEG_cormotif$motif_LR
motif_ER <- DEG_cormotif$motif_ER
  
backGL <- read.csv("data/backGL.txt")
#NRresp <- read_csv("data/cormotif_NRset.txt")

No response motif genes

GO:BP

source term_id term_name intersection_size term_size p_value
GO:BP GO:0002181 cytoplasmic translation 117 155 9.02e-06
GO:BP GO:0019646 aerobic electron transport chain 63 74 9.02e-06
GO:BP GO:0009060 aerobic respiration 133 180 9.02e-06
GO:BP GO:0006119 oxidative phosphorylation 104 134 9.02e-06
GO:BP GO:0022904 respiratory electron transport chain 83 103 9.02e-06
GO:BP GO:0042775 mitochondrial ATP synthesis coupled electron transport 68 82 1.51e-05
GO:BP GO:0042773 ATP synthesis coupled electron transport 68 82 1.51e-05
GO:BP GO:0045333 cellular respiration 158 222 1.67e-05
GO:BP GO:0034645 cellular macromolecule biosynthetic process 624 1030 8.49e-05
GO:BP GO:1901566 organonitrogen compound biosynthetic process 878 1499 7.73e-04
GO:BP GO:0009100 glycoprotein metabolic process 209 317 1.00e-03
GO:BP GO:0022900 electron transport chain 102 141 1.29e-03
GO:BP GO:1901564 organonitrogen compound metabolic process 2774 5018 1.40e-03
GO:BP GO:0043603 amide metabolic process 597 999 1.44e-03
GO:BP GO:0006518 peptide metabolic process 481 793 1.50e-03
GO:BP GO:0015980 energy derivation by oxidation of organic compounds 196 298 1.91e-03
GO:BP GO:0070085 glycosylation 139 204 2.73e-03
GO:BP GO:0033108 mitochondrial respiratory chain complex assembly 71 94 2.73e-03
GO:BP GO:0006486 protein glycosylation 130 189 2.73e-03
GO:BP GO:0043413 macromolecule glycosylation 130 189 2.73e-03
GO:BP GO:0006412 translation 393 644 4.10e-03
GO:BP GO:0006091 generation of precursor metabolites and energy 272 432 4.10e-03
GO:BP GO:0022613 ribonucleoprotein complex biogenesis 281 449 5.52e-03
GO:BP GO:0019538 protein metabolic process 2347 4252 1.54e-02
GO:BP GO:0015986 proton motive force-driven ATP synthesis 51 66 1.54e-02
GO:BP GO:0043043 peptide biosynthetic process 400 664 1.54e-02
GO:BP GO:0043604 amide biosynthetic process 458 767 1.54e-02
GO:BP GO:0009101 glycoprotein biosynthetic process 165 254 1.87e-02
GO:BP GO:0006487 protein N-linked glycosylation 50 65 2.02e-02
GO:BP GO:0006754 ATP biosynthetic process 64 87 2.10e-02
GO:BP GO:1901135 carbohydrate derivative metabolic process 529 899 2.68e-02
GO:BP GO:0010257 NADH dehydrogenase complex assembly 43 55 3.07e-02
GO:BP GO:0032981 mitochondrial respiratory chain complex I assembly 43 55 3.07e-02
GO:BP GO:0010466 negative regulation of peptidase activity 101 149 4.20e-02
GO:BP GO:0042776 proton motive force-driven mitochondrial ATP synthesis 44 57 4.20e-02
KEGG KEGG:05171 Coronavirus disease - COVID-19 122 162 7.18e-07
KEGG KEGG:03010 Ribosome 98 127 1.54e-06
KEGG KEGG:04510 Focal adhesion 126 175 9.65e-06
KEGG KEGG:05208 Chemical carcinogenesis - reactive oxygen species 133 186 9.65e-06
KEGG KEGG:00190 Oxidative phosphorylation 81 106 2.52e-05
KEGG KEGG:04512 ECM-receptor interaction 55 69 1.36e-04
KEGG KEGG:05012 Parkinson disease 153 226 1.36e-04
KEGG KEGG:04714 Thermogenesis 134 195 1.39e-04
KEGG KEGG:05020 Prion disease 148 220 2.52e-04
KEGG KEGG:05415 Diabetic cardiomyopathy 117 169 2.64e-04
KEGG KEGG:00531 Glycosaminoglycan degradation 16 16 1.02e-03
KEGG KEGG:04141 Protein processing in endoplasmic reticulum 110 161 1.02e-03
KEGG KEGG:05016 Huntington disease 165 256 2.07e-03
KEGG KEGG:05010 Alzheimer disease 197 315 5.40e-03
KEGG KEGG:00513 Various types of N-glycan biosynthesis 29 36 1.08e-02
KEGG KEGG:04932 Non-alcoholic fatty liver disease 88 131 1.08e-02
KEGG KEGG:04142 Lysosome 80 118 1.17e-02
KEGG KEGG:00510 N-Glycan biosynthesis 36 48 2.41e-02
KEGG KEGG:04810 Regulation of actin cytoskeleton 114 179 3.22e-02
KEGG KEGG:01200 Carbon metabolism 66 98 3.80e-02
KEGG KEGG:03040 Spliceosome 86 132 3.93e-02
KEGG KEGG:05022 Pathways of neurodegeneration - multiple diseases 230 385 4.28e-02

Late response Top2\(\beta\) inhibitor motif genes

GO:BP/KEGG

source term_id term_name intersection_size term_size p_value
GO:BP GO:0007059 chromosome segregation 207 378 4.07e-06
GO:BP GO:0000280 nuclear division 190 354 8.76e-05
GO:BP GO:0051301 cell division 284 567 1.73e-04
GO:BP GO:0007049 cell cycle 689 1522 4.11e-04
GO:BP GO:0098813 nuclear chromosome segregation 155 287 4.42e-04
GO:BP GO:0007051 spindle organization 107 186 5.13e-04
GO:BP GO:0000070 mitotic sister chromatid segregation 110 193 5.75e-04
GO:BP GO:0140014 mitotic nuclear division 143 264 6.50e-04
GO:BP GO:0006261 DNA-templated DNA replication 88 149 7.42e-04
GO:BP GO:0048285 organelle fission 203 397 7.42e-04
GO:BP GO:0061982 meiosis I cell cycle process 53 80 8.85e-04
GO:BP GO:0022402 cell cycle process 495 1075 9.31e-04
GO:BP GO:0140013 meiotic nuclear division 73 121 1.68e-03
GO:BP GO:0000278 mitotic cell cycle 390 833 1.71e-03
GO:BP GO:0007127 meiosis I 50 76 1.81e-03
GO:BP GO:1903046 meiotic cell cycle process 80 136 1.85e-03
GO:BP GO:0000226 microtubule cytoskeleton organization 268 552 2.03e-03
GO:BP GO:0000819 sister chromatid segregation 126 234 2.07e-03
GO:BP GO:0045132 meiotic chromosome segregation 46 69 2.09e-03
GO:BP GO:1903047 mitotic cell cycle process 331 700 2.51e-03
GO:BP GO:0051276 chromosome organization 261 543 5.74e-03
GO:BP GO:0007017 microtubule-based process 352 756 6.39e-03
GO:BP GO:0006260 DNA replication 134 258 9.24e-03
GO:BP GO:2001251 negative regulation of chromosome organization 55 90 9.83e-03
GO:BP GO:0070925 organelle assembly 370 803 1.06e-02
GO:BP GO:0051716 cellular response to stimulus 2043 4935 1.14e-02
GO:BP GO:0050896 response to stimulus 2360 5741 1.35e-02
GO:BP GO:0032465 regulation of cytokinesis 49 79 1.35e-02
GO:BP GO:1902850 microtubule cytoskeleton organization involved in mitosis 86 156 1.45e-02
GO:BP GO:0045930 negative regulation of mitotic cell cycle 110 208 1.45e-02
GO:BP GO:0045839 negative regulation of mitotic nuclear division 36 54 1.49e-02
GO:BP GO:2000816 negative regulation of mitotic sister chromatid separation 32 47 1.89e-02
GO:BP GO:0033048 negative regulation of mitotic sister chromatid segregation 32 47 1.89e-02
GO:BP GO:0046474 glycerophospholipid biosynthetic process 101 190 1.89e-02
GO:BP GO:0033046 negative regulation of sister chromatid segregation 32 47 1.89e-02
GO:BP GO:0008654 phospholipid biosynthetic process 122 236 1.89e-02
GO:BP GO:0045017 glycerolipid biosynthetic process 114 219 2.09e-02
GO:BP GO:0006996 organelle organization 1253 2971 2.23e-02
GO:BP GO:0051784 negative regulation of nuclear division 37 57 2.23e-02
GO:BP GO:0071174 mitotic spindle checkpoint signaling 30 44 2.59e-02
GO:BP GO:0071173 spindle assembly checkpoint signaling 30 44 2.59e-02
GO:BP GO:0007094 mitotic spindle assembly checkpoint signaling 30 44 2.59e-02
GO:BP GO:0045841 negative regulation of mitotic metaphase/anaphase transition 31 46 2.72e-02
GO:BP GO:1905819 negative regulation of chromosome separation 32 48 2.76e-02
GO:BP GO:0051985 negative regulation of chromosome segregation 32 48 2.76e-02
GO:BP GO:0007093 mitotic cell cycle checkpoint signaling 75 136 2.79e-02
GO:BP GO:0006270 DNA replication initiation 25 35 2.79e-02
GO:BP GO:0033047 regulation of mitotic sister chromatid segregation 34 52 2.85e-02
GO:BP GO:0051304 chromosome separation 45 74 3.10e-02
GO:BP GO:0000075 cell cycle checkpoint signaling 95 180 3.10e-02
GO:BP GO:0007052 mitotic spindle organization 71 128 3.10e-02
GO:BP GO:0021537 telencephalon development 103 198 3.39e-02
GO:BP GO:0051225 spindle assembly 66 118 3.52e-02
GO:BP GO:0031577 spindle checkpoint signaling 30 45 3.79e-02
GO:BP GO:0045786 negative regulation of cell cycle 163 334 3.84e-02
GO:BP GO:1902100 negative regulation of metaphase/anaphase transition of cell cycle 31 47 3.84e-02
GO:BP GO:1901653 cellular response to peptide 139 280 4.26e-02
GO:BP GO:1905818 regulation of chromosome separation 42 69 4.33e-02
GO:BP GO:0051256 mitotic spindle midzone assembly 9 9 4.43e-02
GO:BP GO:0090407 organophosphate biosynthetic process 241 517 4.81e-02
GO:BP GO:0010889 regulation of sequestering of triglyceride 11 12 4.81e-02
GO:BP GO:0019692 deoxyribose phosphate metabolic process 26 38 4.81e-02
GO:BP GO:0051255 spindle midzone assembly 11 12 4.81e-02
GO:BP GO:0009262 deoxyribonucleotide metabolic process 26 38 4.81e-02
KEGG KEGG:00230 Purine metabolism 56 97 2.67e-02
KEGG KEGG:03030 DNA replication 25 35 2.67e-02

