GO and KEGG pathway analysis

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Last updated: 2024-08-05

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Knit directory: ATAC_learning/

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    Modified:   analysis/TSS_ATAC_MRC_DAR_FC_RNA.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/GO_KEGG_analysis.Rmd) and HTML (docs/GO_KEGG_analysis.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	5193b51	reneeisnowhere	2024-08-05	updates to barcharts
html	1933f92	reneeisnowhere	2024-08-02	Build site.
Rmd	50cc96f	reneeisnowhere	2024-08-02	updates using new guidelines
Rmd	5d54017	reneeisnowhere	2024-06-12	adding commit
html	bd33175	reneeisnowhere	2024-06-07	Build site.
Rmd	b5e8a1e	reneeisnowhere	2024-06-07	updates and new analysis
html	021ca5f	reneeisnowhere	2024-06-07	Build site.
Rmd	95e0415	reneeisnowhere	2024-06-07	updates, i think
html	eea0976	reneeisnowhere	2024-06-03	Build site.
Rmd	0672654	reneeisnowhere	2024-06-03	updates to gene lists
html	897af23	reneeisnowhere	2024-05-28	Build site.
Rmd	5c6ef83	reneeisnowhere	2024-05-28	updates to KEGG/GO 20kb lists
html	d1a3829	reneeisnowhere	2024-05-17	Build site.
Rmd	9fb4f9a	reneeisnowhere	2024-05-17	adding in updates from Neargenes and enhncers
html	2d991d7	reneeisnowhere	2024-05-03	Build site.
Rmd	f57f2ee	reneeisnowhere	2024-05-03	first update

---

library(tidyverse)
library(kableExtra)
library(broom)
library(RColorBrewer)
library(gprofiler2)
library(ChIPseeker)
library("TxDb.Hsapiens.UCSC.hg38.knownGene")
library("org.Hs.eg.db")
library(rtracklayer)
library(edgeR)
library(ggfortify)
library(limma)
library(readr)
library(BiocGenerics)
library(gridExtra)
library(VennDiagram)
library(scales)
library(ggVennDiagram)
library(BiocParallel)
library(ggpubr)
library(biomaRt)

data loading

peakAnnoList_n45_motif <- readRDS("data/peakAnnoList_n45_motif.RDS")
# list2env(peakAnnoList_n45_motif, envir = .GlobalEnv)
fills <- c("#C77CFF","#F8766D","#7CAE00",  "#00BFC4" )

EAR_df <- as.data.frame(peakAnnoList_n45_motif$EAR_n45_gr)
ESR_df <- as.data.frame(peakAnnoList_n45_motif$ESR_n45_gr)
LR_df <- as.data.frame(peakAnnoList_n45_motif$LR_n45_gr)
NR_df <- as.data.frame(peakAnnoList_n45_motif$NR_n45_gr)

toplist_ATAC <- readRDS("data/toplist_n45.RDS")

DOX24h_peaks_hypo_list  <- toplist_ATAC %>% 
  dplyr::filter(trt=="DOX" & time=="24 hours" & logFC<0) %>% 
  dplyr::select(trt:logFC)

DOX24h_peaks_hyper_list <- toplist_ATAC %>% 
  dplyr::filter(trt=="DOX" & time=="24 hours" & logFC>0) %>% 
  dplyr::select(trt:logFC)

DOX3h_peaks_hypo_list  <- toplist_ATAC %>% 
  dplyr::filter(trt=="DOX" & time=="3 hours" & logFC<0) %>% 
  dplyr::select(trt:logFC)

DOX3h_peaks_hyper_list <- toplist_ATAC %>% 
  dplyr::filter(trt=="DOX" & time=="3 hours" & logFC>0) %>% 
  dplyr::select(trt:logFC)

# exp_neargene_table <- read_delim("data/n45_bedfiles/exp_neargene_table.tsv", 
#     delim = "\t", escape_double = FALSE, 
#     trim_ws = TRUE)
background_genes <- read.csv("data/other_papers/backgroundRNAlist.csv", row.names = 1)


TSS_NG_data <- read_delim("data/n45_bedfiles/TSS_NG_data.tsv", 
    delim = "\t", escape_double = FALSE, 
    trim_ws = TRUE)
Collapsed_peaks <- read_delim("data/n45_bedfiles/TSS_NG_data_collapsed_peaks.tsv",
                              delim = "\t", 
                              escape_double = FALSE, 
                              trim_ws = TRUE)

EAR_NG_3hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% EAR_df$id) %>%
  dplyr::filter(peakid %in% DOX3h_peaks_hyper_list$peak) %>% 
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
  dplyr::select(entrezgene_id) %>% 
  distinct()

ESR_NG_3hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% ESR_df$id) %>%
   dplyr::filter(peakid %in% DOX3h_peaks_hyper_list$peak) %>% 
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

LR_NG_3hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% LR_df$id) %>%
   dplyr::filter(peakid %in% DOX3h_peaks_hyper_list$peak) %>% 
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

NR_NG_3hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% NR_df$id) %>%
   dplyr::filter(peakid %in% DOX3h_peaks_hyper_list$peak) %>% 
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

EAR_NG_24hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% EAR_df$id) %>%
   dplyr::filter(peakid %in% DOX24h_peaks_hyper_list$peak) %>% 
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
  dplyr::select(entrezgene_id) %>% 
  distinct()

ESR_NG_24hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% ESR_df$id) %>%
  dplyr::filter(peakid %in% DOX24h_peaks_hyper_list$peak) %>%
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

LR_NG_24hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% LR_df$id) %>%
  dplyr::filter(peakid %in% DOX24h_peaks_hyper_list$peak) %>%
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

NR_NG_24hhyper <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% NR_df$id) %>%
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()
EAR_NG_3hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% EAR_df$id) %>%
  dplyr::filter(peakid %in% DOX3h_peaks_hypo_list$peak) %>% 
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
  dplyr::select(entrezgene_id) %>% 
  distinct()

ESR_NG_3hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% ESR_df$id) %>%
   dplyr::filter(peakid %in% DOX3h_peaks_hypo_list$peak) %>% 
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

LR_NG_3hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% LR_df$id) %>%
   dplyr::filter(peakid %in% DOX3h_peaks_hypo_list$peak) %>% 
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

NR_NG_3hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% NR_df$id) %>%
   dplyr::filter(peakid %in% DOX3h_peaks_hypo_list$peak) %>% 
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

EAR_NG_24hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% EAR_df$id) %>%
   dplyr::filter(peakid %in% DOX24h_peaks_hypo_list$peak) %>% 
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
  dplyr::select(entrezgene_id) %>% 
  distinct()

ESR_NG_24hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% ESR_df$id) %>%
  dplyr::filter(peakid %in% DOX24h_peaks_hypo_list$peak) %>%
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

LR_NG_24hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% LR_df$id) %>%
  dplyr::filter(peakid %in% DOX24h_peaks_hypo_list$peak) %>%
  dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

NR_NG_24hhypo <- TSS_NG_data %>% 
    dplyr::filter(peakid %in% NR_df$id) %>%
  dplyr::filter(peakid %in% DOX24h_peaks_hypo_list$peak) %>%
 dplyr::filter(dist_to_NG<20000 & dist_to_NG>-20000) %>% 
 dplyr::select(entrezgene_id) %>% 
  distinct()

Introduction

This is an updated page of GO/KEGG analysis based on previous analysis (link pending). To get this analysis, I took the peaks from my data, assigned them to the nearest RNA expressed gene, then I used my Doxorubicin ATAC peak log fold change(LFC) data at 3 hours and 24 hours to create lists of hyper-accessible peaks (LFC >0) and hypo-accessible peaks (LFC<0) for enrichment testing. Additionally, most peaks fall within multiple response clusters (MRCs) using the Cormotif package. This created lists of EAR-hyper, EAR-hypo, ESR-hyper,ESR-hypo, LR-hyper, LR-hypo, and NR-hyper, NR-hypo peaks at 3 and 24 hours (a total of 16 groups). Enrichment testing was done using the neargenes assigned to each of the MRC hypo and hyper clusters, using the full list of RNA expressed genes (14,084) as the background. This page is broken up into the following sections:
1. Hyper and Hypo MRC response for 3 and 24 hours 2. Hyper and Hypo MRC response within 20kb of neargene 3 and 24 hours 3. Bargraphs of top KEGG/GO terms

EAR response genes

Hyper/hypo-3hr

EAR3h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/EAR_3h_hyper_resgenes.RDS")
EAR3h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/EAR_3h_hypo_resgenes.RDS")
# EAR_3h_hyper_resgenes <- gost(query = EAR_NG_3hhyper$entrezgene_id,
#                     organism = "hsapiens",
#                     significant = FALSE,
#                     ordered_query = FALSE,
#                     domain_scope = "custom",
#                     measure_underrepresentation = FALSE,
#                     evcodes = FALSE,
#                     user_threshold = 0.05,
#                     correction_method = c("fdr"),
#                     custom_bg = background_genes$ENTREZID,
#                     sources=c("GO:BP","KEGG"))
# saveRDS(NR_EAh_hyper_resgenes,"data/GO_KEGG_analysis/final_analysis/EAR_3h_hyper_resgenes.RDS")

EAR3h_hyper_nomtable <-  EAR3h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
EAR3h_hypo_nomtable <-  EAR3h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

EAR3h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in EAR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in EAR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

EAR3h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in EAR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in EAR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

EAR3h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in EAR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in EAR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0072359	circulatory system development	92	896	9.26e-04
GO:BP	GO:0009653	anatomical structure morphogenesis	159	1951	4.40e-02
GO:BP	GO:0007507	heart development	54	515	4.49e-02
GO:BP	GO:0050896	response to stimulus	397	5732	4.49e-02
GO:BP	GO:0048513	animal organ development	169	2130	4.49e-02
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	81	876	4.73e-02

EAR3h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in EAR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in EAR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

Hyper/hypo-24hr

EAR24h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/EAR_24h_hyper_resgenes.RDS")
EAR24h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/EAR_24h_hypo_resgenes.RDS")

EAR24h_hyper_nomtable <-  EAR24h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
EAR24h_hypo_nomtable <-  EAR24h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

EAR24h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr EAR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr EAR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

EAR24h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr EAR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr EAR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

EAR24h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr EAR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr EAR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

EAR24h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr EAR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr EAR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

ESR response genes

Hyper/hypo-3hr

ESR3h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/ESR_3h_hyper_resgenes.RDS")
ESR3h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/ESR_3h_hypo_resgenes.RDS")

ESR3h_hyper_nomtable <-  ESR3h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
ESR3h_hypo_nomtable <-  ESR3h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

ESR3h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in ESR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in ESR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0051716	cellular response to stimulus	627	4933	2.28e-03
GO:BP	GO:0048522	positive regulation of cellular process	543	4198	2.28e-03
GO:BP	GO:0007165	signal transduction	503	3846	2.28e-03
GO:BP	GO:0023051	regulation of signaling	352	2597	2.40e-03
GO:BP	GO:0023052	signaling	538	4180	2.40e-03
GO:BP	GO:0009888	tissue development	210	1425	2.40e-03
GO:BP	GO:0048856	anatomical structure development	532	4130	2.40e-03
GO:BP	GO:0048518	positive regulation of biological process	580	4561	2.40e-03
GO:BP	GO:0007154	cell communication	545	4248	2.40e-03
GO:BP	GO:0050896	response to stimulus	713	5732	2.40e-03
GO:BP	GO:0009966	regulation of signal transduction	317	2307	2.44e-03
GO:BP	GO:0048568	embryonic organ development	62	317	2.68e-03
GO:BP	GO:2000026	regulation of multicellular organismal development	156	1011	2.69e-03
GO:BP	GO:0010646	regulation of cell communication	351	2601	2.70e-03
GO:BP	GO:0009893	positive regulation of metabolic process	372	2780	2.70e-03
GO:BP	GO:0048598	embryonic morphogenesis	79	440	3.18e-03
GO:BP	GO:0008150	biological_process	1371	12051	4.28e-03
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	343	2555	4.28e-03
GO:BP	GO:0009790	embryo development	135	864	4.28e-03
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	314	2311	4.28e-03
GO:BP	GO:0009891	positive regulation of biosynthetic process	273	1974	4.55e-03
GO:BP	GO:0043009	chordate embryonic development	90	529	4.60e-03
GO:BP	GO:0009653	anatomical structure morphogenesis	270	1951	4.60e-03
GO:BP	GO:0050794	regulation of cellular process	916	7651	4.60e-03
GO:BP	GO:0031325	positive regulation of cellular metabolic process	332	2474	4.66e-03
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	92	545	4.66e-03
GO:BP	GO:0032501	multicellular organismal process	604	4830	4.66e-03
GO:BP	GO:0032502	developmental process	563	4475	5.37e-03
GO:BP	GO:0051254	positive regulation of RNA metabolic process	205	1430	5.37e-03
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	189	1301	5.37e-03
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	189	1304	5.70e-03
GO:BP	GO:0048583	regulation of response to stimulus	381	2902	5.70e-03
GO:BP	GO:0042472	inner ear morphogenesis	19	62	5.70e-03
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	269	1959	5.70e-03
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	261	1900	6.64e-03
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	134	876	6.64e-03
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	24	91	6.64e-03
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	105	653	6.64e-03
GO:BP	GO:0060038	cardiac muscle cell proliferation	15	43	6.64e-03
GO:BP	GO:0050793	regulation of developmental process	249	1801	6.64e-03
GO:BP	GO:0009987	cellular process	1309	11450	6.67e-03
GO:BP	GO:0060485	mesenchyme development	50	256	6.68e-03
GO:BP	GO:0060429	epithelium development	128	836	8.55e-03
GO:BP	GO:0042471	ear morphogenesis	21	76	8.55e-03
GO:BP	GO:0055017	cardiac muscle tissue growth	19	65	8.55e-03
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	23	88	9.60e-03
GO:BP	GO:0030154	cell differentiation	387	2987	1.09e-02
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	116	749	1.09e-02
GO:BP	GO:0110110	positive regulation of animal organ morphogenesis	11	27	1.09e-02
GO:BP	GO:0060419	heart growth	20	72	1.09e-02
GO:BP	GO:0048869	cellular developmental process	387	2988	1.10e-02
GO:BP	GO:0071345	cellular response to cytokine stimulus	90	554	1.24e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	39	190	1.24e-02
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	50	265	1.31e-02
GO:BP	GO:0035556	intracellular signal transduction	279	2079	1.33e-02
GO:BP	GO:0048513	animal organ development	285	2130	1.34e-02
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	44	225	1.38e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	257	1900	1.51e-02
GO:BP	GO:1902531	regulation of intracellular signal transduction	193	1376	1.76e-02
GO:BP	GO:0044344	cellular response to fibroblast growth factor stimulus	21	82	2.10e-02
GO:BP	GO:0030855	epithelial cell differentiation	75	452	2.12e-02
GO:BP	GO:0042221	response to chemical	319	2436	2.18e-02
GO:BP	GO:0055023	positive regulation of cardiac muscle tissue growth	10	25	2.18e-02
GO:BP	GO:0033002	muscle cell proliferation	33	157	2.18e-02
GO:BP	GO:0008543	fibroblast growth factor receptor signaling pathway	17	60	2.18e-02
GO:BP	GO:0065007	biological regulation	972	8275	2.20e-02
GO:BP	GO:0061061	muscle structure development	89	559	2.20e-02
GO:BP	GO:0048863	stem cell differentiation	39	198	2.41e-02
GO:BP	GO:0055021	regulation of cardiac muscle tissue growth	14	45	2.56e-02
GO:BP	GO:0007275	multicellular organism development	428	3383	2.56e-02
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	218	1597	2.65e-02
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	148	1027	2.74e-02
GO:BP	GO:0050789	regulation of biological process	945	8037	2.74e-02
GO:BP	GO:0003209	cardiac atrium morphogenesis	10	26	2.77e-02
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	149	1036	2.78e-02
GO:BP	GO:0141124	intracellular signaling cassette	194	1403	2.88e-02
GO:BP	GO:0023057	negative regulation of signaling	158	1111	2.94e-02
GO:BP	GO:0060043	regulation of cardiac muscle cell proliferation	11	31	2.94e-02
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	113	752	2.94e-02
GO:BP	GO:0034097	response to cytokine	96	621	3.05e-02
GO:BP	GO:0048762	mesenchymal cell differentiation	40	209	3.13e-02
GO:BP	GO:0071774	response to fibroblast growth factor	21	86	3.13e-02
GO:BP	GO:0070848	response to growth factor	90	576	3.14e-02
GO:BP	GO:0010954	positive regulation of protein processing	8	18	3.21e-02
GO:BP	GO:0071363	cellular response to growth factor stimulus	87	554	3.24e-02
GO:BP	GO:0001837	epithelial to mesenchymal transition	30	143	3.29e-02
GO:BP	GO:0010648	negative regulation of cell communication	157	1109	3.35e-02
GO:BP	GO:0071310	cellular response to organic substance	189	1370	3.35e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	247	1852	3.35e-02
GO:BP	GO:0048584	positive regulation of response to stimulus	217	1601	3.35e-02
GO:BP	GO:0002009	morphogenesis of an epithelium	65	391	3.54e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	96	626	3.54e-02
GO:BP	GO:0051240	positive regulation of multicellular organismal process	157	1111	3.54e-02
GO:BP	GO:0035265	organ growth	28	132	3.87e-02
GO:BP	GO:0014855	striated muscle cell proliferation	16	59	3.94e-02
GO:BP	GO:0010033	response to organic substance	244	1835	4.06e-02
GO:BP	GO:0060421	positive regulation of heart growth	10	28	4.25e-02
GO:BP	GO:0030510	regulation of BMP signaling pathway	20	83	4.26e-02
GO:BP	GO:1903319	positive regulation of protein maturation	8	19	4.26e-02
GO:BP	GO:0042476	odontogenesis	20	83	4.26e-02
GO:BP	GO:0090596	sensory organ morphogenesis	35	180	4.32e-02
GO:BP	GO:0009887	animal organ morphogenesis	106	710	4.36e-02
GO:BP	GO:0090103	cochlea morphogenesis	7	15	4.37e-02
GO:BP	GO:0006351	DNA-templated transcription	343	2683	4.44e-02
GO:BP	GO:0010718	positive regulation of epithelial to mesenchymal transition	14	49	4.49e-02
GO:BP	GO:0071495	cellular response to endogenous stimulus	153	1088	4.57e-02
GO:BP	GO:0051094	positive regulation of developmental process	138	967	4.60e-02
GO:BP	GO:0006355	regulation of DNA-templated transcription	330	2576	4.79e-02
GO:BP	GO:1904117	cellular response to vasopressin	4	5	4.79e-02
GO:BP	GO:0072282	metanephric nephron tubule morphogenesis	4	5	4.79e-02
GO:BP	GO:0042475	odontogenesis of dentin-containing tooth	15	55	4.79e-02
GO:BP	GO:1904116	response to vasopressin	4	5	4.79e-02
GO:BP	GO:0080090	regulation of primary metabolic process	524	4269	4.79e-02

ESR3h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in ESR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in ESR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

