Cormotifcluster_analysis
ERM
2023-06-02
Last updated: 2023-06-02
Checks: 7 0
Knit directory: Cardiotoxicity/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2aca0d8 | reneeisnowhere | 2023-06-02 | adding in LFC plot to show magnitude of effect |
| Rmd | 2be1117 | reneeisnowhere | 2023-05-31 | updating pie charts and lfc to remove significance test |
| html | 4393a05 | reneeisnowhere | 2023-05-26 | Build site. |
| Rmd | ac69e6e | reneeisnowhere | 2023-05-26 | adding abs LFC of motifs |
| Rmd | f3871a5 | reneeisnowhere | 2023-05-26 | updates |
| html | 71f4c17 | reneeisnowhere | 2023-05-25 | Build site. |
| Rmd | 43b7b74 | reneeisnowhere | 2023-05-25 | update pie chart with ggplot |
| Rmd | e8c82ec | reneeisnowhere | 2023-05-18 | adding other_analysis and genes of interest log2cpm |
| html | 0835f9c | reneeisnowhere | 2023-05-17 | Build site. |
| Rmd | 4edac57 | reneeisnowhere | 2023-05-17 | adding piechart and barchart |
| html | f0bbc78 | reneeisnowhere | 2023-04-19 | Build site. |
| Rmd | 5ce3414 | reneeisnowhere | 2023-04-19 | updated Cormotif |
| html | f4a33f1 | reneeisnowhere | 2023-04-19 | Build site. |
| Rmd | b117da5 | reneeisnowhere | 2023-04-19 | updated Cormotif |
| html | 22246d9 | reneeisnowhere | 2023-04-18 | Build site. |
| Rmd | 6f6aaf4 | reneeisnowhere | 2023-04-18 | new Cormotif analysis with codes |
| html | d0f459b | reneeisnowhere | 2023-04-18 | Build site. |
| Rmd | 67b2a09 | reneeisnowhere | 2023-04-18 | new Cormotif analysis with codes |
| Rmd | a64bbe1 | reneeisnowhere | 2023-04-18 | updated with new cormotif method |
| html | 9e37491 | reneeisnowhere | 2023-04-16 | Build site. |
| Rmd | 6d925a2 | reneeisnowhere | 2023-04-16 | updating cormotif with updated RNAseq counts |
| Rmd | 4e52216 | reneeisnowhere | 2023-03-31 | End of week updates |
| 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$ENTREZID,(union(clust1,union(clust2,union(clust3,clust4))))))
##63 genes not used overall same as (14084-7504-528-444-5545)Pie Chart of overall numbers
#make data frame
Set <- c("Early Response", "Time-Independent Response","Late Response", "No Response")
gene_num <- c(487,589,5596,7409)
fills <- c("#F8766D", "#00BFC4","#7CAE00", "#C77CFF")
pie_chartdata <- data.frame(Set, gene_num, fills)
pie(gene_num,labels =Set ) 
##label computation
pie_chartdata <- pie_chartdata %>%
mutate(prop = gene_num / sum(pie_chartdata$gene_num) *100) %>%
mutate(ypos = (prop)+ 0.5*prop )
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))) ## GO and KEGG of each set
DEG_cormotif <- readRDS("data/DEG_cormotif.RDS")
list2env(DEG_cormotif,envir=.GlobalEnv)<environment: R_GlobalEnv># 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
| 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
| 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
| 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"))
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"))
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"))
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"))
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