Early Response Top2\(\beta\) inhibitor motif genes

GO:BP/KEGG
query significant p_value term_size query_size intersection_size precision recall term_id source term_name effective_domain_size source_order parents
query_1 TRUE 0.0000000 2683 428 2.16e+02 0.5046729 0.0805069 GO:0006351 GO:BP DNA-templated transcription 13587 2189 GO:0097659
query_1 TRUE 0.0000000 2684 428 2.16e+02 0.5046729 0.0804769 GO:0097659 GO:BP nucleic acid-templated transcription 13587 19903 GO:0010467, GO:0032774
query_1 TRUE 0.0000000 2714 428 2.16e+02 0.5046729 0.0795873 GO:0032774 GO:BP RNA biosynthetic process 13587 8281 GO:0009059, GO:0016070, GO:0034654
query_1 TRUE 0.0000000 1991 428 1.83e+02 0.4275701 0.0919136 GO:0006366 GO:BP transcription by RNA polymerase II 13587 2202 GO:0006351
query_1 TRUE 0.0000000 2581 428 2.09e+02 0.4883178 0.0809764 GO:1903506 GO:BP regulation of nucleic acid-templated transcription 13587 24286 GO:0097659, GO:2001141
query_1 TRUE 0.0000000 3105 428 2.31e+02 0.5397196 0.0743961 GO:0019219 GO:BP regulation of nucleobase-containing compound metabolic process 13587 5932 GO:0006139, GO:0031323, GO:0051171, GO:0080090
query_1 TRUE 0.0000000 2579 428 2.09e+02 0.4883178 0.0810392 GO:0006355 GO:BP regulation of DNA-templated transcription 13587 2193 GO:0006351, GO:0010468, GO:1903506
query_1 TRUE 0.0000000 1915 428 1.78e+02 0.4158879 0.0929504 GO:0006357 GO:BP regulation of transcription by RNA polymerase II 13587 2195 GO:0006355, GO:0006366
query_1 TRUE 0.0000000 2598 428 2.09e+02 0.4883178 0.0804465 GO:2001141 GO:BP regulation of RNA biosynthetic process 13587 27809 GO:0010556, GO:0031326, GO:0032774, GO:0051252
query_1 TRUE 0.0000000 2849 428 2.19e+02 0.5116822 0.0768691 GO:0051252 GO:BP regulation of RNA metabolic process 13587 14451 GO:0016070, GO:0019219, GO:0060255
query_1 TRUE 0.0000000 4047 428 2.60e+02 0.6074766 0.0642451 GO:0090304 GO:BP nucleic acid metabolic process 13587 19342 GO:0006139, GO:0043170
query_1 TRUE 0.0000000 3015 428 2.19e+02 0.5116822 0.0726368 GO:0010556 GO:BP regulation of macromolecule biosynthetic process 13587 4326 GO:0009059, GO:0009889, GO:0060255
query_1 TRUE 0.0000000 3593 428 2.41e+02 0.5630841 0.0670749 GO:0016070 GO:BP RNA metabolic process 13587 5254 GO:0090304
query_1 TRUE 0.0000000 4305 428 2.66e+02 0.6214953 0.0617886 GO:0031323 GO:BP regulation of cellular metabolic process 13587 7549 GO:0019222, GO:0044237, GO:0050794
query_1 TRUE 0.0000000 3083 428 2.19e+02 0.5116822 0.0710347 GO:0034654 GO:BP nucleobase-containing compound biosynthetic process 13587 9218 GO:0006139, GO:0018130, GO:0019438, GO:0044271, GO:1901362
query_1 TRUE 0.0000000 3123 428 2.20e+02 0.5140187 0.0704451 GO:0031326 GO:BP regulation of cellular biosynthetic process 13587 7552 GO:0009889, GO:0031323, GO:0044249
query_1 TRUE 0.0000000 3149 428 2.20e+02 0.5140187 0.0698634 GO:0019438 GO:BP aromatic compound biosynthetic process 13587 6132 GO:0006725, GO:0044249
query_1 TRUE 0.0000000 3148 428 2.20e+02 0.5140187 0.0698856 GO:0018130 GO:BP heterocycle biosynthetic process 13587 5537 GO:0044249, GO:0046483
query_1 TRUE 0.0000000 3174 428 2.20e+02 0.5140187 0.0693132 GO:0009889 GO:BP regulation of biosynthetic process 13587 3843 GO:0009058, GO:0019222
query_1 TRUE 0.0000000 3253 428 2.21e+02 0.5163551 0.0679373 GO:1901362 GO:BP organic cyclic compound biosynthetic process 13587 22499 GO:1901360, GO:1901576
query_1 TRUE 0.0000000 3583 428 2.33e+02 0.5443925 0.0650293 GO:0010468 GO:BP regulation of gene expression 13587 4271 GO:0010467, GO:0060255
query_1 TRUE 0.0000000 4440 428 2.63e+02 0.6144860 0.0592342 GO:0080090 GO:BP regulation of primary metabolic process 13587 18924 GO:0019222, GO:0044238
query_1 TRUE 0.0000000 4330 428 2.59e+02 0.6051402 0.0598152 GO:0051171 GO:BP regulation of nitrogen compound metabolic process 13587 14399 GO:0006807, GO:0019222
query_1 TRUE 0.0000000 3730 428 2.36e+02 0.5514019 0.0632708 GO:0009059 GO:BP macromolecule biosynthetic process 13587 3327 GO:0043170, GO:1901576
query_1 TRUE 0.0000000 4503 428 2.63e+02 0.6144860 0.0584055 GO:0006139 GO:BP nucleobase-containing compound metabolic process 13587 2036 GO:0006725, GO:0034641, GO:0044238, GO:0046483, GO:1901360
query_1 TRUE 0.0000000 4640 428 2.65e+02 0.6191589 0.0571121 GO:0060255 GO:BP regulation of macromolecule metabolic process 13587 15399 GO:0019222, GO:0043170
query_1 TRUE 0.0000000 4616 428 2.64e+02 0.6168224 0.0571924 GO:0046483 GO:BP heterocycle metabolic process 13587 12974 GO:0044237
query_1 TRUE 0.0000000 4646 428 2.64e+02 0.6168224 0.0568231 GO:0006725 GO:BP cellular aromatic compound metabolic process 13587 2497 GO:0044237
query_1 TRUE 0.0000000 3758 428 2.31e+02 0.5397196 0.0614689 GO:0044271 GO:BP cellular nitrogen compound biosynthetic process 13587 11656 GO:0034641, GO:0044249
query_1 TRUE 0.0000000 4790 428 2.66e+02 0.6214953 0.0555324 GO:1901360 GO:BP organic cyclic compound metabolic process 13587 22497 GO:0071704
query_1 TRUE 0.0000000 4572 428 2.58e+02 0.6028037 0.0564304 GO:0010467 GO:BP gene expression 13587 4270 GO:0043170
query_1 TRUE 0.0000000 5039 428 2.73e+02 0.6378505 0.0541774 GO:0019222 GO:BP regulation of metabolic process 13587 5935 GO:0008152, GO:0050789
query_1 TRUE 0.0000000 4991 428 2.68e+02 0.6261682 0.0536967 GO:0034641 GO:BP cellular nitrogen compound metabolic process 13587 9210 GO:0006807, GO:0044237
query_1 TRUE 0.0000000 4465 428 2.49e+02 0.5817757 0.0557671 GO:0044249 GO:BP cellular biosynthetic process 13587 11645 GO:0009058, GO:0044237
query_1 TRUE 0.0000000 4537 428 2.49e+02 0.5817757 0.0548821 GO:1901576 GO:BP organic substance biosynthetic process 13587 22687 GO:0009058, GO:0071704
query_1 TRUE 0.0000000 4595 428 2.49e+02 0.5817757 0.0541893 GO:0009058 GO:BP biosynthetic process 13587 3326 GO:0008152
query_1 TRUE 0.0000000 7057 428 3.22e+02 0.7523364 0.0456285 GO:0043170 GO:BP macromolecule metabolic process 13587 11211 GO:0071704
query_1 TRUE 0.0000000 7579 428 3.29e+02 0.7686916 0.0434094 GO:0050794 GO:BP regulation of cellular process 13587 14091 GO:0009987, GO:0050789
query_1 TRUE 0.0000000 1304 428 1.05e+02 0.2453271 0.0805215 GO:1903508 GO:BP positive regulation of nucleic acid-templated transcription 13587 24288 GO:0097659, GO:1902680, GO:1903506
query_1 TRUE 0.0000000 1304 428 1.05e+02 0.2453271 0.0805215 GO:0045893 GO:BP positive regulation of DNA-templated transcription 13587 12467 GO:0006351, GO:0006355, GO:1903508
query_1 TRUE 0.0000000 1431 428 1.11e+02 0.2593458 0.0775681 GO:0051254 GO:BP positive regulation of RNA metabolic process 13587 14453 GO:0010604, GO:0016070, GO:0045935, GO:0051252
query_1 TRUE 0.0000000 1311 428 1.05e+02 0.2453271 0.0800915 GO:1902680 GO:BP positive regulation of RNA biosynthetic process 13587 23603 GO:0010557, GO:0031328, GO:0032774, GO:0051254, GO:2001141
query_1 TRUE 0.0000000 7503 428 3.25e+02 0.7593458 0.0433160 GO:0044237 GO:BP cellular metabolic process 13587 11638 GO:0008152, GO:0009987
query_1 TRUE 0.0000000 1600 428 1.16e+02 0.2710280 0.0725000 GO:0045935 GO:BP positive regulation of nucleobase-containing compound metabolic process 13587 12505 GO:0006139, GO:0019219, GO:0031325, GO:0051173