ESR3h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in ESR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in ESR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0032501	multicellular organismal process	840	4830	4.23e-09
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	201	876	1.08e-08
GO:BP	GO:0048856	anatomical structure development	717	4130	5.65e-07
GO:BP	GO:0009653	anatomical structure morphogenesis	373	1951	1.16e-06
GO:BP	GO:0007275	multicellular organism development	598	3383	1.57e-06
GO:BP	GO:0048869	cellular developmental process	534	2988	2.79e-06
GO:BP	GO:0030154	cell differentiation	534	2987	2.79e-06
GO:BP	GO:0023052	signaling	715	4180	4.49e-06
GO:BP	GO:0007154	cell communication	723	4248	7.14e-06
GO:BP	GO:0050896	response to stimulus	944	5732	7.14e-06
GO:BP	GO:0048731	system development	515	2903	1.22e-05
GO:BP	GO:0007165	signal transduction	659	3846	1.52e-05
GO:BP	GO:0051239	regulation of multicellular organismal process	379	2052	1.89e-05
GO:BP	GO:0032502	developmental process	750	4475	4.00e-05
GO:BP	GO:0051716	cellular response to stimulus	812	4933	2.01e-04
GO:BP	GO:0006937	regulation of muscle contraction	41	129	2.32e-04
GO:BP	GO:0009888	tissue development	269	1425	3.66e-04
GO:BP	GO:0048468	cell development	360	1999	5.13e-04
GO:BP	GO:0086036	regulation of cardiac muscle cell membrane potential	7	7	6.17e-04
GO:BP	GO:0065008	regulation of biological quality	365	2039	7.06e-04
GO:BP	GO:0044057	regulation of system process	92	399	9.16e-04
GO:BP	GO:0048513	animal organ development	376	2130	1.78e-03
GO:BP	GO:1903522	regulation of blood circulation	53	200	1.99e-03
GO:BP	GO:0008285	negative regulation of cell population proliferation	110	508	1.99e-03
GO:BP	GO:0030029	actin filament-based process	139	677	2.30e-03
GO:BP	GO:0072359	circulatory system development	176	896	2.30e-03
GO:BP	GO:0035295	tube development	163	827	3.81e-03
GO:BP	GO:0045321	leukocyte activation	118	563	3.81e-03
GO:BP	GO:0060047	heart contraction	52	200	3.81e-03
GO:BP	GO:0022008	neurogenesis	245	1327	3.81e-03
GO:BP	GO:0001775	cell activation	135	665	4.61e-03
GO:BP	GO:0051240	positive regulation of multicellular organismal process	209	1111	4.81e-03
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	128	625	4.81e-03
GO:BP	GO:0006810	transport	530	3176	7.64e-03
GO:BP	GO:0009790	embryo development	167	864	7.64e-03
GO:BP	GO:0090257	regulation of muscle system process	47	181	7.75e-03
GO:BP	GO:0030001	metal ion transport	114	554	9.67e-03
GO:BP	GO:0030036	actin cytoskeleton organization	122	601	9.67e-03
GO:BP	GO:0003015	heart process	52	210	1.12e-02
GO:BP	GO:0050793	regulation of developmental process	316	1801	1.12e-02
GO:BP	GO:0010959	regulation of metal ion transport	60	254	1.27e-02
GO:BP	GO:0008016	regulation of heart contraction	44	170	1.27e-02
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	25	78	1.29e-02
GO:BP	GO:0001838	embryonic epithelial tube formation	32	111	1.35e-02
GO:BP	GO:0006936	muscle contraction	62	267	1.45e-02
GO:BP	GO:0035239	tube morphogenesis	132	668	1.45e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	330	1900	1.45e-02
GO:BP	GO:0006942	regulation of striated muscle contraction	26	84	1.61e-02
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	129	653	1.62e-02
GO:BP	GO:0042127	regulation of cell population proliferation	210	1146	1.62e-02
GO:BP	GO:0051241	negative regulation of multicellular organismal process	146	756	1.73e-02
GO:BP	GO:0050789	regulation of biological process	1236	8037	1.92e-02
GO:BP	GO:0003008	system process	218	1201	1.99e-02
GO:BP	GO:0021915	neural tube development	37	139	2.00e-02
GO:BP	GO:0035556	intracellular signal transduction	356	2079	2.01e-02
GO:BP	GO:2000026	regulation of multicellular organismal development	187	1011	2.13e-02
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	144	749	2.15e-02
GO:BP	GO:0006811	monoatomic ion transport	147	769	2.37e-02
GO:BP	GO:0060048	cardiac muscle contraction	33	121	2.44e-02
GO:BP	GO:0001843	neural tube closure	26	87	2.44e-02
GO:BP	GO:0141124	intracellular signaling cassette	249	1403	2.44e-02
GO:BP	GO:0048514	blood vessel morphogenesis	96	467	2.44e-02
GO:BP	GO:0001944	vasculature development	114	573	2.44e-02
GO:BP	GO:0007155	cell adhesion	185	1004	2.49e-02
GO:BP	GO:0051146	striated muscle cell differentiation	56	242	2.52e-02
GO:BP	GO:0090184	positive regulation of kidney development	6	8	2.65e-02
GO:BP	GO:0031032	actomyosin structure organization	46	189	2.65e-02
GO:BP	GO:0060606	tube closure	26	88	2.65e-02
GO:BP	GO:0050878	regulation of body fluid levels	56	243	2.66e-02
GO:BP	GO:0014733	regulation of skeletal muscle adaptation	7	11	2.82e-02
GO:BP	GO:0014902	myotube differentiation	26	89	2.82e-02
GO:BP	GO:0051924	regulation of calcium ion transport	40	159	2.82e-02
GO:BP	GO:0016477	cell migration	196	1078	2.82e-02
GO:BP	GO:0031175	neuron projection development	150	794	2.82e-02
GO:BP	GO:0008283	cell population proliferation	245	1386	2.82e-02
GO:BP	GO:0048699	generation of neurons	207	1145	2.82e-02
GO:BP	GO:0048729	tissue morphogenesis	97	478	2.82e-02
GO:BP	GO:0071501	cellular response to sterol depletion	8	14	2.82e-02
GO:BP	GO:0061061	muscle structure development	111	559	2.82e-02
GO:BP	GO:0032933	SREBP signaling pathway	8	14	2.82e-02
GO:BP	GO:0001525	angiogenesis	83	397	2.83e-02
GO:BP	GO:0048666	neuron development	166	894	2.87e-02
GO:BP	GO:0051234	establishment of localization	561	3447	2.88e-02
GO:BP	GO:0007622	rhythmic behavior	13	32	2.89e-02
GO:BP	GO:0016043	cellular component organization	812	5139	2.93e-02
GO:BP	GO:0065007	biological regulation	1265	8275	2.93e-02
GO:BP	GO:0043269	regulation of monoatomic ion transport	66	302	3.08e-02
GO:BP	GO:0007399	nervous system development	325	1903	3.18e-02
GO:BP	GO:0001568	blood vessel development	108	546	3.18e-02
GO:BP	GO:0030239	myofibril assembly	21	67	3.22e-02
GO:BP	GO:0045595	regulation of cell differentiation	204	1134	3.22e-02
GO:BP	GO:0050900	leukocyte migration	49	209	3.22e-02
GO:BP	GO:0051094	positive regulation of developmental process	177	967	3.34e-02
GO:BP	GO:0014020	primary neural tube formation	26	91	3.44e-02
GO:BP	GO:0030182	neuron differentiation	195	1080	3.44e-02
GO:BP	GO:0035148	tube formation	34	131	3.44e-02
GO:BP	GO:0001841	neural tube formation	27	96	3.44e-02
GO:BP	GO:0007267	cell-cell signaling	207	1156	3.50e-02
GO:BP	GO:0055117	regulation of cardiac muscle contraction	21	68	3.71e-02
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	218	1227	3.71e-02
GO:BP	GO:0008015	blood circulation	78	374	3.71e-02
GO:BP	GO:0048870	cell motility	212	1190	3.81e-02
GO:BP	GO:0006941	striated muscle contraction	38	153	3.88e-02
GO:BP	GO:0072175	epithelial tube formation	32	122	3.88e-02
GO:BP	GO:0043217	myelin maintenance	8	15	3.99e-02
GO:BP	GO:0045453	bone resorption	15	42	4.06e-02
GO:BP	GO:0042221	response to chemical	405	2436	4.06e-02
GO:BP	GO:0030030	cell projection organization	223	1262	4.06e-02
GO:BP	GO:0014888	striated muscle adaptation	15	42	4.06e-02
GO:BP	GO:0048598	embryonic morphogenesis	89	440	4.06e-02
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	33	128	4.14e-02
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	31	118	4.23e-02
GO:BP	GO:0048512	circadian behavior	12	30	4.35e-02
GO:BP	GO:0009987	cellular process	1703	11450	4.35e-02
GO:BP	GO:0051049	regulation of transport	207	1164	4.35e-02
GO:BP	GO:0055085	transmembrane transport	179	989	4.39e-02
GO:BP	GO:0001704	formation of primary germ layer	27	99	4.69e-02
GO:BP	GO:0045214	sarcomere organization	15	43	4.69e-02
GO:BP	GO:0051179	localization	636	3978	4.69e-02
GO:BP	GO:0055002	striated muscle cell development	21	70	4.69e-02
GO:BP	GO:0051128	regulation of cellular component organization	336	1992	4.69e-02
GO:BP	GO:0003012	muscle system process	71	339	4.69e-02
GO:BP	GO:0007010	cytoskeleton organization	215	1218	4.69e-02
GO:BP	GO:0007162	negative regulation of cell adhesion	45	193	4.69e-02
GO:BP	GO:0009719	response to endogenous stimulus	221	1256	4.69e-02
GO:BP	GO:0006812	monoatomic cation transport	124	653	4.69e-02
GO:BP	GO:0006816	calcium ion transport	59	271	4.76e-02
GO:BP	GO:0050794	regulation of cellular process	1171	7651	4.85e-02
GO:BP	GO:0030155	regulation of cell adhesion	105	540	4.98e-02

ESR3h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in ESR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in ESR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:04015	Rap1 signaling pathway	45	164	3.43e-03
KEGG	KEGG:04022	cGMP-PKG signaling pathway	36	132	4.87e-03
KEGG	KEGG:04919	Thyroid hormone signaling pathway	33	112	4.87e-03
KEGG	KEGG:04020	Calcium signaling pathway	43	164	4.87e-03
KEGG	KEGG:04024	cAMP signaling pathway	40	151	4.87e-03
KEGG	KEGG:05414	Dilated cardiomyopathy	26	84	4.87e-03
KEGG	KEGG:04151	PI3K-Akt signaling pathway	58	256	1.24e-02
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	33	127	1.86e-02
KEGG	KEGG:04814	Motor proteins	37	149	2.01e-02
KEGG	KEGG:05030	Cocaine addiction	13	35	2.32e-02
KEGG	KEGG:04915	Estrogen signaling pathway	26	96	2.32e-02
KEGG	KEGG:05410	Hypertrophic cardiomyopathy	22	79	2.32e-02
KEGG	KEGG:05031	Amphetamine addiction	16	49	2.32e-02
KEGG	KEGG:04510	Focal adhesion	41	177	2.32e-02
KEGG	KEGG:04923	Regulation of lipolysis in adipocytes	14	41	2.32e-02
KEGG	KEGG:05205	Proteoglycans in cancer	40	170	2.32e-02
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	26	99	2.32e-02
KEGG	KEGG:04670	Leukocyte transendothelial migration	22	79	2.32e-02
KEGG	KEGG:04725	Cholinergic synapse	23	83	2.32e-02
KEGG	KEGG:04921	Oxytocin signaling pathway	30	115	2.32e-02
KEGG	KEGG:04911	Insulin secretion	19	64	2.32e-02
KEGG	KEGG:04976	Bile secretion	14	42	2.52e-02
KEGG	KEGG:04971	Gastric acid secretion	16	52	2.99e-02
KEGG	KEGG:04611	Platelet activation	23	89	4.36e-02
KEGG	KEGG:04380	Osteoclast differentiation	24	94	4.36e-02
KEGG	KEGG:04922	Glucagon signaling pathway	22	84	4.36e-02

Hyper/hypo-24hr

ESR24h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/ESR_24h_hyper_resgenes.RDS")
ESR24h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/ESR_24h_hypo_resgenes.RDS")

ESR24h_hyper_nomtable <-  ESR24h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
ESR24h_hypo_nomtable <-  ESR24h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

ESR24h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr ESR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr ESR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0051716	cellular response to stimulus	682	4933	7.22e-04
GO:BP	GO:0009888	tissue development	231	1425	7.22e-04
GO:BP	GO:0007165	signal transduction	548	3846	7.22e-04
GO:BP	GO:0023052	signaling	588	4180	7.22e-04
GO:BP	GO:0007154	cell communication	595	4248	8.83e-04
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	120	653	9.55e-04
GO:BP	GO:0023051	regulation of signaling	383	2597	1.14e-03
GO:BP	GO:0048856	anatomical structure development	577	4130	1.14e-03
GO:BP	GO:0050896	response to stimulus	775	5732	1.14e-03
GO:BP	GO:2000026	regulation of multicellular organismal development	170	1011	1.14e-03
GO:BP	GO:0048522	positive regulation of cellular process	585	4198	1.14e-03
GO:BP	GO:0010646	regulation of cell communication	382	2601	1.23e-03
GO:BP	GO:0009966	regulation of signal transduction	342	2307	2.03e-03
GO:BP	GO:0008150	biological_process	1493	12051	2.32e-03
GO:BP	GO:0050793	regulation of developmental process	274	1801	2.91e-03
GO:BP	GO:0048518	positive regulation of biological process	624	4561	3.77e-03
GO:BP	GO:0048568	embryonic organ development	65	317	3.83e-03
GO:BP	GO:0009653	anatomical structure morphogenesis	292	1951	4.38e-03
GO:BP	GO:0050794	regulation of cellular process	995	7651	4.39e-03
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	146	876	5.44e-03
GO:BP	GO:0048598	embryonic morphogenesis	83	440	5.44e-03
GO:BP	GO:0048513	animal organ development	314	2130	5.58e-03
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	337	2311	6.20e-03
GO:BP	GO:0009893	positive regulation of metabolic process	397	2780	6.42e-03
GO:BP	GO:0032501	multicellular organismal process	653	4830	6.51e-03
GO:BP	GO:0042472	inner ear morphogenesis	20	62	6.51e-03
GO:BP	GO:0048583	regulation of response to stimulus	412	2902	6.63e-03
GO:BP	GO:1902531	regulation of intracellular signal transduction	213	1376	6.92e-03
GO:BP	GO:0032502	developmental process	608	4475	7.70e-03
GO:BP	GO:0035556	intracellular signal transduction	305	2079	8.33e-03
GO:BP	GO:0009987	cellular process	1423	11450	9.03e-03
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	366	2555	9.03e-03
GO:BP	GO:0060429	epithelium development	138	836	9.43e-03
GO:BP	GO:0031325	positive regulation of cellular metabolic process	355	2474	9.78e-03
GO:BP	GO:0007155	cell adhesion	161	1004	9.78e-03
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	201	1301	1.06e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	42	190	1.10e-02
GO:BP	GO:0051254	positive regulation of RNA metabolic process	218	1430	1.10e-02
GO:BP	GO:0042471	ear morphogenesis	22	76	1.10e-02
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	201	1304	1.10e-02
GO:BP	GO:0009790	embryo development	141	864	1.10e-02
GO:BP	GO:0060038	cardiac muscle cell proliferation	15	43	1.47e-02
GO:BP	GO:0033002	muscle cell proliferation	36	157	1.47e-02
GO:BP	GO:0141124	intracellular signaling cassette	213	1403	1.47e-02
GO:BP	GO:0060485	mesenchyme development	52	256	1.47e-02
GO:BP	GO:0042221	response to chemical	347	2436	1.69e-02
GO:BP	GO:0071345	cellular response to cytokine stimulus	96	554	1.74e-02
GO:BP	GO:0050789	regulation of biological process	1030	8037	1.78e-02
GO:BP	GO:0009891	positive regulation of biosynthetic process	287	1974	1.78e-02
GO:BP	GO:0065007	biological regulation	1058	8275	1.78e-02
GO:BP	GO:0043009	chordate embryonic development	92	529	1.91e-02
GO:BP	GO:0048869	cellular developmental process	416	2988	1.91e-02
GO:BP	GO:0030154	cell differentiation	416	2987	1.91e-02
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	24	91	1.91e-02
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	123	749	1.91e-02
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	94	545	2.05e-02
GO:BP	GO:0110110	positive regulation of animal organ morphogenesis	11	27	2.06e-02
GO:BP	GO:0055017	cardiac muscle tissue growth	19	65	2.06e-02
GO:BP	GO:0007275	multicellular organism development	465	3383	2.06e-02
GO:BP	GO:0048519	negative regulation of biological process	546	4037	2.15e-02
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	276	1900	2.15e-02
GO:BP	GO:0030155	regulation of cell adhesion	93	540	2.15e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	105	626	2.26e-02
GO:BP	GO:0016043	cellular component organization	681	5139	2.26e-02
GO:BP	GO:0030855	epithelial cell differentiation	80	452	2.30e-02
GO:BP	GO:0071310	cellular response to organic substance	206	1370	2.30e-02
GO:BP	GO:0051094	positive regulation of developmental process	152	967	2.30e-02
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	283	1959	2.31e-02
GO:BP	GO:0008285	negative regulation of cell population proliferation	88	508	2.32e-02
GO:BP	GO:0034097	response to cytokine	104	621	2.32e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	269	1852	2.32e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	275	1900	2.37e-02
GO:BP	GO:0072359	circulatory system development	142	896	2.37e-02
GO:BP	GO:0060419	heart growth	20	72	2.39e-02
GO:BP	GO:0061061	muscle structure development	95	559	2.43e-02
GO:BP	GO:0006468	protein phosphorylation	157	1008	2.45e-02
GO:BP	GO:0048863	stem cell differentiation	41	198	3.05e-02
GO:BP	GO:0045927	positive regulation of growth	41	198	3.05e-02
GO:BP	GO:0023056	positive regulation of signaling	194	1292	3.29e-02
GO:BP	GO:0010033	response to organic substance	265	1835	3.34e-02
GO:BP	GO:0045446	endothelial cell differentiation	23	91	3.43e-02
GO:BP	GO:0001944	vasculature development	96	573	3.43e-02
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	45	225	3.43e-02
GO:BP	GO:0010647	positive regulation of cell communication	193	1288	3.58e-02
GO:BP	GO:0048584	positive regulation of response to stimulus	234	1601	3.69e-02
GO:BP	GO:0014855	striated muscle cell proliferation	17	59	3.76e-02
GO:BP	GO:0009605	response to external stimulus	242	1664	3.82e-02
GO:BP	GO:0030307	positive regulation of cell growth	30	133	3.85e-02
GO:BP	GO:0035023	regulation of Rho protein signal transduction	19	70	3.87e-02
GO:BP	GO:0051240	positive regulation of multicellular organismal process	169	1111	3.87e-02
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	233	1597	3.94e-02
GO:BP	GO:0048468	cell development	285	1999	3.95e-02
GO:BP	GO:0048762	mesenchymal cell differentiation	42	209	4.21e-02
GO:BP	GO:0008543	fibroblast growth factor receptor signaling pathway	17	60	4.27e-02
GO:BP	GO:0042475	odontogenesis of dentin-containing tooth	16	55	4.40e-02
GO:BP	GO:0044344	cellular response to fibroblast growth factor stimulus	21	82	4.40e-02
GO:BP	GO:0009967	positive regulation of signal transduction	174	1154	4.51e-02
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	22	88	4.51e-02
GO:BP	GO:0007266	Rho protein signal transduction	27	117	4.51e-02
GO:BP	GO:0002009	morphogenesis of an epithelium	69	391	4.51e-02
GO:BP	GO:0012501	programmed cell death	220	1505	4.69e-02
GO:BP	GO:0042476	odontogenesis	21	83	4.80e-02
GO:BP	GO:0010954	positive regulation of protein processing	8	18	4.80e-02
GO:BP	GO:0045595	regulation of cell differentiation	171	1134	4.80e-02

ESR24h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr ESR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr ESR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