query_1 TRUE 0.0000000 7474 428 3.21e+02 0.7500000 0.0429489 GO:0006807 GO:BP nitrogen compound metabolic process 13587 2557 GO:0008152
query_1 TRUE 0.0000000 7992 428 3.35e+02 0.7827103 0.0419169 GO:0050789 GO:BP regulation of biological process 13587 14087 GO:0008150, GO:0065007
query_1 TRUE 0.0000000 7800 428 3.29e+02 0.7686916 0.0421795 GO:0044238 GO:BP primary metabolic process 13587 11639 GO:0008152
query_1 TRUE 0.0000000 8348 428 3.44e+02 0.8037383 0.0412075 GO:0065007 GO:BP biological regulation 13587 16927 GO:0008150
query_1 TRUE 0.0000000 1499 428 1.09e+02 0.2546729 0.0727151 GO:0010557 GO:BP positive regulation of macromolecule biosynthetic process 13587 4327 GO:0009059, GO:0009891, GO:0010556, GO:0010604
query_1 TRUE 0.0000000 1009 428 8.50e+01 0.1985981 0.0842418 GO:0045892 GO:BP negative regulation of DNA-templated transcription 13587 12466 GO:0006351, GO:0006355, GO:1903507
query_1 TRUE 0.0000000 1011 428 8.50e+01 0.1985981 0.0840752 GO:1903507 GO:BP negative regulation of nucleic acid-templated transcription 13587 24287 GO:0097659, GO:1902679, GO:1903506
query_1 TRUE 0.0000000 1020 428 8.50e+01 0.1985981 0.0833333 GO:1902679 GO:BP negative regulation of RNA biosynthetic process 13587 23602 GO:0010558, GO:0031327, GO:0032774, GO:0051253, GO:2001141
query_1 TRUE 0.0000000 1215 428 9.40e+01 0.2196262 0.0773663 GO:0045934 GO:BP negative regulation of nucleobase-containing compound metabolic process 13587 12504 GO:0006139, GO:0019219, GO:0031324, GO:0051172
query_1 TRUE 0.0000000 1115 428 8.90e+01 0.2079439 0.0798206 GO:0051253 GO:BP negative regulation of RNA metabolic process 13587 14452 GO:0010605, GO:0016070, GO:0045934, GO:0051252
query_1 TRUE 0.0000000 925 428 7.90e+01 0.1845794 0.0854054 GO:0045944 GO:BP positive regulation of transcription by RNA polymerase II 13587 12513 GO:0006357, GO:0006366, GO:0045893
query_1 TRUE 0.0000000 1571 428 1.09e+02 0.2546729 0.0693826 GO:0031328 GO:BP positive regulation of cellular biosynthetic process 13587 7554 GO:0009891, GO:0031325, GO:0031326, GO:0044249
query_1 TRUE 0.0000000 8150 428 3.34e+02 0.7803738 0.0409816 GO:0071704 GO:BP organic substance metabolic process 13587 17953 GO:0008152
query_1 TRUE 0.0000000 1598 428 1.09e+02 0.2546729 0.0682103 GO:0009891 GO:BP positive regulation of biosynthetic process 13587 3845 GO:0009058, GO:0009889, GO:0009893
query_1 TRUE 0.0000000 1780 428 1.16e+02 0.2710280 0.0651685 GO:0031324 GO:BP negative regulation of cellular metabolic process 13587 7550 GO:0009892, GO:0031323, GO:0044237, GO:0048523
query_1 TRUE 0.0000000 1206 428 9.00e+01 0.2102804 0.0746269 GO:0010558 GO:BP negative regulation of macromolecule biosynthetic process 13587 4328 GO:0009059, GO:0009890, GO:0010556, GO:0010605
query_1 TRUE 0.0000000 735 428 6.50e+01 0.1518692 0.0884354 GO:0000122 GO:BP negative regulation of transcription by RNA polymerase II 13587 51 GO:0006357, GO:0006366, GO:0045892
query_1 TRUE 0.0000000 2373 428 1.38e+02 0.3224299 0.0581542 GO:0031325 GO:BP positive regulation of cellular metabolic process 13587 7551 GO:0009893, GO:0031323, GO:0044237, GO:0048522
query_1 TRUE 0.0000000 1249 428 9.00e+01 0.2102804 0.0720576 GO:0031327 GO:BP negative regulation of cellular biosynthetic process 13587 7553 GO:0009890, GO:0031324, GO:0031326, GO:0044249
query_1 TRUE 0.0000000 2425 428 1.40e+02 0.3271028 0.0577320 GO:0051173 GO:BP positive regulation of nitrogen compound metabolic process 13587 14401 GO:0006807, GO:0009893, GO:0051171
query_1 TRUE 0.0000000 1273 428 9.00e+01 0.2102804 0.0706991 GO:0009890 GO:BP negative regulation of biosynthetic process 13587 3844 GO:0009058, GO:0009889, GO:0009892
query_1 TRUE 0.0000000 2648 428 1.47e+02 0.3434579 0.0555136 GO:0010604 GO:BP positive regulation of macromolecule metabolic process 13587 4369 GO:0009893, GO:0043170, GO:0060255
query_1 TRUE 0.0000000 8501 428 3.36e+02 0.7850467 0.0395248 GO:0008152 GO:BP metabolic process 13587 3213 GO:0008150
query_1 TRUE 0.0000000 2306 428 1.30e+02 0.3037383 0.0563747 GO:0009892 GO:BP negative regulation of metabolic process 13587 3846 GO:0008152, GO:0019222, GO:0048519
query_1 TRUE 0.0000000 1866 428 1.12e+02 0.2616822 0.0600214 GO:0051172 GO:BP negative regulation of nitrogen compound metabolic process 13587 14400 GO:0006807, GO:0009892, GO:0051171
query_1 TRUE 0.0000000 2146 428 1.23e+02 0.2873832 0.0573159 GO:0010605 GO:BP negative regulation of macromolecule metabolic process 13587 4370 GO:0009892, GO:0043170, GO:0060255
query_1 TRUE 0.0000000 2884 428 1.49e+02 0.3481308 0.0516644 GO:0009893 GO:BP positive regulation of metabolic process 13587 3847 GO:0008152, GO:0019222, GO:0048518
query_1 TRUE 0.0000000 3628 428 1.75e+02 0.4088785 0.0482359 GO:0048523 GO:BP negative regulation of cellular process 13587 13627 GO:0009987, GO:0048519, GO:0050794
query_1 TRUE 0.0000000 4035 428 1.87e+02 0.4369159 0.0463445 GO:0048519 GO:BP negative regulation of biological process 13587 13623 GO:0008150, GO:0050789
query_1 TRUE 0.0000001 536 428 4.50e+01 0.1051402 0.0839552 GO:0006325 GO:BP chromatin organization 13587 2182 GO:0016043
query_1 TRUE 0.0000027 309 428 3.00e+01 0.0700935 0.0970874 GO:0006338 GO:BP chromatin remodeling 13587 2186 GO:0006325
query_1 TRUE 0.0000562 4148 428 1.77e+02 0.4135514 0.0426712 GO:0048522 GO:BP positive regulation of cellular process 13587 13626 GO:0009987, GO:0048518, GO:0050794
query_1 TRUE 0.0001845 4577 428 1.89e+02 0.4415888 0.0412934 GO:0048518 GO:BP positive regulation of biological process 13587 13622 GO:0008150, GO:0050789
query_1 TRUE 0.0002647 424 428 3.20e+01 0.0747664 0.0754717 GO:0016570 GO:BP histone modification 13587 5415 GO:0036211
query_1 TRUE 0.0011631 12 428 5.00e+00 0.0116822 0.4166667 GO:0010452 GO:BP histone H3-K36 methylation 13587 4257 GO:0034968
query_1 TRUE 0.0013697 1829 428 8.80e+01 0.2056075 0.0481137 GO:0050793 GO:BP regulation of developmental process 13587 14090 GO:0032502, GO:0050789
query_1 TRUE 0.0013866 120 428 1.40e+01 0.0327103 0.1166667 GO:0018022 GO:BP peptidyl-lysine methylation 13587 5494 GO:0006479, GO:0018205
query_1 TRUE 0.0015606 224 428 2.00e+01 0.0467290 0.0892857 GO:0006354 GO:BP DNA-templated transcription elongation 13587 2192 GO:0006351, GO:0032774
query_1 TRUE 0.0017063 107 428 1.30e+01 0.0303738 0.1214953 GO:0034968 GO:BP histone lysine methylation 13587 9262 GO:0016571, GO:0018022
query_1 TRUE 0.0020798 141 428 1.50e+01 0.0350467 0.1063830 GO:0016571 GO:BP histone methylation 13587 5416 GO:0006479, GO:0016570
query_1 TRUE 0.0055369 367 428 2.60e+01 0.0607477 0.0708447 GO:0018205 GO:BP peptidyl-lysine modification 13587 5601 GO:0018193
query_1 TRUE 0.0064837 4 428 3.00e+00 0.0070093 0.7500000 GO:0097676 GO:BP histone H3-K36 dimethylation 13587 19904 GO:0010452, GO:0018027
query_1 TRUE 0.0083303 178 428 1.60e+01 0.0373832 0.0898876 GO:0006479 GO:BP protein methylation 13587 2280 GO:0008213, GO:0043414
query_1 TRUE 0.0083303 178 428 1.60e+01 0.0373832 0.0898876 GO:0008213 GO:BP protein alkylation 13587 3228 GO:0036211
query_1 TRUE 0.0083303 789 428 4.40e+01 0.1028037 0.0557668 GO:0006974 GO:BP cellular response to DNA damage stimulus 13587 2675 GO:0033554
query_1 TRUE 0.0094433 18 428 5.00e+00 0.0116822 0.2777778 GO:0006607 GO:BP NLS-bearing protein import into nucleus 13587 2391 GO:0006606
query_1 TRUE 0.0099108 845 428 4.60e+01 0.1074766 0.0544379 GO:0060429 GO:BP epithelium development 13587 15559 GO:0009888
query_1 TRUE 0.0110510 657 428 3.80e+01 0.0887850 0.0578387 GO:0016071 GO:BP mRNA metabolic process 13587 5255 GO:0016070
query_1 TRUE 0.0147308 84 428 1.00e+01 0.0233645 0.1190476 GO:0045814 GO:BP negative regulation of gene expression, epigenetic 13587 12410 GO:0010629, GO:0040029
query_1 TRUE 0.0151756 227 428 1.80e+01 0.0420561 0.0792952 GO:0030522 GO:BP intracellular receptor signaling pathway 13587 7237 GO:0007165
query_1 TRUE 0.0227542 879 428 4.60e+01 0.1074766 0.0523322 GO:0072359 GO:BP circulatory system development 13587 18474 GO:0048731
query_1 TRUE 0.0231340 177 428 1.50e+01 0.0350467 0.0847458 GO:0090596 GO:BP sensory organ morphogenesis 13587 19524 GO:0007423, GO:0009887
query_1 TRUE 0.0235158 277 428 2.00e+01 0.0467290 0.0722022 GO:1903706 GO:BP regulation of hemopoiesis 13587 24477 GO:0002682, GO:0030097, GO:0060284, GO:2000026
query_1 TRUE 0.0235158 197 428 1.60e+01 0.0373832 0.0812183 GO:1902105 GO:BP regulation of leukocyte differentiation 13587 23159 GO:0002521, GO:1903706
query_1 TRUE 0.0235158 74 428 9.00e+00 0.0210280 0.1216216 GO:2000736 GO:BP regulation of stem cell differentiation 13587 27440 GO:0045595, GO:0048863
query_1 TRUE 0.0235158 141 428 1.30e+01 0.0303738 0.0921986 GO:0040029 GO:BP epigenetic regulation of gene expression 13587 10536 GO:0006325, GO:0010468
query_1 TRUE 0.0263267 6 428 3.00e+00 0.0070093 0.5000000 GO:0086023 GO:BP adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process 13587 19024 GO:0071880, GO:0086103
query_1 TRUE 0.0278172 76 428 9.00e+00 0.0210280 0.1184211 GO:0031507 GO:BP heterochromatin formation 13587 7631 GO:0045814, GO:0070828
query_1 TRUE 0.0306558 164 428 1.40e+01 0.0327103 0.0853659 GO:0007623 GO:BP circadian rhythm 13587 3168 GO:0048511
query_1 TRUE 0.0318091 531 428 3.10e+01 0.0724299 0.0583804 GO:0043009 GO:BP chordate embryonic development 13587 11117 GO:0009792
query_1 TRUE 0.0360655 36 428 6.00e+00 0.0140187 0.1666667 GO:1902275 GO:BP regulation of chromatin organization 13587 23312 GO:0006325, GO:0051128
query_1 TRUE 0.0398125 150 428 1.30e+01 0.0303738 0.0866667 GO:0019827 GO:BP stem cell population maintenance 13587 6416 GO:0032501, GO:0098727
query_1 TRUE 0.0417637 7 428 3.00e+00 0.0070093 0.4285714 GO:1900246 GO:BP positive regulation of RIG-I signaling pathway 13587 21551 GO:0039529, GO:0039535, GO:0062208
query_1 TRUE 0.0417637 2 428 2.00e+00 0.0046729 1.0000000 GO:0032242 GO:BP regulation of nucleoside transport 13587 7889 GO:0015858, GO:0032239
query_1 TRUE 0.0417637 2 428 2.00e+00 0.0046729 1.0000000 GO:1901898 GO:BP negative regulation of relaxation of cardiac muscle 13587 22972 GO:0055119, GO:1901078, GO:1901897
query_1 TRUE 0.0420232 15 428 4.00e+00 0.0093458 0.2666667 GO:0032239 GO:BP regulation of nucleobase-containing compound transport 13587 7886 GO:0015931, GO:0051049
query_1 TRUE 0.0429893 152 428 1.30e+01 0.0303738 0.0855263 GO:0098727 GO:BP maintenance of cell number 13587 20042 GO:0032502
query_1 TRUE 0.0468968 1415 428 6.50e+01 0.1518692 0.0459364 GO:0009888 GO:BP tissue development 13587 3842 GO:0048856
query_1 TRUE 0.0473282 154 428 1.30e+01 0.0303738 0.0844156 GO:0045165 GO:BP cell fate commitment 13587 12071 GO:0030154, GO:0048869
query_1 TRUE 0.0473282 83 428 9.00e+00 0.0210280 0.1084337 GO:0070828 GO:BP heterochromatin organization 13587 17383 GO:0006338
query_1 TRUE 0.0475458 501 428 2.90e+01 0.0677570 0.0578842 GO:0048729 GO:BP tissue morphogenesis 13587 13809 GO:0009653, GO:0009888
query_1 TRUE 0.0475458 234 428 1.70e+01 0.0397196 0.0726496 GO:0048511 GO:BP rhythmic process 13587 13617 GO:0008150
query_1 TRUE 0.0475458 548 428 3.10e+01 0.0724299 0.0565693 GO:0009792 GO:BP embryo development ending in birth or egg hatching 13587 3773 GO:0009790
query_1 TRUE 0.0477912 118 428 1.10e+01 0.0257009 0.0932203 GO:1902107 GO:BP positive regulation of leukocyte differentiation 13587 23161 GO:0002521, GO:1902105, GO:1903708
query_1 TRUE 0.0477912 118 428 1.10e+01 0.0257009 0.0932203 GO:1903708 GO:BP positive regulation of hemopoiesis 13587 24479 GO:0002684, GO:0010720, GO:0030097, GO:0051240, GO:1903706
query_1 TRUE 0.0477912 502 428 2.90e+01 0.0677570 0.0577689 GO:0007507 GO:BP heart development 13587 3080 GO:0048513, GO:0072359
query_1 TRUE 0.0481745 39 428 6.00e+00 0.0140187 0.1538462 GO:2001222 GO:BP regulation of neuron migration 13587 27870 GO:0001764, GO:0030334
query_1 TRUE 0.0481745 871 428 4.40e+01 0.1028037 0.0505166 GO:0009790 GO:BP embryo development 13587 3771 GO:0007275
query_1 TRUE 0.0000000 415 428 4.50e+01 0.1051402 0.1084337 KEGG:05168 KEGG Herpes simplex virus 1 infection 13587 442 KEGG:00000
source term_id term_name intersection_size term_size p_value
GO:BP GO:0006351 DNA-templated transcription 216 2683 4.83e-44
GO:BP GO:0097659 nucleic acid-templated transcription 216 2684 4.83e-44
GO:BP GO:0032774 RNA biosynthetic process 216 2714 1.67e-43
GO:BP GO:0006366 transcription by RNA polymerase II 183 1991 1.67e-43
GO:BP GO:1903506 regulation of nucleic acid-templated transcription 209 2581 6.11e-43
GO:BP GO:0019219 regulation of nucleobase-containing compound metabolic process 231 3105 6.11e-43
GO:BP GO:0006355 regulation of DNA-templated transcription 209 2579 6.11e-43
GO:BP GO:0006357 regulation of transcription by RNA polymerase II 178 1915 6.11e-43
GO:BP GO:2001141 regulation of RNA biosynthetic process 209 2598 1.31e-42
GO:BP GO:0051252 regulation of RNA metabolic process 219 2849 3.56e-42
GO:BP GO:0090304 nucleic acid metabolic process 260 4047 8.30e-39
GO:BP GO:0010556 regulation of macromolecule biosynthetic process 219 3015 4.49e-38
GO:BP GO:0016070 RNA metabolic process 241 3593 1.21e-37
GO:BP GO:0031323 regulation of cellular metabolic process 266 4305 4.72e-37
GO:BP GO:0034654 nucleobase-containing compound biosynthetic process 219 3083 1.48e-36
GO:BP GO:0031326 regulation of cellular biosynthetic process 220 3123 3.12e-36
GO:BP GO:0019438 aromatic compound biosynthetic process 220 3149 1.09e-35
GO:BP GO:0018130 heterocycle biosynthetic process 220 3148 1.09e-35
GO:BP GO:0009889 regulation of biosynthetic process 220 3174 3.81e-35
GO:BP GO:1901362 organic cyclic compound biosynthetic process 221 3253 5.63e-34
GO:BP GO:0010468 regulation of gene expression 233 3583 1.42e-33
GO:BP GO:0080090 regulation of primary metabolic process 263 4440 5.67e-33
GO:BP GO:0051171 regulation of nitrogen compound metabolic process 259 4330 6.53e-33
GO:BP GO:0009059 macromolecule biosynthetic process 236 3730 2.90e-32
GO:BP GO:0006139 nucleobase-containing compound metabolic process 263 4503 7.26e-32