ESR24h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr ESR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr ESR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0032501	multicellular organismal process	797	4830	9.00e-10
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	191	876	1.37e-08
GO:BP	GO:0048856	anatomical structure development	676	4130	7.34e-07
GO:BP	GO:0009653	anatomical structure morphogenesis	353	1951	1.26e-06
GO:BP	GO:0007275	multicellular organism development	565	3383	1.46e-06
GO:BP	GO:0030154	cell differentiation	506	2987	1.66e-06
GO:BP	GO:0048869	cellular developmental process	506	2988	1.66e-06
GO:BP	GO:0048731	system development	488	2903	9.94e-06
GO:BP	GO:0050896	response to stimulus	888	5732	1.10e-05
GO:BP	GO:0023052	signaling	670	4180	1.46e-05
GO:BP	GO:0007154	cell communication	679	4248	1.60e-05
GO:BP	GO:0051239	regulation of multicellular organismal process	359	2052	1.68e-05
GO:BP	GO:0032502	developmental process	709	4475	2.48e-05
GO:BP	GO:0007165	signal transduction	619	3846	2.99e-05
GO:BP	GO:0051716	cellular response to stimulus	762	4933	4.46e-04
GO:BP	GO:0048468	cell development	339	1999	8.59e-04
GO:BP	GO:0006937	regulation of muscle contraction	38	129	9.09e-04
GO:BP	GO:0044057	regulation of system process	86	399	2.85e-03
GO:BP	GO:1903522	regulation of blood circulation	50	200	4.01e-03
GO:BP	GO:0060047	heart contraction	50	200	4.01e-03
GO:BP	GO:0009888	tissue development	247	1425	4.69e-03
GO:BP	GO:0065008	regulation of biological quality	338	2039	5.40e-03
GO:BP	GO:0022008	neurogenesis	231	1327	6.10e-03
GO:BP	GO:0051240	positive regulation of multicellular organismal process	198	1111	6.10e-03
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	121	625	7.30e-03
GO:BP	GO:0045321	leukocyte activation	111	563	7.30e-03
GO:BP	GO:0035295	tube development	153	827	7.54e-03
GO:BP	GO:0008285	negative regulation of cell population proliferation	101	508	1.09e-02
GO:BP	GO:0003015	heart process	50	210	1.13e-02
GO:BP	GO:0006936	muscle contraction	60	267	1.18e-02
GO:BP	GO:0001775	cell activation	126	665	1.18e-02
GO:BP	GO:0048513	animal organ development	347	2130	1.28e-02
GO:BP	GO:0090257	regulation of muscle system process	44	181	1.63e-02
GO:BP	GO:0008016	regulation of heart contraction	42	170	1.63e-02
GO:BP	GO:0006810	transport	496	3176	1.70e-02
GO:BP	GO:0072359	circulatory system development	161	896	1.70e-02
GO:BP	GO:0009790	embryo development	156	864	1.70e-02
GO:BP	GO:0006942	regulation of striated muscle contraction	25	84	1.91e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	311	1900	1.99e-02
GO:BP	GO:0008015	blood circulation	77	374	1.99e-02
GO:BP	GO:0030029	actin filament-based process	126	677	2.02e-02
GO:BP	GO:0042127	regulation of cell population proliferation	198	1146	2.30e-02
GO:BP	GO:0060048	cardiac muscle contraction	32	121	2.37e-02
GO:BP	GO:0051146	striated muscle cell differentiation	54	242	2.39e-02
GO:BP	GO:0003008	system process	206	1201	2.39e-02
GO:BP	GO:0030239	myofibril assembly	21	67	2.39e-02
GO:BP	GO:2000026	regulation of multicellular organismal development	177	1011	2.39e-02
GO:BP	GO:0050793	regulation of developmental process	295	1801	2.39e-02
GO:BP	GO:0007399	nervous system development	310	1903	2.39e-02
GO:BP	GO:0030001	metal ion transport	105	554	3.09e-02
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	23	78	3.09e-02
GO:BP	GO:0035239	tube morphogenesis	123	668	3.09e-02
GO:BP	GO:0014902	myotube differentiation	25	89	3.61e-02
GO:BP	GO:0001525	angiogenesis	79	397	3.61e-02
GO:BP	GO:0001704	formation of primary germ layer	27	99	3.61e-02
GO:BP	GO:0003013	circulatory system process	87	446	3.61e-02
GO:BP	GO:0010876	lipid localization	65	312	3.61e-02
GO:BP	GO:0050789	regulation of biological process	1158	8037	3.63e-02
GO:BP	GO:0006811	monoatomic ion transport	138	769	3.65e-02
GO:BP	GO:0048729	tissue morphogenesis	92	478	3.73e-02
GO:BP	GO:0006941	striated muscle contraction	37	153	3.75e-02
GO:BP	GO:0055002	striated muscle cell development	21	70	3.75e-02
GO:BP	GO:0006869	lipid transport	58	273	3.85e-02
GO:BP	GO:0048514	blood vessel morphogenesis	90	467	3.88e-02
GO:BP	GO:0003012	muscle system process	69	339	3.90e-02
GO:BP	GO:0043217	myelin maintenance	8	15	3.90e-02
GO:BP	GO:0001838	embryonic epithelial tube formation	29	111	3.90e-02
GO:BP	GO:0045214	sarcomere organization	15	43	4.19e-02
GO:BP	GO:0030036	actin cytoskeleton organization	111	601	4.19e-02
GO:BP	GO:0035556	intracellular signal transduction	332	2079	4.19e-02
GO:BP	GO:0048699	generation of neurons	194	1145	4.63e-02
GO:BP	GO:0008283	cell population proliferation	230	1386	4.63e-02

ESR24h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr ESR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr ESR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:04015	Rap1 signaling pathway	44	164	1.52e-03
KEGG	KEGG:04024	cAMP signaling pathway	39	151	4.43e-03
KEGG	KEGG:05414	Dilated cardiomyopathy	26	84	4.43e-03
KEGG	KEGG:04022	cGMP-PKG signaling pathway	34	132	9.92e-03
KEGG	KEGG:04919	Thyroid hormone signaling pathway	30	112	9.92e-03
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	32	127	1.29e-02
KEGG	KEGG:04151	PI3K-Akt signaling pathway	55	256	1.29e-02
KEGG	KEGG:04020	Calcium signaling pathway	39	164	1.29e-02
KEGG	KEGG:05030	Cocaine addiction	13	35	1.43e-02
KEGG	KEGG:05205	Proteoglycans in cancer	39	170	1.43e-02
KEGG	KEGG:04923	Regulation of lipolysis in adipocytes	14	41	1.43e-02
KEGG	KEGG:04921	Oxytocin signaling pathway	29	115	1.43e-02
KEGG	KEGG:04911	Insulin secretion	19	64	1.43e-02
KEGG	KEGG:04814	Motor proteins	35	149	1.43e-02
KEGG	KEGG:05410	Hypertrophic cardiomyopathy	22	79	1.43e-02
KEGG	KEGG:04510	Focal adhesion	40	177	1.43e-02
KEGG	KEGG:04976	Bile secretion	14	42	1.73e-02
KEGG	KEGG:04971	Gastric acid secretion	16	52	1.93e-02
KEGG	KEGG:04611	Platelet activation	23	89	2.52e-02
KEGG	KEGG:05031	Amphetamine addiction	15	49	2.61e-02
KEGG	KEGG:04915	Estrogen signaling pathway	24	96	2.97e-02
KEGG	KEGG:04725	Cholinergic synapse	21	83	4.17e-02
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	24	99	4.17e-02
KEGG	KEGG:04750	Inflammatory mediator regulation of TRP channels	19	72	4.17e-02
KEGG	KEGG:04962	Vasopressin-regulated water reabsorption	12	38	4.49e-02
KEGG	KEGG:04922	Glucagon signaling pathway	21	84	4.49e-02
KEGG	KEGG:04670	Leukocyte transendothelial migration	20	79	4.57e-02
KEGG	KEGG:04512	ECM-receptor interaction	18	69	4.85e-02
KEGG	KEGG:05034	Alcoholism	26	113	4.91e-02

LR response genes

Hyper/hypo-3hr

LR3h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/LR_3h_hyper_resgenes.RDS")
LR3h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/LR_3h_hypo_resgenes.RDS")

LR3h_hyper_nomtable <-  LR3h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
LR3h_hypo_nomtable <-  LR3h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