GO:BP GO:0060255 regulation of macromolecule metabolic process 265 4640 1.81e-30
GO:BP GO:0046483 heterocycle metabolic process 264 4616 2.15e-30
GO:BP GO:0006725 cellular aromatic compound metabolic process 264 4646 6.97e-30
GO:BP GO:0044271 cellular nitrogen compound biosynthetic process 231 3758 3.33e-29
GO:BP GO:1901360 organic cyclic compound metabolic process 266 4790 1.86e-28
GO:BP GO:0010467 gene expression 258 4572 3.44e-28
GO:BP GO:0019222 regulation of metabolic process 273 5039 7.88e-28
GO:BP GO:0034641 cellular nitrogen compound metabolic process 268 4991 3.45e-26
GO:BP GO:0044249 cellular biosynthetic process 249 4465 1.14e-25
GO:BP GO:1901576 organic substance biosynthetic process 249 4537 1.61e-24
GO:BP GO:0009058 biosynthetic process 249 4595 1.28e-23
GO:BP GO:0043170 macromolecule metabolic process 322 7057 9.57e-22
GO:BP GO:0050794 regulation of cellular process 329 7579 2.78e-18
GO:BP GO:1903508 positive regulation of nucleic acid-templated transcription 105 1304 4.26e-18
GO:BP GO:0045893 positive regulation of DNA-templated transcription 105 1304 4.26e-18
GO:BP GO:0051254 positive regulation of RNA metabolic process 111 1431 4.68e-18
GO:BP GO:1902680 positive regulation of RNA biosynthetic process 105 1311 6.07e-18
GO:BP GO:0044237 cellular metabolic process 325 7503 1.55e-17
GO:BP GO:0045935 positive regulation of nucleobase-containing compound metabolic process 116 1600 1.05e-16
GO:BP GO:0006807 nitrogen compound metabolic process 321 7474 3.03e-16
GO:BP GO:0050789 regulation of biological process 335 7992 4.68e-16
GO:BP GO:0044238 primary metabolic process 329 7800 8.56e-16
GO:BP GO:0065007 biological regulation 344 8348 8.56e-16
GO:BP GO:0010557 positive regulation of macromolecule biosynthetic process 109 1499 1.23e-15
GO:BP GO:0045892 negative regulation of DNA-templated transcription 85 1009 2.00e-15
GO:BP GO:1903507 negative regulation of nucleic acid-templated transcription 85 1011 2.21e-15
GO:BP GO:1902679 negative regulation of RNA biosynthetic process 85 1020 3.73e-15
GO:BP GO:0045934 negative regulation of nucleobase-containing compound metabolic process 94 1215 7.17e-15
GO:BP GO:0051253 negative regulation of RNA metabolic process 89 1115 8.33e-15
GO:BP GO:0045944 positive regulation of transcription by RNA polymerase II 79 925 1.42e-14
GO:BP GO:0031328 positive regulation of cellular biosynthetic process 109 1571 3.23e-14
GO:BP GO:0071704 organic substance metabolic process 334 8150 5.29e-14
GO:BP GO:0009891 positive regulation of biosynthetic process 109 1598 1.04e-13
GO:BP GO:0031324 negative regulation of cellular metabolic process 116 1780 2.57e-13
GO:BP GO:0010558 negative regulation of macromolecule biosynthetic process 90 1206 3.13e-13
GO:BP GO:0000122 negative regulation of transcription by RNA polymerase II 65 735 1.83e-12
GO:BP GO:0031325 positive regulation of cellular metabolic process 138 2373 2.39e-12
GO:BP GO:0031327 negative regulation of cellular biosynthetic process 90 1249 2.44e-12
GO:BP GO:0051173 positive regulation of nitrogen compound metabolic process 140 2425 2.46e-12
GO:BP GO:0009890 negative regulation of biosynthetic process 90 1273 7.26e-12
GO:BP GO:0010604 positive regulation of macromolecule metabolic process 147 2648 1.02e-11
GO:BP GO:0008152 metabolic process 336 8501 3.09e-11
GO:BP GO:0009892 negative regulation of metabolic process 130 2306 1.80e-10
GO:BP GO:0051172 negative regulation of nitrogen compound metabolic process 112 1866 2.11e-10
GO:BP GO:0010605 negative regulation of macromolecule metabolic process 123 2146 2.90e-10
GO:BP GO:0009893 positive regulation of metabolic process 149 2884 2.01e-09
GO:BP GO:0048523 negative regulation of cellular process 175 3628 4.49e-09
GO:BP GO:0048519 negative regulation of biological process 187 4035 2.05e-08
GO:BP GO:0006325 chromatin organization 45 536 1.13e-07
GO:BP GO:0006338 chromatin remodeling 30 309 2.71e-06
GO:BP GO:0048522 positive regulation of cellular process 177 4148 5.62e-05
GO:BP GO:0048518 positive regulation of biological process 189 4577 1.85e-04
GO:BP GO:0016570 histone modification 32 424 2.65e-04
GO:BP GO:0010452 histone H3-K36 methylation 5 12 1.16e-03
GO:BP GO:0050793 regulation of developmental process 88 1829 1.37e-03
GO:BP GO:0018022 peptidyl-lysine methylation 14 120 1.39e-03
GO:BP GO:0006354 DNA-templated transcription elongation 20 224 1.56e-03
GO:BP GO:0034968 histone lysine methylation 13 107 1.71e-03
GO:BP GO:0016571 histone methylation 15 141 2.08e-03
GO:BP GO:0018205 peptidyl-lysine modification 26 367 5.54e-03
GO:BP GO:0097676 histone H3-K36 dimethylation 3 4 6.48e-03
GO:BP GO:0006479 protein methylation 16 178 8.33e-03
GO:BP GO:0008213 protein alkylation 16 178 8.33e-03
GO:BP GO:0006974 cellular response to DNA damage stimulus 44 789 8.33e-03
GO:BP GO:0006607 NLS-bearing protein import into nucleus 5 18 9.44e-03
GO:BP GO:0060429 epithelium development 46 845 9.91e-03
GO:BP GO:0016071 mRNA metabolic process 38 657 1.11e-02
GO:BP GO:0045814 negative regulation of gene expression, epigenetic 10 84 1.47e-02
GO:BP GO:0030522 intracellular receptor signaling pathway 18 227 1.52e-02
GO:BP GO:0072359 circulatory system development 46 879 2.28e-02
GO:BP GO:0090596 sensory organ morphogenesis 15 177 2.31e-02
GO:BP GO:1903706 regulation of hemopoiesis 20 277 2.35e-02
GO:BP GO:1902105 regulation of leukocyte differentiation 16 197 2.35e-02
GO:BP GO:2000736 regulation of stem cell differentiation 9 74 2.35e-02
GO:BP GO:0040029 epigenetic regulation of gene expression 13 141 2.35e-02
GO:BP GO:0086023 adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process 3 6 2.63e-02
GO:BP GO:0031507 heterochromatin formation 9 76 2.78e-02
GO:BP GO:0007623 circadian rhythm 14 164 3.07e-02
GO:BP GO:0043009 chordate embryonic development 31 531 3.18e-02
GO:BP GO:1902275 regulation of chromatin organization 6 36 3.61e-02
GO:BP GO:0019827 stem cell population maintenance 13 150 3.98e-02
GO:BP GO:1900246 positive regulation of RIG-I signaling pathway 3 7 4.18e-02
GO:BP GO:0032242 regulation of nucleoside transport 2 2 4.18e-02
GO:BP GO:1901898 negative regulation of relaxation of cardiac muscle 2 2 4.18e-02
GO:BP GO:0032239 regulation of nucleobase-containing compound transport 4 15 4.20e-02
GO:BP GO:0098727 maintenance of cell number 13 152 4.30e-02
GO:BP GO:0009888 tissue development 65 1415 4.69e-02
GO:BP GO:0045165 cell fate commitment 13 154 4.73e-02
GO:BP GO:0070828 heterochromatin organization 9 83 4.73e-02
GO:BP GO:0048729 tissue morphogenesis 29 501 4.75e-02
GO:BP GO:0048511 rhythmic process 17 234 4.75e-02
GO:BP GO:0009792 embryo development ending in birth or egg hatching 31 548 4.75e-02
GO:BP GO:1902107 positive regulation of leukocyte differentiation 11 118 4.78e-02
GO:BP GO:1903708 positive regulation of hemopoiesis 11 118 4.78e-02
GO:BP GO:0007507 heart development 29 502 4.78e-02
GO:BP GO:2001222 regulation of neuron migration 6 39 4.82e-02
GO:BP GO:0009790 embryo development 44 871 4.82e-02
KEGG KEGG:05168 Herpes simplex virus 1 infection 45 415 6.65e-11