LR3h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in LR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in LR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0023052	signaling	1245	4180	3.79e-15
GO:BP	GO:0007154	cell communication	1255	4248	3.31e-14
GO:BP	GO:0007165	signal transduction	1142	3846	4.22e-13
GO:BP	GO:0050896	response to stimulus	1623	5732	8.34e-13
GO:BP	GO:0009653	anatomical structure morphogenesis	628	1951	1.82e-12
GO:BP	GO:0051716	cellular response to stimulus	1413	4933	6.10e-12
GO:BP	GO:0032501	multicellular organismal process	1384	4830	1.23e-11
GO:BP	GO:0010646	regulation of cell communication	786	2601	1.80e-09
GO:BP	GO:0007166	cell surface receptor signaling pathway	595	1900	2.54e-09
GO:BP	GO:0023051	regulation of signaling	783	2597	2.81e-09
GO:BP	GO:0009888	tissue development	462	1425	3.79e-09
GO:BP	GO:0007275	multicellular organism development	988	3383	5.44e-09
GO:BP	GO:0072359	circulatory system development	310	896	5.44e-09
GO:BP	GO:0048856	anatomical structure development	1182	4130	5.44e-09
GO:BP	GO:0051239	regulation of multicellular organismal process	633	2052	5.68e-09
GO:BP	GO:0050793	regulation of developmental process	560	1801	2.90e-08
GO:BP	GO:0048731	system development	855	2903	3.50e-08
GO:BP	GO:0009966	regulation of signal transduction	695	2307	5.20e-08
GO:BP	GO:0048583	regulation of response to stimulus	853	2902	5.36e-08
GO:BP	GO:0048513	animal organ development	646	2130	7.53e-08
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	298	876	7.73e-08
GO:BP	GO:0048518	positive regulation of biological process	1279	4561	1.53e-07
GO:BP	GO:0035295	tube development	282	827	1.73e-07
GO:BP	GO:0048522	positive regulation of cellular process	1185	4198	1.84e-07
GO:BP	GO:0032502	developmental process	1255	4475	2.29e-07
GO:BP	GO:0035239	tube morphogenesis	234	668	3.37e-07
GO:BP	GO:0065007	biological regulation	2199	8275	3.37e-07
GO:BP	GO:0050789	regulation of biological process	2141	8037	3.41e-07
GO:BP	GO:0048870	cell motility	383	1190	3.72e-07
GO:BP	GO:0016477	cell migration	351	1078	4.50e-07
GO:BP	GO:0050794	regulation of cellular process	2043	7651	7.90e-07
GO:BP	GO:0042221	response to chemical	719	2436	8.11e-07
GO:BP	GO:0060429	epithelium development	280	836	1.09e-06
GO:BP	GO:2000026	regulation of multicellular organismal development	329	1011	1.49e-06
GO:BP	GO:2000145	regulation of cell motility	253	745	1.50e-06
GO:BP	GO:0040012	regulation of locomotion	259	766	1.50e-06
GO:BP	GO:0035556	intracellular signal transduction	621	2079	1.65e-06
GO:BP	GO:0048584	positive regulation of response to stimulus	491	1601	2.17e-06
GO:BP	GO:0051179	localization	1116	3978	2.82e-06
GO:BP	GO:0048519	negative regulation of biological process	1129	4037	4.66e-06
GO:BP	GO:0048523	negative regulation of cellular process	1069	3804	4.66e-06
GO:BP	GO:0001944	vasculature development	200	573	5.14e-06
GO:BP	GO:0001568	blood vessel development	192	546	5.14e-06
GO:BP	GO:0051093	negative regulation of developmental process	226	662	5.14e-06
GO:BP	GO:0006810	transport	904	3176	7.90e-06
GO:BP	GO:0030334	regulation of cell migration	238	710	1.17e-05
GO:BP	GO:0141124	intracellular signaling cassette	431	1403	1.38e-05
GO:BP	GO:0032879	regulation of localization	463	1521	1.41e-05
GO:BP	GO:0048514	blood vessel morphogenesis	165	467	3.23e-05
GO:BP	GO:0009719	response to endogenous stimulus	388	1256	3.36e-05
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	219	653	3.52e-05
GO:BP	GO:0016192	vesicle-mediated transport	380	1231	4.80e-05
GO:BP	GO:0051234	establishment of localization	966	3447	5.03e-05
GO:BP	GO:0040011	locomotion	276	858	5.60e-05
GO:BP	GO:0051049	regulation of transport	361	1164	5.60e-05
GO:BP	GO:0008150	biological_process	3065	12051	7.32e-05
GO:BP	GO:0061061	muscle structure development	190	559	7.55e-05
GO:BP	GO:0051128	regulation of cellular component organization	583	1992	8.37e-05
GO:BP	GO:0051240	positive regulation of multicellular organismal process	345	1111	8.47e-05
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	244	749	8.47e-05
GO:BP	GO:0048729	tissue morphogenesis	166	478	8.47e-05
GO:BP	GO:0002009	morphogenesis of an epithelium	140	391	9.29e-05
GO:BP	GO:1902531	regulation of intracellular signal transduction	417	1376	9.29e-05
GO:BP	GO:0070887	cellular response to chemical stimulus	545	1852	9.29e-05
GO:BP	GO:0071495	cellular response to endogenous stimulus	338	1088	9.87e-05
GO:BP	GO:0009967	positive regulation of signal transduction	356	1154	1.02e-04
GO:BP	GO:0098657	import into cell	218	661	1.18e-04
GO:BP	GO:0051094	positive regulation of developmental process	303	967	1.66e-04
GO:BP	GO:0010647	positive regulation of cell communication	391	1288	1.67e-04
GO:BP	GO:0023056	positive regulation of signaling	392	1292	1.69e-04
GO:BP	GO:0007399	nervous system development	556	1903	1.72e-04
GO:BP	GO:0007507	heart development	175	515	1.75e-04
GO:BP	GO:0060537	muscle tissue development	127	353	2.02e-04
GO:BP	GO:0046903	secretion	215	656	2.11e-04
GO:BP	GO:0043067	regulation of programmed cell death	346	1128	2.39e-04
GO:BP	GO:0009987	cellular process	2922	11450	2.90e-04
GO:BP	GO:0140352	export from cell	205	624	2.98e-04
GO:BP	GO:0051241	negative regulation of multicellular organismal process	242	756	3.32e-04
GO:BP	GO:0042981	regulation of apoptotic process	336	1096	3.39e-04
GO:BP	GO:0010033	response to organic substance	535	1835	3.39e-04
GO:BP	GO:0050673	epithelial cell proliferation	115	317	3.59e-04
GO:BP	GO:0007267	cell-cell signaling	352	1156	3.76e-04
GO:BP	GO:0008219	cell death	447	1509	4.21e-04
GO:BP	GO:0007155	cell adhesion	310	1004	4.21e-04
GO:BP	GO:0009887	animal organ morphogenesis	228	710	4.62e-04
GO:BP	GO:0009790	embryo development	271	864	4.62e-04
GO:BP	GO:0030154	cell differentiation	835	2987	4.76e-04
GO:BP	GO:0060627	regulation of vesicle-mediated transport	139	400	4.78e-04
GO:BP	GO:0048869	cellular developmental process	835	2988	4.93e-04
GO:BP	GO:0006816	calcium ion transport	100	271	6.13e-04
GO:BP	GO:0048598	embryonic morphogenesis	150	440	6.54e-04
GO:BP	GO:0012501	programmed cell death	444	1505	6.65e-04
GO:BP	GO:0006915	apoptotic process	431	1459	7.83e-04
GO:BP	GO:0001649	osteoblast differentiation	72	182	7.83e-04
GO:BP	GO:0001525	angiogenesis	137	397	7.83e-04
GO:BP	GO:2000147	positive regulation of cell motility	145	425	8.45e-04
GO:BP	GO:0032940	secretion by cell	189	579	9.26e-04
GO:BP	GO:0040017	positive regulation of locomotion	147	433	9.68e-04
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	237	751	1.04e-03
GO:BP	GO:0045595	regulation of cell differentiation	342	1134	1.09e-03
GO:BP	GO:0002062	chondrocyte differentiation	42	92	1.09e-03
GO:BP	GO:0030155	regulation of cell adhesion	177	540	1.28e-03
GO:BP	GO:0051130	positive regulation of cellular component organization	280	909	1.28e-03
GO:BP	GO:0070848	response to growth factor	187	576	1.39e-03
GO:BP	GO:0008283	cell population proliferation	409	1386	1.40e-03
GO:BP	GO:0001775	cell activation	212	665	1.40e-03
GO:BP	GO:0014706	striated muscle tissue development	82	218	1.57e-03
GO:BP	GO:1901700	response to oxygen-containing compound	343	1145	1.86e-03
GO:BP	GO:0030335	positive regulation of cell migration	139	411	1.88e-03
GO:BP	GO:0016043	cellular component organization	1375	5139	1.93e-03
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	34	71	1.95e-03
GO:BP	GO:0042127	regulation of cell population proliferation	343	1146	1.95e-03
GO:BP	GO:0043010	camera-type eye development	87	236	2.04e-03
GO:BP	GO:0030029	actin filament-based process	214	677	2.18e-03
GO:BP	GO:0051924	regulation of calcium ion transport	63	159	2.21e-03
GO:BP	GO:0032101	regulation of response to external stimulus	222	706	2.21e-03
GO:BP	GO:0045596	negative regulation of cell differentiation	158	479	2.26e-03
GO:BP	GO:0007517	muscle organ development	100	281	2.67e-03
GO:BP	GO:0031032	actomyosin structure organization	72	189	2.80e-03
GO:BP	GO:0048468	cell development	568	1999	2.94e-03
GO:BP	GO:0050678	regulation of epithelial cell proliferation	95	265	2.94e-03
GO:BP	GO:0050921	positive regulation of chemotaxis	39	87	3.06e-03
GO:BP	GO:0016202	regulation of striated muscle tissue development	11	14	3.15e-03
GO:BP	GO:0006812	monoatomic cation transport	206	653	3.26e-03
GO:BP	GO:0009605	response to external stimulus	479	1664	3.37e-03
GO:BP	GO:0048585	negative regulation of response to stimulus	376	1279	3.78e-03
GO:BP	GO:0030036	actin cytoskeleton organization	191	601	3.78e-03
GO:BP	GO:0043069	negative regulation of programmed cell death	215	687	3.78e-03
GO:BP	GO:0050920	regulation of chemotaxis	57	143	3.86e-03
GO:BP	GO:1902893	regulation of miRNA transcription	30	62	3.93e-03
GO:BP	GO:0003013	circulatory system process	147	446	4.00e-03
GO:BP	GO:1901342	regulation of vasculature development	77	208	4.30e-03
GO:BP	GO:0022008	neurogenesis	388	1327	4.56e-03
GO:BP	GO:0023057	negative regulation of signaling	330	1111	4.59e-03
GO:BP	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	154	472	4.61e-03
GO:BP	GO:0030001	metal ion transport	177	554	4.84e-03
GO:BP	GO:0006897	endocytosis	168	522	4.84e-03
GO:BP	GO:0045597	positive regulation of cell differentiation	197	626	5.05e-03
GO:BP	GO:0030855	epithelial cell differentiation	148	452	5.11e-03
GO:BP	GO:0070588	calcium ion transmembrane transport	79	216	5.25e-03
GO:BP	GO:0051641	cellular localization	771	2793	5.25e-03
GO:BP	GO:0061614	miRNA transcription	30	63	5.25e-03
GO:BP	GO:0009968	negative regulation of signal transduction	310	1040	5.49e-03
GO:BP	GO:0001818	negative regulation of cytokine production	66	174	5.63e-03
GO:BP	GO:0051050	positive regulation of transport	191	606	5.63e-03
GO:BP	GO:0043066	negative regulation of apoptotic process	207	664	5.83e-03
GO:BP	GO:0051046	regulation of secretion	137	415	5.85e-03
GO:BP	GO:1903169	regulation of calcium ion transmembrane transport	46	111	5.86e-03
GO:BP	GO:0038127	ERBB signaling pathway	44	105	6.03e-03
GO:BP	GO:0045765	regulation of angiogenesis	75	204	6.09e-03
GO:BP	GO:0010648	negative regulation of cell communication	328	1109	6.17e-03
GO:BP	GO:0071363	cellular response to growth factor stimulus	176	554	6.37e-03
GO:BP	GO:0009611	response to wounding	133	402	6.37e-03
GO:BP	GO:0022604	regulation of cell morphogenesis	76	208	6.74e-03
GO:BP	GO:0042592	homeostatic process	353	1204	6.87e-03
GO:BP	GO:0048634	regulation of muscle organ development	11	15	7.21e-03
GO:BP	GO:0006811	monoatomic ion transport	235	769	7.43e-03
GO:BP	GO:0042692	muscle cell differentiation	113	334	7.43e-03
GO:BP	GO:0048568	embryonic organ development	108	317	7.61e-03
GO:BP	GO:0006874	intracellular calcium ion homeostasis	76	209	7.75e-03
GO:BP	GO:0043068	positive regulation of programmed cell death	133	404	7.76e-03
GO:BP	GO:0006950	response to stress	748	2715	7.97e-03
GO:BP	GO:0098655	monoatomic cation transmembrane transport	167	525	8.35e-03
GO:BP	GO:0045807	positive regulation of endocytosis	43	104	9.47e-03
GO:BP	GO:0006909	phagocytosis	56	145	9.54e-03
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	56	145	9.54e-03
GO:BP	GO:0098662	inorganic cation transmembrane transport	162	509	9.93e-03
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	67	181	1.00e-02
GO:BP	GO:0045321	leukocyte activation	177	563	1.01e-02
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	642	2311	1.02e-02
GO:BP	GO:0014070	response to organic cyclic compound	196	632	1.05e-02
GO:BP	GO:0051246	regulation of protein metabolic process	480	1692	1.10e-02
GO:BP	GO:1903530	regulation of secretion by cell	126	383	1.11e-02
GO:BP	GO:1902105	regulation of leukocyte differentiation	74	205	1.13e-02
GO:BP	GO:0000902	cell morphogenesis	232	764	1.13e-02
GO:BP	GO:0045165	cell fate commitment	60	159	1.13e-02
GO:BP	GO:0060562	epithelial tube morphogenesis	95	276	1.14e-02
GO:BP	GO:0009893	positive regulation of metabolic process	762	2780	1.21e-02
GO:BP	GO:0040013	negative regulation of locomotion	91	263	1.24e-02
GO:BP	GO:0060706	cell differentiation involved in embryonic placenta development	12	18	1.24e-02
GO:BP	GO:2000628	regulation of miRNA metabolic process	33	75	1.24e-02
GO:BP	GO:0071417	cellular response to organonitrogen compound	148	462	1.24e-02
GO:BP	GO:0071840	cellular component organization or biogenesis	1411	5340	1.25e-02
GO:BP	GO:0043065	positive regulation of apoptotic process	129	395	1.25e-02
GO:BP	GO:0008360	regulation of cell shape	46	115	1.27e-02
GO:BP	GO:0071310	cellular response to organic substance	394	1370	1.29e-02
GO:BP	GO:0001503	ossification	108	322	1.29e-02
GO:BP	GO:0055074	calcium ion homeostasis	79	223	1.30e-02
GO:BP	GO:0002376	immune system process	431	1512	1.44e-02
GO:BP	GO:0008544	epidermis development	77	217	1.44e-02
GO:BP	GO:0003205	cardiac chamber development	57	151	1.47e-02
GO:BP	GO:0048880	sensory system development	94	275	1.49e-02
GO:BP	GO:0001654	eye development	93	272	1.58e-02
GO:BP	GO:0043588	skin development	66	181	1.59e-02
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	702	2555	1.61e-02
GO:BP	GO:0002684	positive regulation of immune system process	194	631	1.63e-02
GO:BP	GO:0002682	regulation of immune system process	277	936	1.63e-02
GO:BP	GO:0048699	generation of neurons	333	1145	1.63e-02
GO:BP	GO:0030336	negative regulation of cell migration	79	225	1.69e-02
GO:BP	GO:0051146	striated muscle cell differentiation	84	242	1.69e-02
GO:BP	GO:0034220	monoatomic ion transmembrane transport	193	628	1.71e-02
GO:BP	GO:0044087	regulation of cellular component biogenesis	244	815	1.73e-02
GO:BP	GO:0150063	visual system development	93	273	1.73e-02
GO:BP	GO:0008015	blood circulation	122	374	1.74e-02
GO:BP	GO:0010243	response to organonitrogen compound	217	716	1.74e-02
GO:BP	GO:0032103	positive regulation of response to external stimulus	123	378	1.82e-02
GO:BP	GO:0032409	regulation of transporter activity	59	159	1.82e-02
GO:BP	GO:0060707	trophoblast giant cell differentiation	7	8	1.85e-02
GO:BP	GO:0032412	regulation of monoatomic ion transmembrane transporter activity	54	143	1.91e-02
GO:BP	GO:0002688	regulation of leukocyte chemotaxis	30	68	1.93e-02
GO:BP	GO:0030216	keratinocyte differentiation	33	77	1.93e-02
GO:BP	GO:0048738	cardiac muscle tissue development	73	206	1.93e-02
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	60	163	2.01e-02
GO:BP	GO:0007162	negative regulation of cell adhesion	69	193	2.03e-02
GO:BP	GO:0022898	regulation of transmembrane transporter activity	56	150	2.03e-02
GO:BP	GO:0010959	regulation of metal ion transport	87	254	2.03e-02
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	56	150	2.03e-02
GO:BP	GO:1901698	response to nitrogen compound	232	774	2.08e-02
GO:BP	GO:0097006	regulation of plasma lipoprotein particle levels	23	48	2.08e-02
GO:BP	GO:0008016	regulation of heart contraction	62	170	2.10e-02
GO:BP	GO:0090596	sensory organ morphogenesis	65	180	2.10e-02
GO:BP	GO:2000146	negative regulation of cell motility	81	234	2.12e-02
GO:BP	GO:0010640	regulation of platelet-derived growth factor receptor signaling pathway	12	19	2.12e-02
GO:BP	GO:1903131	mononuclear cell differentiation	99	296	2.14e-02
GO:BP	GO:0097435	supramolecular fiber organization	207	683	2.15e-02
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	90	265	2.15e-02
GO:BP	GO:0048565	digestive tract development	37	90	2.19e-02
GO:BP	GO:0045445	myoblast differentiation	37	90	2.19e-02
GO:BP	GO:0042063	gliogenesis	87	255	2.22e-02
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	545	1959	2.26e-02
GO:BP	GO:0006887	exocytosis	86	252	2.34e-02
GO:BP	GO:0001937	negative regulation of endothelial cell proliferation	17	32	2.45e-02
GO:BP	GO:0045214	sarcomere organization	21	43	2.50e-02
GO:BP	GO:0001936	regulation of endothelial cell proliferation	40	100	2.50e-02
GO:BP	GO:0065008	regulation of biological quality	565	2039	2.58e-02
GO:BP	GO:0044093	positive regulation of molecular function	248	837	2.58e-02
GO:BP	GO:0040008	regulation of growth	154	493	2.58e-02
GO:BP	GO:0034383	low-density lipoprotein particle clearance	11	17	2.58e-02
GO:BP	GO:0043408	regulation of MAPK cascade	142	450	2.59e-02
GO:BP	GO:1902895	positive regulation of miRNA transcription	22	46	2.60e-02
GO:BP	GO:0030865	cortical cytoskeleton organization	22	46	2.60e-02
GO:BP	GO:0003008	system process	345	1201	2.72e-02
GO:BP	GO:0042110	T cell activation	106	323	2.73e-02
GO:BP	GO:0043269	regulation of monoatomic ion transport	100	302	2.73e-02
GO:BP	GO:0003148	outflow tract septum morphogenesis	13	22	2.77e-02
GO:BP	GO:1901019	regulation of calcium ion transmembrane transporter activity	24	52	2.80e-02
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	168	545	2.84e-02
GO:BP	GO:0042633	hair cycle	33	79	2.85e-02
GO:BP	GO:0042303	molting cycle	33	79	2.85e-02
GO:BP	GO:0030856	regulation of epithelial cell differentiation	41	104	2.85e-02
GO:BP	GO:0072001	renal system development	86	254	2.85e-02
GO:BP	GO:0022405	hair cycle process	30	70	2.91e-02
GO:BP	GO:0022404	molting cycle process	30	70	2.91e-02
GO:BP	GO:0008284	positive regulation of cell population proliferation	193	637	2.98e-02
GO:BP	GO:1901699	cellular response to nitrogen compound	157	506	2.98e-02
GO:BP	GO:0016310	phosphorylation	347	1211	3.00e-02
GO:BP	GO:0034349	glial cell apoptotic process	10	15	3.06e-02
GO:BP	GO:1904062	regulation of monoatomic cation transmembrane transport	70	200	3.07e-02
GO:BP	GO:0007423	sensory organ development	127	399	3.15e-02
GO:BP	GO:0060341	regulation of cellular localization	241	815	3.17e-02
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	166	540	3.31e-02
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	57	157	3.33e-02
GO:BP	GO:0140747	regulation of ncRNA transcription	34	83	3.42e-02
GO:BP	GO:0009891	positive regulation of biosynthetic process	546	1974	3.44e-02
GO:BP	GO:0098739	import across plasma membrane	49	131	3.50e-02
GO:BP	GO:0099537	trans-synaptic signaling	155	501	3.53e-02
GO:BP	GO:0040007	growth	220	739	3.54e-02
GO:BP	GO:0030098	lymphocyte differentiation	88	263	3.55e-02
GO:BP	GO:0002683	negative regulation of immune system process	102	312	3.58e-02
GO:BP	GO:0046649	lymphocyte activation	148	476	3.58e-02
GO:BP	GO:0003231	cardiac ventricle development	44	115	3.58e-02
GO:BP	GO:0035461	vitamin transmembrane transport	9	13	3.61e-02
GO:BP	GO:0050764	regulation of phagocytosis	25	56	3.61e-02
GO:BP	GO:0001942	hair follicle development	29	68	3.61e-02
GO:BP	GO:0048592	eye morphogenesis	43	112	3.67e-02
GO:BP	GO:0097178	ruffle assembly	18	36	3.67e-02
GO:BP	GO:0001501	skeletal system development	118	369	3.67e-02
GO:BP	GO:0002521	leukocyte differentiation	125	394	3.69e-02
GO:BP	GO:0031099	regeneration	54	148	3.70e-02
GO:BP	GO:0010632	regulation of epithelial cell migration	68	195	3.73e-02
GO:BP	GO:0000165	MAPK cascade	164	535	3.79e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	98	299	3.89e-02
GO:BP	GO:0060443	mammary gland morphogenesis	19	39	3.90e-02
GO:BP	GO:0030100	regulation of endocytosis	72	209	3.90e-02
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	35	87	3.92e-02
GO:BP	GO:0019725	cellular homeostasis	180	594	3.92e-02
GO:BP	GO:0061337	cardiac conduction	35	87	3.92e-02
GO:BP	GO:0001822	kidney development	83	247	3.94e-02
GO:BP	GO:0098660	inorganic ion transmembrane transport	169	554	3.95e-02
GO:BP	GO:0007015	actin filament organization	121	381	4.05e-02
GO:BP	GO:0032688	negative regulation of interferon-beta production	8	11	4.05e-02
GO:BP	GO:0043009	chordate embryonic development	162	529	4.05e-02
GO:BP	GO:0035108	limb morphogenesis	44	116	4.05e-02
GO:BP	GO:0043584	nose development	8	11	4.05e-02
GO:BP	GO:0035107	appendage morphogenesis	44	116	4.05e-02
GO:BP	GO:0017157	regulation of exocytosis	51	139	4.12e-02
GO:BP	GO:0045649	regulation of macrophage differentiation	11	18	4.12e-02
GO:BP	GO:0055085	transmembrane transport	286	989	4.22e-02
GO:BP	GO:0003015	heart process	72	210	4.26e-02
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	349	1227	4.26e-02
GO:BP	GO:0035051	cardiocyte differentiation	50	136	4.26e-02
GO:BP	GO:0006468	protein phosphorylation	291	1008	4.26e-02
GO:BP	GO:0048732	gland development	105	325	4.26e-02
GO:BP	GO:0034762	regulation of transmembrane transport	103	318	4.27e-02
GO:BP	GO:0001892	embryonic placenta development	29	69	4.28e-02
GO:BP	GO:0060047	heart contraction	69	200	4.29e-02
GO:BP	GO:0002690	positive regulation of leukocyte chemotaxis	23	51	4.29e-02
GO:BP	GO:1903522	regulation of blood circulation	69	200	4.29e-02
GO:BP	GO:0034765	regulation of monoatomic ion transmembrane transport	76	224	4.29e-02
GO:BP	GO:0030030	cell projection organization	358	1262	4.29e-02
GO:BP	GO:0031325	positive regulation of cellular metabolic process	673	2474	4.29e-02
GO:BP	GO:0008543	fibroblast growth factor receptor signaling pathway	26	60	4.29e-02
GO:BP	GO:0045661	regulation of myoblast differentiation	26	60	4.29e-02
GO:BP	GO:0003143	embryonic heart tube morphogenesis	25	57	4.29e-02
GO:BP	GO:0010759	positive regulation of macrophage chemotaxis	7	9	4.30e-02
GO:BP	GO:0110020	regulation of actomyosin structure organization	36	91	4.32e-02
GO:BP	GO:0048593	camera-type eye morphogenesis	36	91	4.32e-02
GO:BP	GO:0050680	negative regulation of epithelial cell proliferation	41	107	4.32e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	66	190	4.32e-02
GO:BP	GO:0060326	cell chemotaxis	58	163	4.32e-02
GO:BP	GO:0051216	cartilage development	55	153	4.32e-02
GO:BP	GO:0009913	epidermal cell differentiation	45	120	4.32e-02
GO:BP	GO:0098771	inorganic ion homeostasis	116	365	4.43e-02
GO:BP	GO:0033036	macromolecule localization	667	2453	4.50e-02
GO:BP	GO:0080134	regulation of response to stress	288	999	4.54e-02
GO:BP	GO:0033993	response to lipid	181	601	4.55e-02
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	85	256	4.55e-02
GO:BP	GO:0040036	regulation of fibroblast growth factor receptor signaling pathway	14	26	4.55e-02
GO:BP	GO:1901653	cellular response to peptide	93	284	4.55e-02
GO:BP	GO:0030866	cortical actin cytoskeleton organization	18	37	4.57e-02
GO:BP	GO:0022612	gland morphogenesis	39	101	4.57e-02
GO:BP	GO:1903034	regulation of response to wounding	47	127	4.57e-02
GO:BP	GO:0071705	nitrogen compound transport	430	1539	4.65e-02
GO:BP	GO:0055123	digestive system development	38	98	4.73e-02
GO:BP	GO:0030858	positive regulation of epithelial cell differentiation	19	40	4.83e-02
GO:BP	GO:0003007	heart morphogenesis	75	222	4.84e-02
GO:BP	GO:0045762	positive regulation of adenylate cyclase activity	10	16	4.84e-02
GO:BP	GO:0061138	morphogenesis of a branching epithelium	52	144	4.89e-02
GO:BP	GO:0098659	inorganic cation import across plasma membrane	30	73	4.91e-02
GO:BP	GO:0099587	inorganic ion import across plasma membrane	30	73	4.91e-02
GO:BP	GO:0030900	forebrain development	95	292	4.94e-02
GO:BP	GO:0043547	positive regulation of GTPase activity	45	121	4.94e-02
GO:BP	GO:0035050	embryonic heart tube development	29	70	4.98e-02

LR3h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in LR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in LR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:04010	MAPK signaling pathway	93	246	6.02e-04
KEGG	KEGG:05205	Proteoglycans in cancer	70	170	6.02e-04
KEGG	KEGG:04270	Vascular smooth muscle contraction	43	94	8.85e-04
KEGG	KEGG:04022	cGMP-PKG signaling pathway	54	132	2.76e-03
KEGG	KEGG:04927	Cortisol synthesis and secretion	24	48	7.84e-03
KEGG	KEGG:04925	Aldosterone synthesis and secretion	34	77	7.84e-03
KEGG	KEGG:05211	Renal cell carcinoma	30	65	7.84e-03
KEGG	KEGG:04510	Focal adhesion	65	177	8.94e-03
KEGG	KEGG:04918	Thyroid hormone synthesis	26	55	8.94e-03
KEGG	KEGG:04934	Cushing syndrome	48	121	8.94e-03
KEGG	KEGG:04921	Oxytocin signaling pathway	45	115	1.05e-02
KEGG	KEGG:05200	Pathways in cancer	131	408	1.05e-02
KEGG	KEGG:05165	Human papillomavirus infection	92	271	1.05e-02
KEGG	KEGG:04668	TNF signaling pathway	36	87	1.05e-02
KEGG	KEGG:04151	PI3K-Akt signaling pathway	88	256	1.05e-02
KEGG	KEGG:04915	Estrogen signaling pathway	39	96	1.05e-02
KEGG	KEGG:05160	Hepatitis C	45	116	1.17e-02
KEGG	KEGG:04550	Signaling pathways regulating pluripotency of stem cells	41	104	1.23e-02
KEGG	KEGG:04971	Gastric acid secretion	24	52	1.23e-02
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	48	127	1.32e-02
KEGG	KEGG:05215	Prostate cancer	35	86	1.37e-02
KEGG	KEGG:01521	EGFR tyrosine kinase inhibitor resistance	31	74	1.44e-02
KEGG	KEGG:04371	Apelin signaling pathway	41	106	1.59e-02
KEGG	KEGG:04750	Inflammatory mediator regulation of TRP channels	30	72	1.76e-02
KEGG	KEGG:04928	Parathyroid hormone synthesis, secretion and action	33	82	2.01e-02
KEGG	KEGG:04611	Platelet activation	35	89	2.21e-02
KEGG	KEGG:04970	Salivary secretion	24	55	2.21e-02
KEGG	KEGG:04725	Cholinergic synapse	33	83	2.25e-02
KEGG	KEGG:04014	Ras signaling pathway	60	172	2.25e-02
KEGG	KEGG:04210	Apoptosis	43	117	3.02e-02
KEGG	KEGG:01522	Endocrine resistance	33	85	3.15e-02
KEGG	KEGG:04024	cAMP signaling pathway	53	151	3.15e-02
KEGG	KEGG:04976	Bile secretion	19	42	3.25e-02
KEGG	KEGG:05167	Kaposi sarcoma-associated herpesvirus infection	51	145	3.33e-02
KEGG	KEGG:05163	Human cytomegalovirus infection	60	176	3.34e-02
KEGG	KEGG:05207	Chemical carcinogenesis - receptor activation	50	142	3.34e-02
KEGG	KEGG:05161	Hepatitis B	48	136	3.67e-02
KEGG	KEGG:05218	Melanoma	24	58	3.68e-02
KEGG	KEGG:05219	Bladder cancer	17	37	3.68e-02
KEGG	KEGG:05231	Choline metabolism in cancer	32	84	4.06e-02
KEGG	KEGG:04390	Hippo signaling pathway	47	134	4.15e-02
KEGG	KEGG:04810	Regulation of actin cytoskeleton	60	179	4.32e-02
KEGG	KEGG:04530	Tight junction	48	138	4.35e-02
KEGG	KEGG:04961	Endocrine and other factor-regulated calcium reabsorption	18	41	4.57e-02
KEGG	KEGG:04713	Circadian entrainment	27	69	4.57e-02
KEGG	KEGG:05417	Lipid and atherosclerosis	52	153	4.85e-02
KEGG	KEGG:04912	GnRH signaling pathway	29	76	4.85e-02
KEGG	KEGG:04726	Serotonergic synapse	25	63	4.85e-02
KEGG	KEGG:04015	Rap1 signaling pathway	55	164	4.99e-02
KEGG	KEGG:04020	Calcium signaling pathway	55	164	4.99e-02