Time-independent Top2\(\beta\) inhibitor motif genes

GO:BP/KEGG

source term_id term_name intersection_size term_size p_value
GO:BP GO:0006357 regulation of transcription by RNA polymerase II 178 1915 4.27e-29
GO:BP GO:0006366 transcription by RNA polymerase II 180 1991 3.00e-28
GO:BP GO:0051252 regulation of RNA metabolic process 217 2849 2.60e-25
GO:BP GO:1903506 regulation of nucleic acid-templated transcription 204 2581 2.60e-25
GO:BP GO:0006355 regulation of DNA-templated transcription 204 2579 2.60e-25
GO:BP GO:2001141 regulation of RNA biosynthetic process 204 2598 4.68e-25
GO:BP GO:0097659 nucleic acid-templated transcription 206 2684 3.74e-24
GO:BP GO:0006351 DNA-templated transcription 206 2683 3.74e-24
GO:BP GO:0032774 RNA biosynthetic process 206 2714 1.52e-23
GO:BP GO:0019219 regulation of nucleobase-containing compound metabolic process 224 3105 2.64e-23
GO:BP GO:0010556 regulation of macromolecule biosynthetic process 213 3015 1.79e-20
GO:BP GO:0031326 regulation of cellular biosynthetic process 216 3123 1.09e-19
GO:BP GO:0090304 nucleic acid metabolic process 257 4047 1.14e-19
GO:BP GO:0009889 regulation of biosynthetic process 218 3174 1.29e-19
GO:BP GO:0034654 nucleobase-containing compound biosynthetic process 213 3083 2.52e-19
GO:BP GO:0010468 regulation of gene expression 235 3583 4.29e-19
GO:BP GO:0019438 aromatic compound biosynthetic process 215 3149 5.36e-19
GO:BP GO:0018130 heterocycle biosynthetic process 215 3148 5.36e-19
GO:BP GO:0016070 RNA metabolic process 235 3593 5.36e-19
GO:BP GO:1901362 organic cyclic compound biosynthetic process 217 3253 5.69e-18
GO:BP GO:0051171 regulation of nitrogen compound metabolic process 260 4330 1.50e-16
GO:BP GO:0080090 regulation of primary metabolic process 263 4440 5.17e-16
GO:BP GO:0060255 regulation of macromolecule metabolic process 271 4640 6.15e-16
GO:BP GO:0031323 regulation of cellular metabolic process 255 4305 3.04e-15
GO:BP GO:0006139 nucleobase-containing compound metabolic process 261 4503 1.65e-14
GO:BP GO:0046483 heterocycle metabolic process 264 4616 5.52e-14
GO:BP GO:0019222 regulation of metabolic process 281 5039 6.07e-14
GO:BP GO:0006725 cellular aromatic compound metabolic process 264 4646 1.27e-13
GO:BP GO:0009059 macromolecule biosynthetic process 225 3730 1.70e-13
GO:BP GO:0044271 cellular nitrogen compound biosynthetic process 225 3758 4.06e-13
GO:BP GO:0051253 negative regulation of RNA metabolic process 97 1115 7.31e-13
GO:BP GO:1901360 organic cyclic compound metabolic process 267 4790 8.90e-13
GO:BP GO:0010467 gene expression 256 4572 3.76e-12
GO:BP GO:0045892 negative regulation of DNA-templated transcription 89 1009 5.07e-12
GO:BP GO:1903507 negative regulation of nucleic acid-templated transcription 89 1011 5.53e-12
GO:BP GO:1902679 negative regulation of RNA biosynthetic process 89 1020 9.04e-12
GO:BP GO:0000122 negative regulation of transcription by RNA polymerase II 72 735 1.15e-11
GO:BP GO:0045934 negative regulation of nucleobase-containing compound metabolic process 99 1215 1.89e-11
GO:BP GO:0034641 cellular nitrogen compound metabolic process 270 4991 2.48e-11
GO:BP GO:0045944 positive regulation of transcription by RNA polymerase II 79 925 7.99e-10
GO:BP GO:0010558 negative regulation of macromolecule biosynthetic process 93 1206 2.62e-09
GO:BP GO:0031327 negative regulation of cellular biosynthetic process 95 1249 3.21e-09
GO:BP GO:0009890 negative regulation of biosynthetic process 96 1273 3.90e-09
GO:BP GO:0044249 cellular biosynthetic process 240 4465 5.35e-09
GO:BP GO:1901576 organic substance biosynthetic process 242 4537 9.24e-09
GO:BP GO:0050789 regulation of biological process 373 7992 1.06e-08
GO:BP GO:0009058 biosynthetic process 244 4595 1.10e-08
GO:BP GO:0043170 macromolecule metabolic process 339 7057 1.24e-08
GO:BP GO:0045893 positive regulation of DNA-templated transcription 95 1304 2.89e-08
GO:BP GO:1903508 positive regulation of nucleic acid-templated transcription 95 1304 2.89e-08
GO:BP GO:1902680 positive regulation of RNA biosynthetic process 95 1311 3.78e-08
GO:BP GO:0050794 regulation of cellular process 355 7579 6.74e-08
GO:BP GO:0051254 positive regulation of RNA metabolic process 99 1431 1.79e-07
GO:BP GO:0065007 biological regulation 380 8348 2.54e-07
GO:BP GO:0010557 positive regulation of macromolecule biosynthetic process 100 1499 9.63e-07
GO:BP GO:0031324 negative regulation of cellular metabolic process 113 1780 1.33e-06
GO:BP GO:0031328 positive regulation of cellular biosynthetic process 103 1571 1.33e-06
GO:BP GO:0009891 positive regulation of biosynthetic process 104 1598 1.60e-06
GO:BP GO:0045935 positive regulation of nucleobase-containing compound metabolic process 104 1600 1.68e-06
GO:BP GO:0031325 positive regulation of cellular metabolic process 139 2373 2.94e-06
GO:BP GO:0051173 positive regulation of nitrogen compound metabolic process 141 2425 3.53e-06
GO:BP GO:0010605 negative regulation of macromolecule metabolic process 127 2146 7.92e-06
GO:BP GO:0051172 negative regulation of nitrogen compound metabolic process 114 1866 8.40e-06
GO:BP GO:0010604 positive regulation of macromolecule metabolic process 149 2648 9.95e-06
GO:BP GO:0009893 positive regulation of metabolic process 159 2884 1.16e-05
GO:BP GO:0009892 negative regulation of metabolic process 133 2306 1.52e-05
GO:BP GO:0006807 nitrogen compound metabolic process 339 7474 3.21e-05
GO:BP GO:0044238 primary metabolic process 350 7800 4.85e-05
GO:BP GO:0071704 organic substance metabolic process 360 8150 1.64e-04
GO:BP GO:0003007 heart morphogenesis 23 212 4.45e-04
GO:BP GO:0044237 cellular metabolic process 334 7503 4.56e-04
GO:BP GO:0045595 regulation of cell differentiation 72 1134 7.05e-04
GO:BP GO:0048523 negative regulation of cellular process 180 3628 1.47e-03
GO:BP GO:0048645 animal organ formation 10 52 1.52e-03
GO:BP GO:0009952 anterior/posterior pattern specification 16 126 1.55e-03
GO:BP GO:0045597 positive regulation of cell differentiation 45 619 1.55e-03
GO:BP GO:0140467 integrated stress response signaling 8 34 2.11e-03
GO:BP GO:0060411 cardiac septum morphogenesis 11 67 2.67e-03
GO:BP GO:0008152 metabolic process 364 8501 5.44e-03
GO:BP GO:0060914 heart formation 7 30 6.77e-03
GO:BP GO:0007389 pattern specification process 26 305 6.79e-03
GO:BP GO:0035914 skeletal muscle cell differentiation 9 52 8.36e-03
GO:BP GO:0014706 striated muscle tissue development 20 210 9.46e-03
GO:BP GO:0051094 positive regulation of developmental process 59 958 9.56e-03
GO:BP GO:0045596 negative regulation of cell differentiation 35 478 9.88e-03
GO:BP GO:2000026 regulation of multicellular organismal development 61 1007 1.13e-02
GO:BP GO:0048738 cardiac muscle tissue development 19 198 1.19e-02
GO:BP GO:0021546 rhombomere development 3 4 1.24e-02
GO:BP GO:0048518 positive regulation of biological process 212 4577 1.37e-02
GO:BP GO:0060537 muscle tissue development 27 340 1.46e-02
GO:BP GO:0048519 negative regulation of biological process 190 4035 1.48e-02
GO:BP GO:0043009 chordate embryonic development 37 531 1.60e-02
GO:BP GO:0003002 regionalization 23 272 1.64e-02
GO:BP GO:0051726 regulation of cell cycle 57 950 2.16e-02
GO:BP GO:0001756 somitogenesis 8 48 2.22e-02
GO:BP GO:0051239 regulation of multicellular organismal process 105 2023 2.26e-02
GO:BP GO:0030336 negative regulation of cell migration 20 227 2.27e-02
GO:BP GO:0048522 positive regulation of cellular process 193 4148 2.34e-02
GO:BP GO:0002293 alpha-beta T cell differentiation involved in immune response 7 38 2.53e-02
GO:BP GO:0042093 T-helper cell differentiation 7 38 2.53e-02
GO:BP GO:0002287 alpha-beta T cell activation involved in immune response 7 38 2.53e-02
GO:BP GO:0002294 CD4-positive, alpha-beta T cell differentiation involved in immune response 7 38 2.53e-02
GO:BP GO:0035282 segmentation 10 75 2.59e-02
GO:BP GO:0009792 embryo development ending in birth or egg hatching 37 548 2.59e-02
GO:BP GO:0045598 regulation of fat cell differentiation 12 103 2.60e-02
GO:BP GO:0050793 regulation of developmental process 96 1829 2.61e-02
GO:BP GO:0048483 autonomic nervous system development 6 28 2.61e-02
GO:BP GO:1902893 regulation of miRNA transcription 8 51 2.98e-02
GO:BP GO:0007049 cell cycle 82 1522 3.18e-02
GO:BP GO:0060412 ventricular septum morphogenesis 7 40 3.20e-02
GO:BP GO:2000146 negative regulation of cell motility 20 236 3.20e-02
GO:BP GO:0002292 T cell differentiation involved in immune response 7 40 3.20e-02
GO:BP GO:0060429 epithelium development 51 845 3.20e-02
GO:BP GO:0051241 negative regulation of multicellular organismal process 46 741 3.21e-02
GO:BP GO:0061614 miRNA transcription 8 52 3.21e-02
GO:BP GO:0051093 negative regulation of developmental process 42 659 3.22e-02
GO:BP GO:0055017 cardiac muscle tissue growth 9 65 3.28e-02
GO:BP GO:0060284 regulation of cell development 39 600 3.37e-02
GO:BP GO:0048486 parasympathetic nervous system development 4 12 3.42e-02
GO:BP GO:0048729 tissue morphogenesis 34 501 3.42e-02
GO:BP GO:0045444 fat cell differentiation 17 187 3.42e-02
GO:BP GO:0007507 heart development 34 502 3.48e-02
GO:BP GO:0003151 outflow tract morphogenesis 9 66 3.50e-02
GO:BP GO:0003206 cardiac chamber morphogenesis 12 109 3.68e-02
GO:BP GO:0043954 cellular component maintenance 8 54 3.78e-02
GO:BP GO:0060562 epithelial tube morphogenesis 22 277 3.78e-02
GO:BP GO:0003197 endocardial cushion development 7 42 3.81e-02
GO:BP GO:0042127 regulation of cell population proliferation 64 1141 4.12e-02
GO:BP GO:0060840 artery development 10 82 4.25e-02
GO:BP GO:1900744 regulation of p38MAPK cascade 6 32 4.55e-02
GO:BP GO:0003281 ventricular septum development 9 69 4.55e-02
GO:BP GO:0010628 positive regulation of gene expression 47 781 4.71e-02
GO:BP GO:0040013 negative regulation of locomotion 21 265 4.78e-02
GO:BP GO:0060038 cardiac muscle cell proliferation 7 44 4.80e-02
KEGG KEGG:05168 Herpes simplex virus 1 infection 47 415 3.76e-09
KEGG KEGG:04115 p53 signaling pathway 11 65 3.17e-03
KEGG KEGG:05217 Basal cell carcinoma 9 49 5.76e-03
KEGG KEGG:05224 Breast cancer 14 117 5.91e-03
KEGG KEGG:05225 Hepatocellular carcinoma 16 145 5.91e-03
KEGG KEGG:05226 Gastric cancer 13 117 1.76e-02
KEGG KEGG:05202 Transcriptional misregulation in cancer 13 128 3.52e-02

long GO:BP frame

###long go KEGG frame

## Example of genes from each cluster

Motif_NR

[1] 72

#### Log-Fold Change of Motif_NR

lfc_nums <- readRDS("data/toplistall.RDS")
lfc_nums %>% 
  dplyr::filter(ENTREZID %in% motif_NR) %>% 
  mutate(absFC=abs(logFC)) %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  ggplot(., aes(x=id,y=absFC))+
  geom_boxplot(aes(fill=id))+
  fill_palette(palette =drug_palNoVeh)+
  guides(fill=guide_legend(title = "Treatment"))+
  facet_wrap(~time)+
  theme_bw()+
  xlab("")+
  ylab("|Log Fold Change|")+
  theme_bw()+
  ggtitle("|Log Fold| for all genes in NR set")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.line = element_line(linewidth = 1.5),
        strip.background = element_rect(fill = "#C77CFF"),
        axis.text = element_text(size = 8, color = "black", angle = 15),         strip.text.x = element_text(size = 12, color = "black", face = "bold"))+
  geom_signif(comparisons = list(c("Daunorubicin", "Doxorubicin"),
                                 c("Epirubicin", "Doxorubicin"),
                                 c("Mitoxantrone", "Doxorubicin"),
                                 c("Trastuzumab","Doxorubicin")),
              test = "t.test",
              map_signif_level = TRUE,
              step_increase = 0.1,
              textsize = 4)