LR3h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in LR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in LR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0008150	biological_process	3173	12051	1.31e-06
GO:BP	GO:0023052	signaling	1204	4180	1.50e-05
GO:BP	GO:0032501	multicellular organismal process	1373	4830	1.50e-05
GO:BP	GO:0065007	biological regulation	2251	8275	1.81e-05
GO:BP	GO:0007154	cell communication	1217	4248	2.07e-05
GO:BP	GO:0050789	regulation of biological process	2186	8037	4.23e-05
GO:BP	GO:0007165	signal transduction	1104	3846	7.86e-05
GO:BP	GO:0048518	positive regulation of biological process	1289	4561	9.76e-05
GO:BP	GO:0048731	system development	851	2903	9.76e-05
GO:BP	GO:0009987	cellular process	3016	11450	9.76e-05
GO:BP	GO:0072359	circulatory system development	296	896	9.76e-05
GO:BP	GO:0010646	regulation of cell communication	769	2601	9.76e-05
GO:BP	GO:0032502	developmental process	1262	4475	1.94e-04
GO:BP	GO:0048856	anatomical structure development	1172	4130	1.94e-04
GO:BP	GO:0023051	regulation of signaling	764	2597	1.94e-04
GO:BP	GO:0044057	regulation of system process	146	399	2.90e-04
GO:BP	GO:0030154	cell differentiation	866	2987	3.26e-04
GO:BP	GO:0048869	cellular developmental process	866	2988	3.28e-04
GO:BP	GO:0007275	multicellular organism development	970	3383	4.02e-04
GO:BP	GO:0050794	regulation of cellular process	2072	7651	4.57e-04
GO:BP	GO:0048522	positive regulation of cellular process	1183	4198	5.41e-04
GO:BP	GO:0009966	regulation of signal transduction	680	2307	5.64e-04
GO:BP	GO:0065008	regulation of biological quality	605	2039	9.89e-04
GO:BP	GO:0141124	intracellular signaling cassette	430	1403	1.13e-03
GO:BP	GO:0001944	vasculature development	194	573	1.37e-03
GO:BP	GO:0048583	regulation of response to stimulus	835	2902	1.43e-03
GO:BP	GO:0007166	cell surface receptor signaling pathway	565	1900	1.49e-03
GO:BP	GO:0009653	anatomical structure morphogenesis	578	1951	1.79e-03
GO:BP	GO:0001568	blood vessel development	185	546	1.89e-03
GO:BP	GO:0010647	positive regulation of cell communication	394	1288	3.07e-03
GO:BP	GO:0051239	regulation of multicellular organismal process	601	2052	4.71e-03
GO:BP	GO:0048519	negative regulation of biological process	1127	4037	5.26e-03
GO:BP	GO:0023056	positive regulation of signaling	393	1292	5.26e-03
GO:BP	GO:0009967	positive regulation of signal transduction	354	1154	6.22e-03
GO:BP	GO:0051716	cellular response to stimulus	1359	4933	6.32e-03
GO:BP	GO:0050793	regulation of developmental process	531	1801	6.44e-03
GO:BP	GO:0050896	response to stimulus	1565	5732	6.44e-03
GO:BP	GO:0048523	negative regulation of cellular process	1059	3804	1.63e-02
GO:BP	GO:0035295	tube development	258	827	2.23e-02
GO:BP	GO:0031016	pancreas development	26	51	2.23e-02
GO:BP	GO:0006810	transport	891	3176	2.58e-02
GO:BP	GO:0051179	localization	1101	3978	2.70e-02
GO:BP	GO:0016477	cell migration	327	1078	2.70e-02
GO:BP	GO:1901564	organonitrogen compound metabolic process	1272	4637	2.82e-02
GO:BP	GO:0048468	cell development	577	1999	2.82e-02
GO:BP	GO:0035239	tube morphogenesis	212	668	2.82e-02
GO:BP	GO:0048870	cell motility	357	1190	3.12e-02
GO:BP	GO:0048514	blood vessel morphogenesis	154	467	3.19e-02
GO:BP	GO:0051240	positive regulation of multicellular organismal process	335	1111	3.20e-02
GO:BP	GO:0032879	regulation of localization	447	1521	3.22e-02
GO:BP	GO:0045595	regulation of cell differentiation	341	1134	3.36e-02
GO:BP	GO:0042391	regulation of membrane potential	104	299	3.98e-02
GO:BP	GO:0051247	positive regulation of protein metabolic process	293	963	4.02e-02
GO:BP	GO:0003008	system process	358	1201	4.56e-02
GO:BP	GO:0009888	tissue development	419	1425	4.59e-02
GO:BP	GO:0035556	intracellular signal transduction	595	2079	4.71e-02

LR3h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in LR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in LR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
NA	NA	NA	NA	NA	NA
:——	:——-	:———	—————–:	———:	:——-

Hyper/hypo-24hr

LR24h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/LR_24h_hyper_resgenes.RDS")
LR24h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/LR_24h_hypo_resgenes.RDS")

LR24h_hyper_nomtable <-  LR24h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
LR24h_hypo_nomtable <-  LR24h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

LR24h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr LR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr LR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0023052	signaling	1429	4180	1.82e-10
GO:BP	GO:0007154	cell communication	1442	4248	3.39e-10
GO:BP	GO:0007166	cell surface receptor signaling pathway	703	1900	3.39e-10
GO:BP	GO:0009653	anatomical structure morphogenesis	718	1951	3.39e-10
GO:BP	GO:0007165	signal transduction	1319	3846	3.39e-10
GO:BP	GO:0032501	multicellular organismal process	1622	4830	3.39e-10
GO:BP	GO:0007275	multicellular organism development	1172	3383	4.36e-10
GO:BP	GO:0048731	system development	1021	2903	4.36e-10
GO:BP	GO:0050896	response to stimulus	1889	5732	7.78e-10
GO:BP	GO:0048856	anatomical structure development	1400	4130	1.06e-09
GO:BP	GO:0051716	cellular response to stimulus	1645	4933	1.21e-09
GO:BP	GO:0009888	tissue development	538	1425	2.70e-09
GO:BP	GO:0050793	regulation of developmental process	658	1801	9.03e-09
GO:BP	GO:0048870	cell motility	456	1190	1.15e-08
GO:BP	GO:0010646	regulation of cell communication	911	2601	2.40e-08
GO:BP	GO:0023051	regulation of signaling	909	2597	2.82e-08
GO:BP	GO:0032502	developmental process	1489	4475	6.25e-08
GO:BP	GO:0035295	tube development	328	827	1.01e-07
GO:BP	GO:0016477	cell migration	412	1078	1.40e-07
GO:BP	GO:0060429	epithelium development	330	836	1.51e-07
GO:BP	GO:0051239	regulation of multicellular organismal process	729	2052	1.72e-07
GO:BP	GO:0141124	intracellular signaling cassette	518	1403	2.26e-07
GO:BP	GO:0007399	nervous system development	680	1903	2.33e-07
GO:BP	GO:0072359	circulatory system development	349	896	2.40e-07
GO:BP	GO:0009966	regulation of signal transduction	807	2307	3.99e-07
GO:BP	GO:0048513	animal organ development	750	2130	4.78e-07
GO:BP	GO:0030154	cell differentiation	1020	2987	4.88e-07
GO:BP	GO:0048869	cellular developmental process	1020	2988	5.11e-07
GO:BP	GO:0048583	regulation of response to stimulus	993	2902	5.11e-07
GO:BP	GO:0035239	tube morphogenesis	269	668	5.23e-07
GO:BP	GO:0001568	blood vessel development	225	546	1.16e-06
GO:BP	GO:0008150	biological_process	3672	12051	1.97e-06
GO:BP	GO:0009967	positive regulation of signal transduction	429	1154	2.22e-06
GO:BP	GO:0001944	vasculature development	233	573	2.25e-06
GO:BP	GO:0006810	transport	1072	3176	2.30e-06
GO:BP	GO:0023056	positive regulation of signaling	474	1292	2.30e-06
GO:BP	GO:0048518	positive regulation of biological process	1497	4561	2.43e-06
GO:BP	GO:2000026	regulation of multicellular organismal development	381	1011	2.49e-06
GO:BP	GO:0010647	positive regulation of cell communication	472	1288	2.73e-06
GO:BP	GO:0040012	regulation of locomotion	298	766	3.35e-06
GO:BP	GO:0022008	neurogenesis	484	1327	3.37e-06
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	292	749	3.55e-06
GO:BP	GO:0048522	positive regulation of cellular process	1384	4198	3.57e-06
GO:BP	GO:2000145	regulation of cell motility	290	745	4.52e-06
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	334	876	4.67e-06
GO:BP	GO:0051179	localization	1314	3978	6.21e-06
GO:BP	GO:0048584	positive regulation of response to stimulus	570	1601	7.34e-06
GO:BP	GO:0016192	vesicle-mediated transport	450	1231	7.34e-06
GO:BP	GO:0065007	biological regulation	2596	8275	8.55e-06
GO:BP	GO:0050789	regulation of biological process	2526	8037	9.22e-06
GO:BP	GO:0035556	intracellular signal transduction	721	2079	1.07e-05
GO:BP	GO:0050794	regulation of cellular process	2410	7651	1.59e-05
GO:BP	GO:0040011	locomotion	324	858	2.02e-05
GO:BP	GO:0048514	blood vessel morphogenesis	191	467	2.03e-05
GO:BP	GO:0009719	response to endogenous stimulus	454	1256	2.67e-05
GO:BP	GO:0030334	regulation of cell migration	273	710	3.42e-05
GO:BP	GO:0061061	muscle structure development	221	559	4.68e-05
GO:BP	GO:0051234	establishment of localization	1141	3447	4.68e-05
GO:BP	GO:0042221	response to chemical	826	2436	6.30e-05
GO:BP	GO:0051240	positive regulation of multicellular organismal process	404	1111	6.30e-05
GO:BP	GO:0009987	cellular process	3494	11450	6.42e-05
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	285	751	6.42e-05
GO:BP	GO:0002009	morphogenesis of an epithelium	162	391	6.42e-05
GO:BP	GO:0032879	regulation of localization	535	1521	9.29e-05
GO:BP	GO:0048519	negative regulation of biological process	1318	4037	9.33e-05
GO:BP	GO:0048523	negative regulation of cellular process	1246	3804	1.06e-04
GO:BP	GO:0002062	chondrocyte differentiation	50	92	1.06e-04
GO:BP	GO:0051094	positive regulation of developmental process	355	967	1.06e-04
GO:BP	GO:0098657	import into cell	253	661	1.23e-04
GO:BP	GO:0071495	cellular response to endogenous stimulus	394	1088	1.23e-04
GO:BP	GO:0045595	regulation of cell differentiation	409	1134	1.23e-04
GO:BP	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	188	472	1.66e-04
GO:BP	GO:0048468	cell development	684	1999	1.71e-04
GO:BP	GO:1902531	regulation of intracellular signal transduction	486	1376	1.71e-04
GO:BP	GO:0070848	response to growth factor	222	576	3.06e-04
GO:BP	GO:2000147	positive regulation of cell motility	170	425	3.78e-04
GO:BP	GO:0046903	secretion	248	656	4.27e-04
GO:BP	GO:0048699	generation of neurons	408	1145	4.76e-04
GO:BP	GO:0007155	cell adhesion	362	1004	5.16e-04
GO:BP	GO:0040017	positive regulation of locomotion	172	433	5.17e-04
GO:BP	GO:0008283	cell population proliferation	485	1386	5.23e-04
GO:BP	GO:0048729	tissue morphogenesis	187	478	6.07e-04
GO:BP	GO:0140352	export from cell	236	624	6.66e-04
GO:BP	GO:0006915	apoptotic process	507	1459	7.23e-04
GO:BP	GO:0030036	actin cytoskeleton organization	228	601	7.35e-04
GO:BP	GO:0071363	cellular response to growth factor stimulus	212	554	7.95e-04
GO:BP	GO:0051049	regulation of transport	412	1164	8.15e-04
GO:BP	GO:0051093	negative regulation of developmental process	248	662	8.17e-04
GO:BP	GO:0006897	endocytosis	201	522	8.40e-04
GO:BP	GO:0030855	epithelial cell differentiation	177	452	9.26e-04
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	244	653	1.16e-03
GO:BP	GO:0042063	gliogenesis	108	255	1.18e-03
GO:BP	GO:0070887	cellular response to chemical stimulus	629	1852	1.18e-03
GO:BP	GO:0043588	skin development	81	181	1.35e-03
GO:BP	GO:0030335	positive regulation of cell migration	162	411	1.37e-03
GO:BP	GO:0008219	cell death	520	1509	1.37e-03
GO:BP	GO:0030029	actin filament-based process	251	677	1.56e-03
GO:BP	GO:0012501	programmed cell death	518	1505	1.62e-03
GO:BP	GO:0042981	regulation of apoptotic process	387	1096	1.79e-03
GO:BP	GO:0032940	secretion by cell	218	579	1.79e-03
GO:BP	GO:0007267	cell-cell signaling	406	1156	1.91e-03
GO:BP	GO:0060537	muscle tissue development	141	353	2.15e-03
GO:BP	GO:0001525	angiogenesis	156	397	2.24e-03
GO:BP	GO:0043067	regulation of programmed cell death	396	1128	2.48e-03
GO:BP	GO:0007264	small GTPase-mediated signal transduction	165	425	2.79e-03
GO:BP	GO:0009887	animal organ morphogenesis	260	710	2.79e-03
GO:BP	GO:0042127	regulation of cell population proliferation	401	1146	2.99e-03
GO:BP	GO:0038127	ERBB signaling pathway	51	105	3.52e-03
GO:BP	GO:0043010	camera-type eye development	99	236	3.66e-03
GO:BP	GO:0043085	positive regulation of catalytic activity	214	574	3.98e-03
GO:BP	GO:0048568	embryonic organ development	127	317	4.27e-03
GO:BP	GO:0000902	cell morphogenesis	276	764	4.65e-03
GO:BP	GO:0060627	regulation of vesicle-mediated transport	155	400	5.05e-03
GO:BP	GO:0060707	trophoblast giant cell differentiation	8	8	5.88e-03
GO:BP	GO:0045597	positive regulation of cell differentiation	230	626	5.88e-03
GO:BP	GO:0060284	regulation of cell development	223	605	5.99e-03
GO:BP	GO:0042692	muscle cell differentiation	132	334	6.00e-03
GO:BP	GO:0060562	epithelial tube morphogenesis	112	276	6.00e-03
GO:BP	GO:0048598	embryonic morphogenesis	168	440	6.00e-03
GO:BP	GO:0007015	actin filament organization	148	381	6.06e-03
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	839	2555	6.07e-03
GO:BP	GO:0065008	regulation of biological quality	679	2039	6.09e-03
GO:BP	GO:0009893	positive regulation of metabolic process	908	2780	6.35e-03
GO:BP	GO:0042633	hair cycle	40	79	6.49e-03
GO:BP	GO:0042303	molting cycle	40	79	6.49e-03
GO:BP	GO:0009790	embryo development	307	864	6.56e-03
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	78	181	7.04e-03
GO:BP	GO:0031175	neuron projection development	284	794	7.13e-03
GO:BP	GO:0030182	neuron differentiation	376	1080	7.22e-03
GO:BP	GO:0001503	ossification	127	322	8.32e-03
GO:BP	GO:0051241	negative regulation of multicellular organismal process	271	756	8.56e-03
GO:BP	GO:0097435	supramolecular fiber organization	247	683	9.04e-03
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	104	256	9.04e-03
GO:BP	GO:0010033	response to organic substance	613	1835	9.20e-03
GO:BP	GO:0006816	calcium ion transport	109	271	9.88e-03
GO:BP	GO:0072001	renal system development	103	254	1.03e-02
GO:BP	GO:0032101	regulation of response to external stimulus	254	706	1.03e-02
GO:BP	GO:0008544	epidermis development	90	217	1.04e-02
GO:BP	GO:0051345	positive regulation of hydrolase activity	113	283	1.04e-02
GO:BP	GO:0016310	phosphorylation	416	1211	1.04e-02
GO:BP	GO:0060443	mammary gland morphogenesis	23	39	1.06e-02
GO:BP	GO:0031032	actomyosin structure organization	80	189	1.06e-02
GO:BP	GO:0043065	positive regulation of apoptotic process	151	395	1.07e-02
GO:BP	GO:0043068	positive regulation of programmed cell death	154	404	1.08e-02
GO:BP	GO:0007507	heart development	191	515	1.08e-02
GO:BP	GO:0045596	negative regulation of cell differentiation	179	479	1.09e-02
GO:BP	GO:0048008	platelet-derived growth factor receptor signaling pathway	28	51	1.11e-02
GO:BP	GO:0044093	positive regulation of molecular function	296	837	1.11e-02
GO:BP	GO:0009725	response to hormone	230	634	1.11e-02
GO:BP	GO:0007517	muscle organ development	112	281	1.11e-02
GO:BP	GO:0045165	cell fate commitment	69	159	1.15e-02
GO:BP	GO:0048666	neuron development	314	894	1.19e-02
GO:BP	GO:0051128	regulation of cellular component organization	660	1992	1.19e-02
GO:BP	GO:0043547	positive regulation of GTPase activity	55	121	1.21e-02
GO:BP	GO:0016043	cellular component organization	1618	5139	1.33e-02
GO:BP	GO:0048286	lung alveolus development	24	42	1.33e-02
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	106	265	1.33e-02
GO:BP	GO:0035914	skeletal muscle cell differentiation	29	54	1.33e-02
GO:BP	GO:2000009	negative regulation of protein localization to cell surface	10	12	1.33e-02
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	758	2311	1.34e-02
GO:BP	GO:1902105	regulation of leukocyte differentiation	85	205	1.37e-02
GO:BP	GO:0030900	forebrain development	115	292	1.49e-02
GO:BP	GO:2001236	regulation of extrinsic apoptotic signaling pathway	55	122	1.49e-02
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	198	540	1.49e-02
GO:BP	GO:0051247	positive regulation of protein metabolic process	335	963	1.49e-02
GO:BP	GO:0030879	mammary gland development	49	106	1.52e-02
GO:BP	GO:0001654	eye development	108	272	1.54e-02
GO:BP	GO:0048880	sensory system development	109	275	1.56e-02
GO:BP	GO:0060706	cell differentiation involved in embryonic placenta development	13	18	1.57e-02
GO:BP	GO:0043408	regulation of MAPK cascade	168	450	1.57e-02
GO:BP	GO:0021915	neural tube development	61	139	1.65e-02
GO:BP	GO:0022404	molting cycle process	35	70	1.74e-02
GO:BP	GO:0051050	positive regulation of transport	219	606	1.74e-02
GO:BP	GO:0150063	visual system development	108	273	1.74e-02
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	418	1227	1.74e-02
GO:BP	GO:0050673	epithelial cell proliferation	123	317	1.74e-02
GO:BP	GO:0022405	hair cycle process	35	70	1.74e-02
GO:BP	GO:0001822	kidney development	99	247	1.74e-02
GO:BP	GO:0007224	smoothened signaling pathway	55	123	1.75e-02
GO:BP	GO:0001775	cell activation	238	665	1.82e-02
GO:BP	GO:0030155	regulation of cell adhesion	197	540	1.92e-02
GO:BP	GO:0051146	striated muscle cell differentiation	97	242	1.95e-02
GO:BP	GO:0008589	regulation of smoothened signaling pathway	36	73	1.96e-02
GO:BP	GO:0001649	osteoblast differentiation	76	182	1.97e-02
GO:BP	GO:0001942	hair follicle development	34	68	2.01e-02
GO:BP	GO:0030336	negative regulation of cell migration	91	225	2.01e-02
GO:BP	GO:0050730	regulation of peptidyl-tyrosine phosphorylation	62	143	2.02e-02
GO:BP	GO:0018212	peptidyl-tyrosine modification	72	171	2.04e-02
GO:BP	GO:0001501	skeletal system development	140	369	2.05e-02
GO:BP	GO:0030030	cell projection organization	428	1262	2.08e-02
GO:BP	GO:0040013	negative regulation of locomotion	104	263	2.08e-02
GO:BP	GO:0043066	negative regulation of apoptotic process	237	664	2.10e-02
GO:BP	GO:0035108	limb morphogenesis	52	116	2.17e-02
GO:BP	GO:0035107	appendage morphogenesis	52	116	2.17e-02
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	35	71	2.23e-02
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	224	625	2.28e-02
GO:BP	GO:0018108	peptidyl-tyrosine phosphorylation	71	169	2.30e-02
GO:BP	GO:0043069	negative regulation of programmed cell death	244	687	2.34e-02
GO:BP	GO:0061138	morphogenesis of a branching epithelium	62	144	2.38e-02
GO:BP	GO:0010720	positive regulation of cell development	125	326	2.41e-02
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	41	87	2.41e-02
GO:BP	GO:0009605	response to external stimulus	553	1664	2.42e-02
GO:BP	GO:0031344	regulation of cell projection organization	200	553	2.60e-02
GO:BP	GO:0001892	embryonic placenta development	34	69	2.60e-02
GO:BP	GO:0023057	negative regulation of signaling	379	1111	2.61e-02
GO:BP	GO:0060538	skeletal muscle organ development	60	139	2.61e-02
GO:BP	GO:0048730	epidermis morphogenesis	14	21	2.69e-02
GO:BP	GO:0051246	regulation of protein metabolic process	561	1692	2.72e-02
GO:BP	GO:0061564	axon development	150	402	2.75e-02
GO:BP	GO:0009611	response to wounding	150	402	2.75e-02
GO:BP	GO:0042592	homeostatic process	408	1204	2.77e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	40	85	2.77e-02
GO:BP	GO:0006909	phagocytosis	62	145	2.77e-02
GO:BP	GO:0007163	establishment or maintenance of cell polarity	80	196	2.80e-02
GO:BP	GO:0010640	regulation of platelet-derived growth factor receptor signaling pathway	13	19	2.84e-02
GO:BP	GO:0031069	hair follicle morphogenesis	13	19	2.84e-02
GO:BP	GO:0031099	regeneration	63	148	2.85e-02
GO:BP	GO:0051641	cellular localization	900	2793	2.88e-02
GO:BP	GO:0045807	positive regulation of endocytosis	47	104	2.88e-02
GO:BP	GO:0031325	positive regulation of cellular metabolic process	802	2474	2.95e-02
GO:BP	GO:2000146	negative regulation of cell motility	93	234	2.95e-02
GO:BP	GO:0002521	leukocyte differentiation	147	394	2.95e-02
GO:BP	GO:0051130	positive regulation of cellular component organization	314	909	2.96e-02
GO:BP	GO:0035590	purinergic nucleotide receptor signaling pathway	11	15	3.02e-02
GO:BP	GO:0006811	monoatomic ion transport	269	769	3.11e-02
GO:BP	GO:0048806	genitalia development	17	28	3.12e-02
GO:BP	GO:0006887	exocytosis	99	252	3.12e-02
GO:BP	GO:0098773	skin epidermis development	42	91	3.14e-02
GO:BP	GO:0010648	negative regulation of cell communication	377	1109	3.23e-02
GO:BP	GO:0071310	cellular response to organic substance	459	1370	3.30e-02
GO:BP	GO:0000165	MAPK cascade	193	535	3.30e-02
GO:BP	GO:0071774	response to fibroblast growth factor	40	86	3.39e-02
GO:BP	GO:0001764	neuron migration	59	138	3.42e-02
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	642	1959	3.45e-02
GO:BP	GO:0008543	fibroblast growth factor receptor signaling pathway	30	60	3.50e-02
GO:BP	GO:0031401	positive regulation of protein modification process	205	573	3.64e-02
GO:BP	GO:0007519	skeletal muscle tissue development	56	130	3.65e-02
GO:BP	GO:0048771	tissue remodeling	52	119	3.68e-02
GO:BP	GO:0001935	endothelial cell proliferation	52	119	3.68e-02
GO:BP	GO:0014070	response to organic cyclic compound	224	632	3.73e-02
GO:BP	GO:0071702	organic substance transport	598	1819	3.77e-02
GO:BP	GO:0090066	regulation of anatomical structure size	150	406	3.90e-02
GO:BP	GO:0051960	regulation of nervous system development	134	358	3.95e-02
GO:BP	GO:0070588	calcium ion transmembrane transport	86	216	3.95e-02
GO:BP	GO:0099177	regulation of trans-synaptic signaling	129	343	3.95e-02
GO:BP	GO:0051216	cartilage development	64	153	3.97e-02
GO:BP	GO:1901700	response to oxygen-containing compound	387	1145	4.07e-02
GO:BP	GO:0006898	receptor-mediated endocytosis	79	196	4.07e-02
GO:BP	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	43	95	4.10e-02
GO:BP	GO:0007266	Rho protein signal transduction	51	117	4.21e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	114	299	4.26e-02
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	61	145	4.26e-02
GO:BP	GO:0003008	system process	404	1201	4.54e-02
GO:BP	GO:0010001	glial cell differentiation	77	191	4.54e-02
GO:BP	GO:0003205	cardiac chamber development	63	151	4.54e-02
GO:BP	GO:0098609	cell-cell adhesion	215	607	4.58e-02
GO:BP	GO:0033993	response to lipid	213	601	4.63e-02
GO:BP	GO:0048589	developmental growth	189	527	4.63e-02
GO:BP	GO:0006468	protein phosphorylation	343	1008	4.63e-02
GO:BP	GO:0007423	sensory organ development	147	399	4.65e-02
GO:BP	GO:0009968	negative regulation of signal transduction	353	1040	4.72e-02
GO:BP	GO:0042733	embryonic digit morphogenesis	26	51	4.72e-02
GO:BP	GO:0050804	modulation of chemical synaptic transmission	128	342	4.72e-02
GO:BP	GO:0007409	axonogenesis	135	363	4.72e-02
GO:BP	GO:0090596	sensory organ morphogenesis	73	180	4.72e-02
GO:BP	GO:0048536	spleen development	17	29	4.72e-02
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	36	77	4.72e-02
GO:BP	GO:0050920	regulation of chemotaxis	60	143	4.72e-02
GO:BP	GO:0030856	regulation of epithelial cell differentiation	46	104	4.72e-02
GO:BP	GO:0006874	intracellular calcium ion homeostasis	83	209	4.73e-02
GO:BP	GO:0030100	regulation of endocytosis	83	209	4.73e-02
GO:BP	GO:0009891	positive regulation of biosynthetic process	644	1974	4.75e-02
GO:BP	GO:0060430	lung saccule development	7	8	4.93e-02

LR24h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr LR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr LR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:05205	Proteoglycans in cancer	77	170	3.78e-03
KEGG	KEGG:04010	MAPK signaling pathway	102	246	8.38e-03
KEGG	KEGG:04510	Focal adhesion	76	177	1.31e-02
KEGG	KEGG:04015	Rap1 signaling pathway	69	164	2.56e-02
KEGG	KEGG:05200	Pathways in cancer	152	408	2.56e-02
KEGG	KEGG:04270	Vascular smooth muscle contraction	44	94	2.56e-02
KEGG	KEGG:01521	EGFR tyrosine kinase inhibitor resistance	36	74	2.56e-02
KEGG	KEGG:04550	Signaling pathways regulating pluripotency of stem cells	46	104	2.71e-02
KEGG	KEGG:05132	Salmonella infection	85	214	2.71e-02
KEGG	KEGG:04390	Hippo signaling pathway	57	134	2.71e-02
KEGG	KEGG:05165	Human papillomavirus infection	105	271	2.71e-02
KEGG	KEGG:04810	Regulation of actin cytoskeleton	73	179	2.71e-02
KEGG	KEGG:05211	Renal cell carcinoma	32	65	2.71e-02
KEGG	KEGG:04151	PI3K-Akt signaling pathway	99	256	2.71e-02
KEGG	KEGG:04750	Inflammatory mediator regulation of TRP channels	34	72	2.71e-02
KEGG	KEGG:04934	Cushing syndrome	52	121	2.71e-02
KEGG	KEGG:05231	Choline metabolism in cancer	38	84	3.67e-02
KEGG	KEGG:04530	Tight junction	57	138	4.20e-02
KEGG	KEGG:04072	Phospholipase D signaling pathway	47	110	4.20e-02
KEGG	KEGG:04925	Aldosterone synthesis and secretion	35	77	4.20e-02
KEGG	KEGG:05160	Hepatitis C	49	116	4.33e-02
KEGG	KEGG:05130	Pathogenic Escherichia coli infection	61	151	4.85e-02
KEGG	KEGG:04210	Apoptosis	49	117	4.88e-02

LR24h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr LR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr LR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0008150	biological_process	2398	12051	2.95e-06
GO:BP	GO:0044057	regulation of system process	121	399	1.89e-04
GO:BP	GO:0009987	cellular process	2279	11450	6.19e-04
GO:BP	GO:0023052	signaling	905	4180	1.59e-03
GO:BP	GO:0065007	biological regulation	1694	8275	1.59e-03
GO:BP	GO:0007154	cell communication	915	4248	2.50e-03
GO:BP	GO:0032501	multicellular organismal process	1023	4830	6.85e-03
GO:BP	GO:0090257	regulation of muscle system process	60	181	6.85e-03
GO:BP	GO:0030001	metal ion transport	148	554	6.85e-03
GO:BP	GO:0050789	regulation of biological process	1639	8037	7.03e-03
GO:BP	GO:0003012	muscle system process	97	339	1.19e-02
GO:BP	GO:0072359	circulatory system development	221	896	1.20e-02
GO:BP	GO:0006812	monoatomic cation transport	168	653	1.20e-02
GO:BP	GO:0006941	striated muscle contraction	51	153	1.49e-02
GO:BP	GO:0003015	heart process	65	210	1.56e-02
GO:BP	GO:0010646	regulation of cell communication	573	2601	1.56e-02
GO:BP	GO:0008016	regulation of heart contraction	55	170	1.56e-02
GO:BP	GO:0007165	signal transduction	821	3846	1.80e-02
GO:BP	GO:0006811	monoatomic ion transport	191	769	1.85e-02
GO:BP	GO:0060047	heart contraction	62	200	1.85e-02
GO:BP	GO:0048518	positive regulation of biological process	961	4561	1.85e-02
GO:BP	GO:0098662	inorganic cation transmembrane transport	133	509	2.36e-02
GO:BP	GO:0023051	regulation of signaling	569	2597	2.36e-02
GO:BP	GO:1903522	regulation of blood circulation	61	200	2.98e-02
GO:BP	GO:0016043	cellular component organization	1070	5139	3.16e-02
GO:BP	GO:0098660	inorganic ion transmembrane transport	142	554	3.16e-02
GO:BP	GO:0098655	monoatomic cation transmembrane transport	135	525	3.87e-02
GO:BP	GO:0003013	circulatory system process	117	446	4.44e-02
GO:BP	GO:0086019	cell-cell signaling involved in cardiac conduction	15	30	4.45e-02
GO:BP	GO:0050896	response to stimulus	1182	5732	4.45e-02
GO:BP	GO:0006936	muscle contraction	76	267	4.45e-02

LR24h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr LR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr LR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	42	127	4.65e-02

NR response genes

Hyper/hypo-3hr

NR3h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/NR_3h_hyper_resgenes.RDS")
NR3h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/NR_3h_hypo_resgenes.RDS")

NR3h_hyper_nomtable <-  NR3h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
NR3h_hypo_nomtable <-  NR3h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

NR3h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in NR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in NR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0008150	biological_process	7095	12051	6.42e-15
GO:BP	GO:0009987	cellular process	6746	11450	1.48e-10
GO:BP	GO:0048518	positive regulation of biological process	2778	4561	3.17e-05
GO:BP	GO:0009893	positive regulation of metabolic process	1726	2780	6.69e-05
GO:BP	GO:0048522	positive regulation of cellular process	2560	4198	6.69e-05
GO:BP	GO:0023051	regulation of signaling	1611	2597	2.56e-04
GO:BP	GO:0010646	regulation of cell communication	1611	2601	3.83e-04
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	1437	2311	4.82e-04
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	1582	2555	4.82e-04
GO:BP	GO:0051716	cellular response to stimulus	2974	4933	5.90e-04
GO:BP	GO:0009966	regulation of signal transduction	1432	2307	7.27e-04
GO:BP	GO:0051254	positive regulation of RNA metabolic process	908	1430	7.27e-04
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	1007	1597	9.60e-04
GO:BP	GO:0031325	positive regulation of cellular metabolic process	1528	2474	1.14e-03
GO:BP	GO:0008152	metabolic process	4999	8464	1.50e-03
GO:BP	GO:0061061	muscle structure development	374	559	1.77e-03
GO:BP	GO:0023056	positive regulation of signaling	820	1292	2.12e-03
GO:BP	GO:0010647	positive regulation of cell communication	817	1288	2.37e-03
GO:BP	GO:0009967	positive regulation of signal transduction	736	1154	2.40e-03
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	826	1304	2.45e-03
GO:BP	GO:0006915	apoptotic process	919	1459	2.45e-03
GO:BP	GO:0050794	regulation of cellular process	4529	7651	2.47e-03
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	823	1301	2.83e-03
GO:BP	GO:0044238	primary metabolic process	4556	7701	2.83e-03
GO:BP	GO:0032502	developmental process	2694	4475	2.83e-03
GO:BP	GO:0023052	signaling	2521	4180	3.09e-03
GO:BP	GO:0050896	response to stimulus	3421	5732	3.38e-03
GO:BP	GO:0006810	transport	1933	3176	3.38e-03
GO:BP	GO:0007154	cell communication	2559	4248	3.55e-03
GO:BP	GO:0065007	biological regulation	4882	8275	3.55e-03
GO:BP	GO:0048583	regulation of response to stimulus	1769	2902	5.31e-03
GO:BP	GO:0048584	positive regulation of response to stimulus	999	1601	5.53e-03
GO:BP	GO:0050789	regulation of biological process	4742	8037	5.53e-03
GO:BP	GO:0048856	anatomical structure development	2487	4130	5.53e-03
GO:BP	GO:0007165	signal transduction	2321	3846	5.53e-03
GO:BP	GO:0072359	circulatory system development	575	896	5.56e-03
GO:BP	GO:0071495	cellular response to endogenous stimulus	691	1088	5.56e-03
GO:BP	GO:0007166	cell surface receptor signaling pathway	1176	1900	5.71e-03
GO:BP	GO:0044237	cellular metabolic process	4459	7545	5.97e-03
GO:BP	GO:0008219	cell death	942	1509	7.18e-03
GO:BP	GO:0071704	organic substance metabolic process	4773	8096	7.18e-03
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	484	749	7.49e-03
GO:BP	GO:0012501	programmed cell death	939	1505	7.49e-03
GO:BP	GO:0071772	response to BMP	94	125	7.49e-03
GO:BP	GO:0009891	positive regulation of biosynthetic process	1218	1974	7.49e-03
GO:BP	GO:0045595	regulation of cell differentiation	717	1134	7.49e-03
GO:BP	GO:0071773	cellular response to BMP stimulus	94	125	7.49e-03
GO:BP	GO:0006807	nitrogen compound metabolic process	4359	7376	7.68e-03
GO:BP	GO:1902531	regulation of intracellular signal transduction	861	1376	8.80e-03
GO:BP	GO:0009719	response to endogenous stimulus	789	1256	9.06e-03
GO:BP	GO:0048523	negative regulation of cellular process	2291	3804	9.45e-03
GO:BP	GO:0070848	response to growth factor	377	576	1.07e-02
GO:BP	GO:0043065	positive regulation of apoptotic process	265	395	1.11e-02
GO:BP	GO:0071840	cellular component organization or biogenesis	3182	5340	1.11e-02
GO:BP	GO:0051234	establishment of localization	2081	3447	1.11e-02
GO:BP	GO:0045663	positive regulation of myoblast differentiation	32	36	1.11e-02
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	1171	1900	1.11e-02
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	1205	1959	1.33e-02
GO:BP	GO:0045661	regulation of myoblast differentiation	49	60	1.42e-02
GO:BP	GO:0043170	macromolecule metabolic process	4131	6990	1.52e-02
GO:BP	GO:0042981	regulation of apoptotic process	690	1096	1.64e-02
GO:BP	GO:0044271	cellular nitrogen compound biosynthetic process	2242	3730	1.96e-02
GO:BP	GO:0030509	BMP signaling pathway	87	117	2.18e-02
GO:BP	GO:0071363	cellular response to growth factor stimulus	361	554	2.18e-02
GO:BP	GO:0045445	myoblast differentiation	69	90	2.19e-02
GO:BP	GO:0071702	organic substance transport	1119	1819	2.19e-02
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	647	1027	2.25e-02
GO:BP	GO:0051179	localization	2385	3978	2.26e-02
GO:BP	GO:0009058	biosynthetic process	3514	5927	2.52e-02
GO:BP	GO:1901576	organic substance biosynthetic process	3490	5886	2.60e-02
GO:BP	GO:0043068	positive regulation of programmed cell death	268	404	2.62e-02
GO:BP	GO:0030510	regulation of BMP signaling pathway	64	83	2.62e-02
GO:BP	GO:0008283	cell population proliferation	860	1386	3.00e-02
GO:BP	GO:0044249	cellular biosynthetic process	3454	5828	3.41e-02
GO:BP	GO:1904019	epithelial cell apoptotic process	77	103	3.41e-02
GO:BP	GO:0030154	cell differentiation	1803	2987	3.42e-02
GO:BP	GO:0007275	multicellular organism development	2034	3383	3.57e-02
GO:BP	GO:0048869	cellular developmental process	1803	2988	3.57e-02
GO:BP	GO:0050793	regulation of developmental process	1105	1801	3.57e-02
GO:BP	GO:0043067	regulation of programmed cell death	705	1128	3.57e-02
GO:BP	GO:0035556	intracellular signal transduction	1269	2079	3.58e-02
GO:BP	GO:0051253	negative regulation of RNA metabolic process	709	1135	3.60e-02
GO:BP	GO:0051641	cellular localization	1688	2793	3.90e-02
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	649	1036	4.19e-02
GO:BP	GO:0051239	regulation of multicellular organismal process	1252	2052	4.19e-02
GO:BP	GO:0016043	cellular component organization	3053	5139	4.20e-02
GO:BP	GO:0030856	regulation of epithelial cell differentiation	77	104	4.96e-02

NR3h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in NR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in NR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:00000	KEGG root term	3465	5802	1.45e-03
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	254	384	4.93e-02