Motif_TI

#### Log-Fold Change of TI response

lfc_nums %>% 
  dplyr::filter(ENTREZID %in% motif_TI) %>% 
  mutate(absFC=abs(logFC)) %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  ggplot(., aes(x=id,y=absFC))+
  geom_boxplot(aes(fill=id))+
  fill_palette(palette =drug_palNoVeh)+
  guides(fill=guide_legend(title = "Treatment"))+
  facet_wrap(~time)+
  theme_bw()+
  xlab("")+
  ylab("|Log Fold Change|")+
  theme_bw()+
  ggtitle("|Log Fold| for genes in TI response set")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.line = element_line(linewidth = 1.5),
        strip.background = element_rect(fill = "#00BFC4"),
        axis.text = element_text(size = 8, color = "black", angle = 10),         strip.text.x = element_text(size = 12, color = "black", face = "bold"))+
  geom_signif(comparisons = list(c("Daunorubicin", "Doxorubicin"),
                                 c("Epirubicin", "Doxorubicin"),
                                 c("Mitoxantrone", "Doxorubicin"),
                                 c("Trastuzumab","Doxorubicin")),
              test = "t.test",
              map_signif_level = TRUE,
              step_increase = 0.1,
              textsize = 4)

Motif_LR

#### Log-Fold Change of Late Response

lfc_nums %>% 
  dplyr::filter(ENTREZID %in% motif_LR) %>% 
  mutate(absFC=abs(logFC)) %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  ggplot(., aes(x=id,y=absFC))+
  geom_boxplot(aes(fill=id))+
  fill_palette(palette =drug_palNoVeh)+
  guides(fill=guide_legend(title = "Treatment"))+
  facet_wrap(~time)+
  theme_bw()+
  xlab("")+
  ylab("|Log Fold Change|")+
  theme_bw()+
  ggtitle("|Log Fold| for genes in LR set")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.line = element_line(linewidth = 1.5),
        strip.background = element_rect(fill = "#7CAE00"),
        axis.text = element_text(size = 8, color = "black", angle = 10),         strip.text.x = element_text(size = 12, color = "black", face = "bold"))+
  geom_signif(comparisons = list(c("Daunorubicin", "Doxorubicin"),
                                 c("Epirubicin", "Doxorubicin"),
                                 c("Mitoxantrone", "Doxorubicin"),
                                 c("Trastuzumab","Doxorubicin")),
              test = "t.test",
              map_signif_level = TRUE,
              step_increase = 0.1,
              textsize = 4)

Motif_ER

#### Log-Fold Change of Early Response

lfc_nums %>% 
  dplyr::filter(ENTREZID %in% motif_ER) %>% 
  mutate(absFC=abs(logFC)) %>% 
  mutate(id = as.factor(id)) %>%
  mutate(time=factor(time, levels=c("3_hours","24_hours"))) %>%
  ggplot(., aes(x=id,y=absFC))+
  geom_boxplot(aes(fill=id))+
  fill_palette(palette =drug_palNoVeh)+
  guides(fill=guide_legend(title = "Treatment"))+
  facet_wrap(~time)+
  theme_bw()+
  xlab("")+
  ylab("|Log Fold Change|")+
  theme_bw()+
  ggtitle("|Log Fold| for genes in ER set")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.line = element_line(linewidth = 1.5),
        strip.background = element_rect(fill = "#F8766D"),
        axis.text = element_text(size = 8, color = "black", angle = 10),         strip.text.x = element_text(size = 12, color = "black", face = "bold"))+
  geom_signif(comparisons = list(c("Daunorubicin", "Doxorubicin"),
                                 c("Epirubicin", "Doxorubicin"),
                                 c("Mitoxantrone", "Doxorubicin"),
                                 c("Trastuzumab","Doxorubicin")),
              test = "t.test",
              map_signif_level = TRUE,
              step_increase = 0.1,
              textsize = 4)


sessionInfo()
R version 4.2.2 (2022-10-31 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    

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

other attached packages:
 [1] biomaRt_2.52.0      ggpubr_0.6.0        RColorBrewer_1.1-3 
 [4] Cormotif_1.42.0     limma_3.52.4        affy_1.74.0        
 [7] Biobase_2.56.0      ggVennDiagram_1.2.2 scales_1.2.1       
[10] kableExtra_1.3.4    VennDiagram_1.7.3   futile.logger_1.4.3
[13] gridExtra_2.3       BiocGenerics_0.42.0 gprofiler2_0.2.1   
[16] lubridate_1.9.2     forcats_1.0.0       stringr_1.5.0      
[19] dplyr_1.1.0         purrr_1.0.1         readr_2.1.4        
[22] tidyr_1.3.0         tibble_3.1.8        ggplot2_3.4.1      
[25] tidyverse_2.0.0     workflowr_1.7.0    

loaded via a namespace (and not attached):
  [1] colorspace_2.1-0       ggsignif_0.6.4         ellipsis_0.3.2        
  [4] rprojroot_2.0.3        XVector_0.36.0         fs_1.6.1              
  [7] rstudioapi_0.14        farver_2.1.1           affyio_1.66.0         
 [10] bit64_4.0.5            AnnotationDbi_1.58.0   fansi_1.0.4           
 [13] xml2_1.3.3             cachem_1.0.7           knitr_1.42            
 [16] jsonlite_1.8.4         broom_1.0.3            dbplyr_2.3.1          
 [19] png_0.1-8              shiny_1.7.4            BiocManager_1.30.20   
 [22] compiler_4.2.2         httr_1.4.5             backports_1.4.1       
 [25] fastmap_1.1.1          lazyeval_0.2.2         cli_3.6.0             
 [28] later_1.3.0            formatR_1.14           prettyunits_1.1.1     
 [31] htmltools_0.5.4        tools_4.2.2            GenomeInfoDbData_1.2.8
 [34] gtable_0.3.1           glue_1.6.2             rappdirs_0.3.3        
 [37] Rcpp_1.0.10            carData_3.0-5          jquerylib_0.1.4       
 [40] Biostrings_2.64.1      vctrs_0.5.2            svglite_2.1.1         
 [43] preprocessCore_1.58.0  crosstalk_1.2.0        xfun_0.37             
 [46] ps_1.7.2               rvest_1.0.3            timechange_0.2.0      
 [49] mime_0.12              lifecycle_1.0.3        rstatix_0.7.2         
 [52] XML_3.99-0.13          getPass_0.2-2          zlibbioc_1.42.0       
 [55] hms_1.1.2              promises_1.2.0.1       lambda.r_1.2.4        
 [58] curl_5.0.0             yaml_2.3.7             memoise_2.0.1         
 [61] sass_0.4.5             stringi_1.7.12         RSQLite_2.3.0         
 [64] highr_0.10             S4Vectors_0.34.0       filelock_1.0.2        
 [67] GenomeInfoDb_1.32.4    bitops_1.0-7           rlang_1.0.6           
 [70] pkgconfig_2.0.3        systemfonts_1.0.4      evaluate_0.20         
 [73] htmlwidgets_1.6.1      labeling_0.4.2         bit_4.0.5             
 [76] processx_3.8.0         tidyselect_1.2.0       magrittr_2.0.3        
 [79] R6_2.5.1               IRanges_2.30.1         generics_0.1.3        
 [82] DBI_1.1.3              pillar_1.8.1           whisker_0.4.1         
 [85] withr_2.5.0            RCurl_1.98-1.10        KEGGREST_1.36.3       
 [88] abind_1.4-5            crayon_1.5.2           car_3.1-1             
 [91] futile.options_1.0.1   utf8_1.2.3             BiocFileCache_2.4.0   
 [94] plotly_4.10.1          RVenn_1.1.0            tzdb_0.3.0            
 [97] rmarkdown_2.20         progress_1.2.2         data.table_1.14.8     
[100] blob_1.2.3             callr_3.7.3            git2r_0.31.0          
[103] digest_0.6.31          webshot_0.5.4          xtable_1.8-4          
[106] httpuv_1.6.9           stats4_4.2.2           munsell_0.5.0         
[109] viridisLite_0.4.1      bslib_0.4.2