NR3h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in NR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in NR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0050896	response to stimulus	3112	5732	7.99e-18
GO:BP	GO:0051716	cellular response to stimulus	2696	4933	3.57e-16
GO:BP	GO:0007154	cell communication	2338	4248	6.32e-15
GO:BP	GO:0023052	signaling	2302	4180	7.26e-15
GO:BP	GO:0008150	biological_process	6120	12051	3.54e-14
GO:BP	GO:0032501	multicellular organismal process	2625	4830	4.74e-14
GO:BP	GO:0007165	signal transduction	2119	3846	2.17e-13
GO:BP	GO:0048518	positive regulation of biological process	2458	4561	2.61e-10
GO:BP	GO:0051239	regulation of multicellular organismal process	1164	2052	7.61e-10
GO:BP	GO:0009653	anatomical structure morphogenesis	1111	1951	7.61e-10
GO:BP	GO:0050789	regulation of biological process	4181	8037	7.61e-10
GO:BP	GO:0048731	system development	1604	2903	1.39e-09
GO:BP	GO:0009987	cellular process	5815	11450	1.39e-09
GO:BP	GO:0007275	multicellular organism development	1849	3383	2.04e-09
GO:BP	GO:0048856	anatomical structure development	2229	4130	2.36e-09
GO:BP	GO:0065007	biological regulation	4286	8275	8.57e-09
GO:BP	GO:0048522	positive regulation of cellular process	2258	4198	8.57e-09
GO:BP	GO:0048869	cellular developmental process	1638	2988	1.58e-08
GO:BP	GO:0042221	response to chemical	1353	2436	1.58e-08
GO:BP	GO:0030154	cell differentiation	1637	2987	1.69e-08
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	527	876	2.19e-08
GO:BP	GO:0050794	regulation of cellular process	3973	7651	3.42e-08
GO:BP	GO:0022008	neurogenesis	767	1327	5.69e-08
GO:BP	GO:0048519	negative regulation of biological process	2164	4037	1.30e-07
GO:BP	GO:0070887	cellular response to chemical stimulus	1041	1852	1.34e-07
GO:BP	GO:0032502	developmental process	2385	4475	1.34e-07
GO:BP	GO:0048523	negative regulation of cellular process	2044	3804	1.75e-07
GO:BP	GO:0010033	response to organic substance	1031	1835	1.75e-07
GO:BP	GO:0048468	cell development	1114	1999	3.75e-07
GO:BP	GO:0071310	cellular response to organic substance	782	1370	7.37e-07
GO:BP	GO:0048513	animal organ development	1178	2130	1.15e-06
GO:BP	GO:0009888	tissue development	809	1425	1.38e-06
GO:BP	GO:0007399	nervous system development	1059	1903	1.46e-06
GO:BP	GO:0007166	cell surface receptor signaling pathway	1057	1900	1.62e-06
GO:BP	GO:0001568	blood vessel development	336	546	1.72e-06
GO:BP	GO:0035239	tube morphogenesis	403	668	1.72e-06
GO:BP	GO:0001944	vasculature development	351	573	1.72e-06
GO:BP	GO:0023051	regulation of signaling	1417	2597	1.72e-06
GO:BP	GO:1901700	response to oxygen-containing compound	659	1145	2.15e-06
GO:BP	GO:0010646	regulation of cell communication	1417	2601	2.65e-06
GO:BP	GO:0048583	regulation of response to stimulus	1571	2902	2.76e-06
GO:BP	GO:0035295	tube development	488	827	2.76e-06
GO:BP	GO:0030182	neuron differentiation	621	1080	6.79e-06
GO:BP	GO:0048699	generation of neurons	655	1145	7.90e-06
GO:BP	GO:0009966	regulation of signal transduction	1258	2307	1.67e-05
GO:BP	GO:0009719	response to endogenous stimulus	710	1256	2.53e-05
GO:BP	GO:0071495	cellular response to endogenous stimulus	621	1088	2.75e-05
GO:BP	GO:0016477	cell migration	615	1078	3.42e-05
GO:BP	GO:0072359	circulatory system development	517	896	5.38e-05
GO:BP	GO:0048514	blood vessel morphogenesis	285	467	5.70e-05
GO:BP	GO:0035556	intracellular signal transduction	1134	2079	7.49e-05
GO:BP	GO:0050793	regulation of developmental process	990	1801	7.87e-05
GO:BP	GO:0051179	localization	2101	3978	7.87e-05
GO:BP	GO:0051234	establishment of localization	1832	3447	8.44e-05
GO:BP	GO:0006810	transport	1694	3176	9.09e-05
GO:BP	GO:0048870	cell motility	670	1190	1.10e-04
GO:BP	GO:0051240	positive regulation of multicellular organismal process	628	1111	1.24e-04
GO:BP	GO:0048666	neuron development	513	894	1.30e-04
GO:BP	GO:0051128	regulation of cellular component organization	1084	1992	2.27e-04
GO:BP	GO:0010243	response to organonitrogen compound	416	716	2.66e-04
GO:BP	GO:1901701	cellular response to oxygen-containing compound	478	833	3.04e-04
GO:BP	GO:0007267	cell-cell signaling	648	1156	3.51e-04
GO:BP	GO:0006796	phosphate-containing compound metabolic process	1089	2006	3.59e-04
GO:BP	GO:0009725	response to hormone	371	634	3.68e-04
GO:BP	GO:0051241	negative regulation of multicellular organismal process	436	756	4.08e-04
GO:BP	GO:1901564	organonitrogen compound metabolic process	2421	4637	5.13e-04
GO:BP	GO:0033993	response to lipid	352	601	5.78e-04
GO:BP	GO:0098657	import into cell	384	661	6.16e-04
GO:BP	GO:0006950	response to stress	1449	2715	6.16e-04
GO:BP	GO:1901698	response to nitrogen compound	444	774	6.65e-04
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	246	407	7.60e-04
GO:BP	GO:0007155	cell adhesion	565	1004	7.85e-04
GO:BP	GO:0008283	cell population proliferation	764	1386	9.28e-04
GO:BP	GO:0014070	response to organic cyclic compound	367	632	9.83e-04
GO:BP	GO:0048585	negative regulation of response to stimulus	708	1279	9.83e-04
GO:BP	GO:0006793	phosphorus metabolic process	1095	2028	9.88e-04
GO:BP	GO:0048584	positive regulation of response to stimulus	875	1601	9.88e-04
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	680	1227	1.21e-03
GO:BP	GO:0045595	regulation of cell differentiation	631	1134	1.35e-03
GO:BP	GO:0060840	artery development	62	85	1.36e-03
GO:BP	GO:0002376	immune system process	827	1512	1.52e-03
GO:BP	GO:0030030	cell projection organization	697	1262	1.60e-03
GO:BP	GO:0023057	negative regulation of signaling	618	1111	1.67e-03
GO:BP	GO:0003008	system process	665	1201	1.67e-03
GO:BP	GO:0010648	negative regulation of cell communication	616	1109	2.15e-03
GO:BP	GO:0042127	regulation of cell population proliferation	635	1146	2.31e-03
GO:BP	GO:0030029	actin filament-based process	388	677	2.48e-03
GO:BP	GO:0009611	response to wounding	240	402	2.74e-03
GO:BP	GO:0009790	embryo development	486	864	3.23e-03
GO:BP	GO:0009893	positive regulation of metabolic process	1472	2780	3.26e-03
GO:BP	GO:0006897	endocytosis	304	522	3.71e-03
GO:BP	GO:0141124	intracellular signaling cassette	766	1403	4.02e-03
GO:BP	GO:0030036	actin cytoskeleton organization	346	601	4.02e-03
GO:BP	GO:0048729	tissue morphogenesis	280	478	4.11e-03
GO:BP	GO:0006816	calcium ion transport	167	271	4.39e-03
GO:BP	GO:0001525	angiogenesis	236	397	4.41e-03
GO:BP	GO:0036075	replacement ossification	23	26	4.49e-03
GO:BP	GO:0048844	artery morphogenesis	44	58	4.49e-03
GO:BP	GO:0001958	endochondral ossification	23	26	4.49e-03
GO:BP	GO:0051049	regulation of transport	641	1164	4.84e-03
GO:BP	GO:0009968	negative regulation of signal transduction	576	1040	5.34e-03
GO:BP	GO:0032870	cellular response to hormone stimulus	265	452	5.64e-03
GO:BP	GO:0032879	regulation of localization	825	1521	5.70e-03
GO:BP	GO:0021915	neural tube development	92	139	5.72e-03
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	423	749	5.72e-03
GO:BP	GO:1902531	regulation of intracellular signal transduction	750	1376	5.72e-03
GO:BP	GO:0009605	response to external stimulus	898	1664	6.28e-03
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	357	625	6.29e-03
GO:BP	GO:0051094	positive regulation of developmental process	537	967	6.29e-03
GO:BP	GO:0048598	embryonic morphogenesis	258	440	6.47e-03
GO:BP	GO:0030335	positive regulation of cell migration	242	411	7.41e-03
GO:BP	GO:0010876	lipid localization	188	312	8.07e-03
GO:BP	GO:0016043	cellular component organization	2651	5139	8.20e-03
GO:BP	GO:0001775	cell activation	377	665	8.80e-03
GO:BP	GO:0031175	neuron projection development	445	794	8.80e-03
GO:BP	GO:0060350	endochondral bone morphogenesis	37	48	8.92e-03
GO:BP	GO:0009410	response to xenobiotic stimulus	169	278	9.16e-03
GO:BP	GO:0040017	positive regulation of locomotion	253	433	9.74e-03
GO:BP	GO:0071396	cellular response to lipid	239	407	9.74e-03
GO:BP	GO:0030334	regulation of cell migration	400	710	1.07e-02
GO:BP	GO:0060429	epithelium development	466	836	1.12e-02
GO:BP	GO:0040007	growth	415	739	1.14e-02
GO:BP	GO:0002682	regulation of immune system process	518	936	1.19e-02
GO:BP	GO:0030001	metal ion transport	317	554	1.19e-02
GO:BP	GO:2000147	positive regulation of cell motility	248	425	1.21e-02
GO:BP	GO:0044057	regulation of system process	234	399	1.21e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	355	626	1.24e-02
GO:BP	GO:0035148	tube formation	86	131	1.27e-02
GO:BP	GO:0006909	phagocytosis	94	145	1.27e-02
GO:BP	GO:0009887	animal organ morphogenesis	399	710	1.33e-02
GO:BP	GO:0006955	immune response	515	932	1.43e-02
GO:BP	GO:0048864	stem cell development	53	75	1.46e-02
GO:BP	GO:0060349	bone morphogenesis	53	75	1.46e-02
GO:BP	GO:0014032	neural crest cell development	50	70	1.46e-02
GO:BP	GO:0036211	protein modification process	1280	2423	1.46e-02
GO:BP	GO:0002009	morphogenesis of an epithelium	229	391	1.48e-02
GO:BP	GO:0030217	T cell differentiation	119	190	1.51e-02
GO:BP	GO:0001501	skeletal system development	217	369	1.54e-02
GO:BP	GO:0042110	T cell activation	192	323	1.60e-02
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	311	545	1.60e-02
GO:BP	GO:0031325	positive regulation of cellular metabolic process	1305	2474	1.63e-02
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	368	653	1.64e-02
GO:BP	GO:0030155	regulation of cell adhesion	308	540	1.76e-02
GO:BP	GO:0031099	regeneration	95	148	1.77e-02
GO:BP	GO:0040012	regulation of locomotion	427	766	1.77e-02
GO:BP	GO:2000145	regulation of cell motility	416	745	1.77e-02
GO:BP	GO:1903131	mononuclear cell differentiation	177	296	1.77e-02
GO:BP	GO:0009967	positive regulation of signal transduction	629	1154	1.77e-02
GO:BP	GO:0043009	chordate embryonic development	302	529	1.78e-02
GO:BP	GO:0019538	protein metabolic process	1997	3848	1.86e-02
GO:BP	GO:0010893	positive regulation of steroid biosynthetic process	15	16	1.86e-02
GO:BP	GO:0016310	phosphorylation	658	1211	1.87e-02
GO:BP	GO:0072073	kidney epithelium development	76	115	1.87e-02
GO:BP	GO:0019935	cyclic-nucleotide-mediated signaling	38	51	1.90e-02
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	267	464	1.97e-02
GO:BP	GO:0042592	homeostatic process	654	1204	2.00e-02
GO:BP	GO:0006869	lipid transport	164	273	2.00e-02
GO:BP	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	271	472	2.12e-02
GO:BP	GO:0040011	locomotion	474	858	2.20e-02
GO:BP	GO:0019222	regulation of metabolic process	2529	4914	2.20e-02
GO:BP	GO:0030301	cholesterol transport	57	83	2.36e-02
GO:BP	GO:0008219	cell death	810	1509	2.38e-02
GO:BP	GO:0051093	negative regulation of developmental process	371	662	2.41e-02
GO:BP	GO:0030098	lymphocyte differentiation	158	263	2.45e-02
GO:BP	GO:0043434	response to peptide hormone	191	324	2.58e-02
GO:BP	GO:0000902	cell morphogenesis	424	764	2.68e-02
GO:BP	GO:1901186	positive regulation of ERBB signaling pathway	19	22	2.68e-02
GO:BP	GO:0009187	cyclic nucleotide metabolic process	25	31	2.68e-02
GO:BP	GO:0031032	actomyosin structure organization	117	189	2.72e-02
GO:BP	GO:0033036	macromolecule localization	1290	2453	2.78e-02
GO:BP	GO:0061061	muscle structure development	316	559	2.86e-02
GO:BP	GO:0046903	secretion	367	656	2.92e-02
GO:BP	GO:0065009	regulation of molecular function	747	1389	2.96e-02
GO:BP	GO:0071702	organic substance transport	967	1819	3.01e-02
GO:BP	GO:0012501	programmed cell death	806	1505	3.25e-02
GO:BP	GO:0072175	epithelial tube formation	79	122	3.26e-02
GO:BP	GO:0014902	myotube differentiation	60	89	3.26e-02
GO:BP	GO:0001841	neural tube formation	64	96	3.41e-02
GO:BP	GO:0006915	apoptotic process	782	1459	3.45e-02
GO:BP	GO:0009891	positive regulation of biosynthetic process	1045	1974	3.48e-02
GO:BP	GO:0007409	axonogenesis	211	363	3.50e-02
GO:BP	GO:0001755	neural crest cell migration	36	49	3.71e-02
GO:BP	GO:0008285	negative regulation of cell population proliferation	288	508	3.72e-02
GO:BP	GO:0060485	mesenchyme development	153	256	3.74e-02
GO:BP	GO:0052652	cyclic purine nucleotide metabolic process	24	30	3.96e-02
GO:BP	GO:0048871	multicellular organismal-level homeostasis	321	571	3.96e-02
GO:BP	GO:0071363	cellular response to growth factor stimulus	312	554	3.99e-02
GO:BP	GO:0035886	vascular associated smooth muscle cell differentiation	22	27	4.11e-02
GO:BP	GO:0032868	response to insulin	127	209	4.11e-02
GO:BP	GO:0023056	positive regulation of signaling	695	1292	4.11e-02
GO:BP	GO:0032940	secretion by cell	325	579	4.11e-02
GO:BP	GO:0045940	positive regulation of steroid metabolic process	18	21	4.11e-02
GO:BP	GO:0072009	nephron epithelium development	59	88	4.11e-02
GO:BP	GO:0097306	cellular response to alcohol	52	76	4.11e-02
GO:BP	GO:0042981	regulation of apoptotic process	594	1096	4.12e-02
GO:BP	GO:0051146	striated muscle cell differentiation	145	242	4.15e-02
GO:BP	GO:0048534	hematopoietic or lymphoid organ development	49	71	4.21e-02
GO:BP	GO:0071417	cellular response to organonitrogen compound	263	462	4.22e-02
GO:BP	GO:0090497	mesenchymal cell migration	37	51	4.28e-02
GO:BP	GO:0061564	axon development	231	402	4.33e-02
GO:BP	GO:0065008	regulation of biological quality	1076	2039	4.41e-02
GO:BP	GO:0070848	response to growth factor	323	576	4.41e-02
GO:BP	GO:0001503	ossification	188	322	4.54e-02
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	76	118	4.54e-02
GO:BP	GO:0001838	embryonic epithelial tube formation	72	111	4.55e-02
GO:BP	GO:0044281	small molecule metabolic process	725	1352	4.55e-02
GO:BP	GO:0060562	epithelial tube morphogenesis	163	276	4.83e-02
GO:BP	GO:0031290	retinal ganglion cell axon guidance	13	14	4.86e-02

NR3h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in NR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in NR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:00000	KEGG root term	2990	5802	7.34e-03

Hyper/hypo-24hr

NR24h_hyper_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/NR_24h_hyper_resgenes.RDS")
NR24h_hypo_nomtable <- readRDS("data/GO_KEGG_analysis/final_analysis/NR_24h_hypo_resgenes.RDS")

NR24h_hyper_nomtable <-  NR24h_hyper_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))# %>% 
NR24h_hypo_nomtable <-  NR24h_hypo_nomtable$result %>% 
  dplyr::select(c(source, term_id,
                  term_name,intersection_size, 
                   term_size, p_value))

NR24h_hyper_nomtable %>%
  filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr NR-hyper accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr NR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0008150	biological_process	9427	12051	3.45e-26
GO:BP	GO:0009987	cellular process	8969	11450	8.49e-21
GO:BP	GO:0048518	positive regulation of biological process	3677	4561	1.75e-11
GO:BP	GO:0051716	cellular response to stimulus	3960	4933	9.39e-11
GO:BP	GO:0050896	response to stimulus	4577	5732	1.07e-10
GO:BP	GO:0007154	cell communication	3419	4248	1.05e-09
GO:BP	GO:0048522	positive regulation of cellular process	3380	4198	1.05e-09
GO:BP	GO:0023052	signaling	3363	4180	2.41e-09
GO:BP	GO:0050789	regulation of biological process	6329	8037	7.81e-09
GO:BP	GO:0065007	biological regulation	6506	8275	2.47e-08
GO:BP	GO:0007165	signal transduction	3092	3846	5.46e-08
GO:BP	GO:0023051	regulation of signaling	2115	2597	5.46e-08
GO:BP	GO:0010646	regulation of cell communication	2116	2601	1.07e-07
GO:BP	GO:0050794	regulation of cellular process	6023	7651	1.10e-07
GO:BP	GO:0051179	localization	3187	3978	4.01e-07
GO:BP	GO:0006810	transport	2561	3176	5.09e-07
GO:BP	GO:0008152	metabolic process	6636	8464	6.17e-07
GO:BP	GO:0051234	establishment of localization	2771	3447	7.10e-07
GO:BP	GO:0007166	cell surface receptor signaling pathway	1557	1900	8.56e-07
GO:BP	GO:0071702	organic substance transport	1493	1819	8.56e-07
GO:BP	GO:0048856	anatomical structure development	3301	4130	9.05e-07
GO:BP	GO:0009966	regulation of signal transduction	1876	2307	1.41e-06
GO:BP	GO:0042221	response to chemical	1973	2436	5.51e-06
GO:BP	GO:0048523	negative regulation of cellular process	3040	3804	6.44e-06
GO:BP	GO:0009893	positive regulation of metabolic process	2241	2780	7.49e-06
GO:BP	GO:0033036	macromolecule localization	1985	2453	7.49e-06
GO:BP	GO:0032502	developmental process	3559	4475	8.58e-06
GO:BP	GO:0009653	anatomical structure morphogenesis	1589	1951	1.17e-05
GO:BP	GO:0032501	multicellular organismal process	3830	4830	1.96e-05
GO:BP	GO:0007275	multicellular organism development	2707	3383	2.12e-05
GO:BP	GO:0051641	cellular localization	2247	2793	2.12e-05
GO:BP	GO:0048583	regulation of response to stimulus	2332	2902	2.12e-05
GO:BP	GO:0044238	primary metabolic process	6036	7701	2.21e-05
GO:BP	GO:1901564	organonitrogen compound metabolic process	3677	4637	4.02e-05
GO:BP	GO:0051239	regulation of multicellular organismal process	1664	2052	4.02e-05
GO:BP	GO:0007267	cell-cell signaling	956	1156	4.45e-05
GO:BP	GO:0044237	cellular metabolic process	5912	7545	5.52e-05
GO:BP	GO:0048519	negative regulation of biological process	3210	4037	6.31e-05
GO:BP	GO:0071704	organic substance metabolic process	6331	8096	8.31e-05
GO:BP	GO:0070887	cellular response to chemical stimulus	1504	1852	8.58e-05
GO:BP	GO:0032879	regulation of localization	1243	1521	8.67e-05
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	2055	2555	8.67e-05
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	629	749	9.19e-05
GO:BP	GO:0031325	positive regulation of cellular metabolic process	1991	2474	9.76e-05
GO:BP	GO:0019538	protein metabolic process	3060	3848	1.20e-04
GO:BP	GO:1902531	regulation of intracellular signal transduction	1127	1376	1.32e-04
GO:BP	GO:0006915	apoptotic process	1192	1459	1.59e-04
GO:BP	GO:0008104	protein localization	1718	2128	1.64e-04
GO:BP	GO:0042592	homeostatic process	990	1204	1.68e-04
GO:BP	GO:0009719	response to endogenous stimulus	1031	1256	1.78e-04
GO:BP	GO:0060341	regulation of cellular localization	680	815	1.91e-04
GO:BP	GO:0070727	cellular macromolecule localization	1725	2138	1.93e-04
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	1860	2311	2.15e-04
GO:BP	GO:0051049	regulation of transport	957	1164	2.49e-04
GO:BP	GO:0042981	regulation of apoptotic process	903	1096	2.51e-04
GO:BP	GO:0048731	system development	2321	2903	2.68e-04
GO:BP	GO:0006807	nitrogen compound metabolic process	5773	7376	2.68e-04
GO:BP	GO:0071705	nitrogen compound transport	1253	1539	2.68e-04
GO:BP	GO:0048869	cellular developmental process	2387	2988	2.75e-04
GO:BP	GO:0048513	animal organ development	1717	2130	2.75e-04
GO:BP	GO:0008219	cell death	1229	1509	2.78e-04
GO:BP	GO:0030154	cell differentiation	2386	2987	2.78e-04
GO:BP	GO:1901700	response to oxygen-containing compound	941	1145	3.05e-04
GO:BP	GO:0010033	response to organic substance	1485	1835	3.11e-04
GO:BP	GO:0035556	intracellular signal transduction	1676	2079	3.41e-04
GO:BP	GO:0012501	programmed cell death	1225	1505	3.44e-04
GO:BP	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	402	472	4.58e-04
GO:BP	GO:0045184	establishment of protein localization	1192	1465	5.42e-04
GO:BP	GO:0048584	positive regulation of response to stimulus	1299	1601	5.47e-04
GO:BP	GO:0009967	positive regulation of signal transduction	946	1154	6.05e-04
GO:BP	GO:1901701	cellular response to oxygen-containing compound	691	833	6.09e-04
GO:BP	GO:0015031	protein transport	991	1211	6.09e-04
GO:BP	GO:0043067	regulation of programmed cell death	925	1128	6.75e-04
GO:BP	GO:0050793	regulation of developmental process	1455	1801	7.08e-04
GO:BP	GO:0071310	cellular response to organic substance	1116	1370	7.08e-04
GO:BP	GO:0071495	cellular response to endogenous stimulus	893	1088	7.30e-04
GO:BP	GO:0023056	positive regulation of signaling	1054	1292	8.03e-04
GO:BP	GO:0045595	regulation of cell differentiation	929	1134	8.29e-04
GO:BP	GO:0009058	biosynthetic process	4653	5927	9.12e-04
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	724	876	9.17e-04
GO:BP	GO:0030029	actin filament-based process	565	677	1.02e-03
GO:BP	GO:0010243	response to organonitrogen compound	596	716	1.09e-03
GO:BP	GO:0043170	macromolecule metabolic process	5468	6990	1.09e-03
GO:BP	GO:1901576	organic substance biosynthetic process	4620	5886	1.13e-03
GO:BP	GO:0022008	neurogenesis	1080	1327	1.24e-03
GO:BP	GO:0016043	cellular component organization	4044	5139	1.26e-03
GO:BP	GO:0009891	positive regulation of biosynthetic process	1588	1974	1.26e-03
GO:BP	GO:0010647	positive regulation of cell communication	1049	1288	1.30e-03
GO:BP	GO:0043065	positive regulation of apoptotic process	337	395	1.64e-03
GO:BP	GO:0051254	positive regulation of RNA metabolic process	1160	1430	1.67e-03
GO:BP	GO:1901698	response to nitrogen compound	641	774	1.70e-03
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	1291	1597	1.77e-03
GO:BP	GO:0061061	muscle structure development	469	559	1.77e-03
GO:BP	GO:0043434	response to peptide hormone	279	324	1.88e-03
GO:BP	GO:0071840	cellular component organization or biogenesis	4196	5340	1.99e-03
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	1528	1900	1.99e-03
GO:BP	GO:0061919	process utilizing autophagic mechanism	438	521	2.14e-03
GO:BP	GO:0006914	autophagy	438	521	2.14e-03
GO:BP	GO:0044249	cellular biosynthetic process	4571	5828	2.15e-03
GO:BP	GO:0030036	actin cytoskeleton organization	502	601	2.27e-03
GO:BP	GO:0051649	establishment of localization in cell	1340	1661	2.30e-03
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	73	77	2.39e-03
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	1573	1959	2.52e-03
GO:BP	GO:0032880	regulation of protein localization	602	727	2.85e-03
GO:BP	GO:0051223	regulation of protein transport	291	340	3.23e-03
GO:BP	GO:1901652	response to peptide	324	381	3.67e-03
GO:BP	GO:0072359	circulatory system development	735	896	4.44e-03
GO:BP	GO:0023057	negative regulation of signaling	905	1111	4.44e-03
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	1057	1304	4.48e-03
GO:BP	GO:0070201	regulation of establishment of protein localization	359	425	4.74e-03
GO:BP	GO:0010648	negative regulation of cell communication	903	1109	4.94e-03
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	1054	1301	5.28e-03
GO:BP	GO:0044271	cellular nitrogen compound biosynthetic process	2946	3730	5.82e-03
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	619	751	6.04e-03
GO:BP	GO:0019222	regulation of metabolic process	3860	4914	6.45e-03
GO:BP	GO:0001944	vasculature development	477	573	6.45e-03
GO:BP	GO:0046903	secretion	543	656	6.98e-03
GO:BP	GO:0044248	cellular catabolic process	1052	1300	7.18e-03
GO:BP	GO:0031329	regulation of cellular catabolic process	491	591	7.38e-03
GO:BP	GO:0009888	tissue development	1150	1425	7.46e-03
GO:BP	GO:0006950	response to stress	2157	2715	7.48e-03
GO:BP	GO:0009968	negative regulation of signal transduction	847	1040	7.48e-03
GO:BP	GO:0043068	positive regulation of programmed cell death	341	404	7.54e-03
GO:BP	GO:0048468	cell development	1599	1999	7.75e-03
GO:BP	GO:0036211	protein modification process	1929	2423	8.67e-03
GO:BP	GO:0051128	regulation of cellular component organization	1593	1992	8.67e-03
GO:BP	GO:0010506	regulation of autophagy	272	319	8.84e-03
GO:BP	GO:0009611	response to wounding	339	402	8.90e-03
GO:BP	GO:0006996	organelle organization	2378	3001	8.92e-03
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	343	407	8.92e-03
GO:BP	GO:0051240	positive regulation of multicellular organismal process	902	1111	9.46e-03
GO:BP	GO:0045597	positive regulation of cell differentiation	518	626	9.76e-03
GO:BP	GO:0003281	ventricular septum development	65	69	1.01e-02
GO:BP	GO:1904019	epithelial cell apoptotic process	94	103	1.03e-02
GO:BP	GO:0046907	intracellular transport	999	1235	1.09e-02
GO:BP	GO:0022411	cellular component disassembly	381	455	1.12e-02
GO:BP	GO:0032940	secretion by cell	480	579	1.18e-02
GO:BP	GO:0009887	animal organ morphogenesis	584	710	1.27e-02
GO:BP	GO:0009894	regulation of catabolic process	728	892	1.32e-02
GO:BP	GO:0080090	regulation of primary metabolic process	3357	4269	1.32e-02
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	138	156	1.32e-02
GO:BP	GO:0030182	neuron differentiation	876	1080	1.42e-02
GO:BP	GO:0071692	protein localization to extracellular region	228	266	1.44e-02
GO:BP	GO:0001568	blood vessel development	453	546	1.50e-02
GO:BP	GO:0198738	cell-cell signaling by wnt	320	380	1.54e-02
GO:BP	GO:0007010	cytoskeleton organization	984	1218	1.62e-02
GO:BP	GO:0031331	positive regulation of cellular catabolic process	244	286	1.62e-02
GO:BP	GO:0019725	cellular homeostasis	491	594	1.62e-02
GO:BP	GO:0016055	Wnt signaling pathway	319	379	1.66e-02
GO:BP	GO:0016192	vesicle-mediated transport	994	1231	1.67e-02
GO:BP	GO:1901566	organonitrogen compound biosynthetic process	1166	1451	1.92e-02
GO:BP	GO:0048878	chemical homeostasis	581	708	1.95e-02
GO:BP	GO:0007399	nervous system development	1519	1903	2.04e-02
GO:BP	GO:0009306	protein secretion	224	262	2.11e-02
GO:BP	GO:0009725	response to hormone	522	634	2.11e-02
GO:BP	GO:0051246	regulation of protein metabolic process	1354	1692	2.11e-02
GO:BP	GO:0035592	establishment of protein localization to extracellular region	224	262	2.11e-02
GO:BP	GO:0007015	actin filament organization	320	381	2.13e-02
GO:BP	GO:0051093	negative regulation of developmental process	544	662	2.26e-02
GO:BP	GO:0051155	positive regulation of striated muscle cell differentiation	31	31	2.27e-02
GO:BP	GO:0010035	response to inorganic substance	331	395	2.35e-02
GO:BP	GO:0071363	cellular response to growth factor stimulus	458	554	2.37e-02
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	235	276	2.50e-02
GO:BP	GO:0007423	sensory organ development	334	399	2.55e-02
GO:BP	GO:0030111	regulation of Wnt signaling pathway	234	275	2.74e-02
GO:BP	GO:0048880	sensory system development	234	275	2.74e-02
GO:BP	GO:0070848	response to growth factor	475	576	2.81e-02
GO:BP	GO:0048699	generation of neurons	924	1145	2.96e-02
GO:BP	GO:0071417	cellular response to organonitrogen compound	384	462	2.99e-02
GO:BP	GO:0006796	phosphate-containing compound metabolic process	1597	2006	3.01e-02
GO:BP	GO:0040007	growth	604	739	3.01e-02
GO:BP	GO:0048585	negative regulation of response to stimulus	1029	1279	3.01e-02
GO:BP	GO:0006793	phosphorus metabolic process	1614	2028	3.08e-02
GO:BP	GO:1904035	regulation of epithelial cell apoptotic process	70	76	3.10e-02
GO:BP	GO:0051171	regulation of nitrogen compound metabolic process	3274	4170	3.16e-02
GO:BP	GO:0150063	visual system development	232	273	3.23e-02
GO:BP	GO:0051098	regulation of binding	180	209	3.33e-02
GO:BP	GO:0001654	eye development	231	272	3.56e-02
GO:BP	GO:0045596	negative regulation of cell differentiation	397	479	3.59e-02
GO:BP	GO:0009056	catabolic process	1645	2069	3.60e-02
GO:BP	GO:0008610	lipid biosynthetic process	463	562	3.64e-02
GO:BP	GO:0035239	tube morphogenesis	547	668	3.73e-02
GO:BP	GO:0009059	macromolecule biosynthetic process	4032	5155	3.74e-02
GO:BP	GO:0141124	intracellular signaling cassette	1125	1403	3.74e-02
GO:BP	GO:0048871	multicellular organismal-level homeostasis	470	571	3.77e-02
GO:BP	GO:0097720	calcineurin-mediated signaling	37	38	3.79e-02
GO:BP	GO:0048870	cell motility	958	1190	3.79e-02
GO:BP	GO:0140352	export from cell	512	624	3.79e-02
GO:BP	GO:0032386	regulation of intracellular transport	200	234	3.82e-02
GO:BP	GO:0031667	response to nutrient levels	308	368	3.82e-02
GO:BP	GO:0050708	regulation of protein secretion	160	185	4.11e-02
GO:BP	GO:0009991	response to extracellular stimulus	327	392	4.20e-02
GO:BP	GO:0008283	cell population proliferation	1111	1386	4.21e-02
GO:BP	GO:0032970	regulation of actin filament-based process	266	316	4.23e-02
GO:BP	GO:0006886	intracellular protein transport	506	617	4.31e-02
GO:BP	GO:0006629	lipid metabolic process	793	981	4.58e-02
GO:BP	GO:0033173	calcineurin-NFAT signaling cascade	36	37	4.58e-02
GO:BP	GO:0060255	regulation of macromolecule metabolic process	3537	4515	4.60e-02
GO:BP	GO:0030514	negative regulation of BMP signaling pathway	43	45	4.64e-02
GO:BP	GO:0060324	face development	43	45	4.64e-02
GO:BP	GO:0007155	cell adhesion	811	1004	4.64e-02
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	829	1027	4.67e-02
GO:BP	GO:0016477	cell migration	869	1078	4.71e-02
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	836	1036	4.71e-02
GO:BP	GO:0043069	negative regulation of programmed cell death	561	687	4.72e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	252	299	4.72e-02
GO:BP	GO:0042594	response to starvation	158	183	4.88e-02
GO:BP	GO:0009410	response to xenobiotic stimulus	235	278	4.88e-02
GO:BP	GO:0042692	muscle cell differentiation	280	334	4.95e-02
GO:BP	GO:0042127	regulation of cell population proliferation	922	1146	5.00e-02

NR24h_hyper_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr NR-hyper accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr NR-hyper accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:00000	KEGG root term	4595	5802	3.90e-07
KEGG	KEGG:04140	Autophagy - animal	139	157	2.01e-02
KEGG	KEGG:04015	Rap1 signaling pathway	144	164	2.01e-02
KEGG	KEGG:05200	Pathways in cancer	342	408	2.01e-02

NR24h_hypo_nomtable %>%
   filter(source=="GO:BP", p_value < 0.05) %>% 
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(.,caption = " Significant (p<0.05) GO:BP terms found in 24 hr NR-hypo accesible neargenes" ) %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) GO:BP terms found in 24 hr NR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0008150	biological_process	7368	12051	7.73e-16
GO:BP	GO:0009987	cellular process	7006	11450	2.45e-11
GO:BP	GO:0008152	metabolic process	5231	8464	1.12e-06
GO:BP	GO:0071704	organic substance metabolic process	4987	8096	1.80e-04
GO:BP	GO:1901564	organonitrogen compound metabolic process	2914	4637	1.80e-04
GO:BP	GO:0048518	positive regulation of biological process	2863	4561	4.06e-04
GO:BP	GO:0044237	cellular metabolic process	4651	7545	5.08e-04
GO:BP	GO:0044238	primary metabolic process	4744	7701	5.08e-04
GO:BP	GO:0006807	nitrogen compound metabolic process	4541	7376	2.33e-03
GO:BP	GO:0051716	cellular response to stimulus	3074	4933	3.09e-03
GO:BP	GO:0050896	response to stimulus	3553	5732	3.91e-03
GO:BP	GO:0030029	actin filament-based process	460	677	4.19e-03
GO:BP	GO:0050789	regulation of biological process	4928	8037	4.69e-03
GO:BP	GO:0050794	regulation of cellular process	4696	7651	6.01e-03
GO:BP	GO:0048522	positive regulation of cellular process	2624	4198	6.01e-03
GO:BP	GO:0065007	biological regulation	5065	8275	7.74e-03
GO:BP	GO:0030036	actin cytoskeleton organization	409	601	8.08e-03
GO:BP	GO:0019538	protein metabolic process	2406	3848	1.34e-02
GO:BP	GO:0071702	organic substance transport	1166	1819	1.70e-02
GO:BP	GO:0006810	transport	1996	3176	1.70e-02
GO:BP	GO:0051179	localization	2480	3978	2.52e-02
GO:BP	GO:0051234	establishment of localization	2157	3447	2.91e-02
GO:BP	GO:0009893	positive regulation of metabolic process	1749	2780	4.19e-02
GO:BP	GO:0061061	muscle structure development	377	559	4.21e-02

NR24h_hypo_nomtable %>%
  filter(source=="KEGG", p_value < 0.05) %>%
  mutate_at(.vars = 6, .funs = scientific_format()) %>%
  kable(., caption = "Significant (p<0.05) KEGG terms found in 24 hr NR-hypo accesible neargenes") %>%
  kable_paper("striped", full_width = FALSE) %>%
  kable_styling(
    full_width = FALSE,
    position = "left",
    bootstrap_options = c("striped", "hover")
  ) %>%
  scroll_box(width = "100%", height = "400px")

Significant (p<0.05) KEGG terms found in 24 hr NR-hypo accesible neargenes

source	term_id	term_name	intersection_size	term_size	p_value
KEGG	KEGG:00000	KEGG root term	3577	5802	1.95e-02
KEGG	KEGG:01100	Metabolic pathways	745	1149	2.20e-02

3 hr and 24 hour Near-genes shared between hyper/hypo

Past versions of EARhypo-hyper-1.png

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02
bd33175	reneeisnowhere	2024-06-07

Past versions of EARhypo-hyper-2.png

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02
bd33175	reneeisnowhere	2024-06-07

Past versions of EARhypo-hyper-3.png

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02
bd33175	reneeisnowhere	2024-06-07

Past versions of EARhypo-hyper-4.png

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR3h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 EAR_hyper accessible GO:BP terms")

Past versions of "bargraph EAR 3hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR3h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 EAR_hyper accessible KEGG pathways")

Past versions of "bargraph EAR 3hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR3h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 EAR_hypo accessible GO:BP terms")

Past versions of "bargraph EAR 3hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR3h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 EAR_hypo accessible KEGG pathways")

Past versions of "bargraph EAR 3hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR24h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 EAR_hyper accessible GO:BP terms")

Past versions of "bargraph EAR 24hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR24h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 EAR_hyper accessible KEGG pathways")

Past versions of "bargraph EAR 24hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR24h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 EAR_hypo accessible GO:BP terms")

Past versions of "bargraph EAR 24hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

EAR24h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill="#F8766D")+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 EAR_hypo accessible KEGG pathways")

Past versions of "bargraph EAR 24hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR3h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 ESR_hyper accessible GO:BP terms")

Past versions of "bargraph ESR 3hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR3h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
      geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 ESR_hyper accessible KEGG pathways")

Past versions of "bargraph ESR 3hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR3h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
     geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 ESR_hypo accessible GO:BP terms")

Past versions of "bargraph ESR 3hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR3h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
     geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 ESR_hypo accessible KEGG pathways")

Past versions of "bargraph ESR 3hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR24h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 ESR_hyper accessible GO:BP terms")

Past versions of "bargraph ESR 24hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR24h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 ESR_hyper accessible KEGG pathways")

Past versions of "bargraph ESR 24hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR24h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 ESR_hypo accessible GO:BP terms")

Past versions of "bargraph ESR 24hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

ESR24h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
      geom_col(fill=fills[3])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 ESR_hypo accessible KEGG pathways")

Past versions of "bargraph ESR 24hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR3h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 LR_hyper accessible GO:BP terms")

Past versions of "bargraph LR 3hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR3h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
      geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 LR_hyper accessible KEGG pathways")

Past versions of "bargraph LR 3hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR3h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
     geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 LR_hypo accessible GO:BP terms")

Past versions of "bargraph LR 3hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR3h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
     geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 LR_hypo accessible KEGG pathways")

Past versions of "bargraph LR 3hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR24h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 LR_hyper accessible GO:BP terms")

Past versions of "bargraph LR 24hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR24h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 LR_hyper accessible KEGG pathways")

Past versions of "bargraph LR 24hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR24h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 LR_hypo accessible GO:BP terms")

Past versions of "bargraph LR 24hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

LR24h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
      geom_col(fill=fills[4])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 LR_hypo accessible KEGG pathways")

Past versions of "bargraph LR 24hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR3h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 NR_hyper accessible GO:BP terms")

Past versions of "bargraph NR 3hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR3h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
      geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 NR_hyper accessible KEGG pathways")

Past versions of "bargraph NR 3hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR3h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
     geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 NR_hypo accessible GO:BP terms")

Past versions of "bargraph NR 3hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR3h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
     geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("3 NR_hypo accessible KEGG pathways")

Past versions of "bargraph NR 3hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR24h_hyper_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 NR_hyper accessible GO:BP terms")

Past versions of "bargraph NR 24hr-1.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR24h_hyper_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=20) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
    geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 NR_hyper accessible KEGG pathways")

Past versions of "bargraph NR 24hr-2.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR24h_hypo_nomtable %>%
filter(source=="GO:BP") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
       geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 NR_hypo accessible GO:BP terms")

Past versions of "bargraph NR 24hr-3.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

NR24h_hypo_nomtable %>%
filter(source=="KEGG") %>% 
  slice_head(n=10) %>% 
  mutate(log10_p=(-log(p_value, base=10))) %>% 
  ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
      geom_col(fill=fills[1])+
  geom_vline(aes(xintercept=-log(0.05,base = 10)), col="red",linetype = 2)+
  theme_bw()+
  ylab("")+
  xlab(paste0("-log10 p-value"))+
  guides(fill="none")+
  theme(axis.text.y = element_text(color="black"))+
  ggtitle("24 NR_hypo accessible KEGG pathways")

Past versions of "bargraph NR 24hr-4.png"

Version	Author	Date
1933f92	reneeisnowhere	2024-08-02

experimental GO

Session information

sessionInfo()

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


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

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] biomaRt_2.60.1                          
 [2] ggpubr_0.6.0                            
 [3] BiocParallel_1.38.0                     
 [4] ggVennDiagram_1.5.2                     
 [5] scales_1.3.0                            
 [6] VennDiagram_1.7.3                       
 [7] futile.logger_1.4.3                     
 [8] gridExtra_2.3                           
 [9] ggfortify_0.4.17                        
[10] edgeR_4.2.1                             
[11] limma_3.60.4                            
[12] rtracklayer_1.64.0                      
[13] org.Hs.eg.db_3.19.1                     
[14] TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0
[15] GenomicFeatures_1.56.0                  
[16] AnnotationDbi_1.66.0                    
[17] Biobase_2.64.0                          
[18] GenomicRanges_1.56.1                    
[19] GenomeInfoDb_1.40.1                     
[20] IRanges_2.38.1                          
[21] S4Vectors_0.42.1                        
[22] BiocGenerics_0.50.0                     
[23] ChIPseeker_1.40.0                       
[24] gprofiler2_0.2.3                        
[25] RColorBrewer_1.1-3                      
[26] broom_1.0.6                             
[27] kableExtra_1.4.0                        
[28] lubridate_1.9.3                         
[29] forcats_1.0.0                           
[30] stringr_1.5.1                           
[31] dplyr_1.1.4                             
[32] purrr_1.0.2                             
[33] readr_2.1.5                             
[34] tidyr_1.3.1                             
[35] tibble_3.2.1                            
[36] ggplot2_3.5.1                           
[37] tidyverse_2.0.0                         
[38] workflowr_1.7.1                         

loaded via a namespace (and not attached):
  [1] fs_1.6.4                               
  [2] matrixStats_1.3.0                      
  [3] bitops_1.0-8                           
  [4] enrichplot_1.24.2                      
  [5] HDO.db_0.99.1                          
  [6] httr_1.4.7                             
  [7] tools_4.4.1                            
  [8] backports_1.5.0                        
  [9] utf8_1.2.4                             
 [10] R6_2.5.1                               
 [11] lazyeval_0.2.2                         
 [12] withr_3.0.0                            
 [13] prettyunits_1.2.0                      
 [14] cli_3.6.3                              
 [15] formatR_1.14                           
 [16] scatterpie_0.2.3                       
 [17] labeling_0.4.3                         
 [18] sass_0.4.9                             
 [19] Rsamtools_2.20.0                       
 [20] systemfonts_1.1.0                      
 [21] yulab.utils_0.1.5                      
 [22] DOSE_3.30.2                            
 [23] svglite_2.1.3                          
 [24] plotrix_3.8-4                          
 [25] rstudioapi_0.16.0                      
 [26] RSQLite_2.3.7                          
 [27] generics_0.1.3                         
 [28] gridGraphics_0.5-1                     
 [29] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [30] BiocIO_1.14.0                          
 [31] vroom_1.6.5                            
 [32] gtools_3.9.5                           
 [33] car_3.1-2                              
 [34] GO.db_3.19.1                           
 [35] Matrix_1.7-0                           
 [36] fansi_1.0.6                            
 [37] abind_1.4-5                            
 [38] lifecycle_1.0.4                        
 [39] whisker_0.4.1                          
 [40] yaml_2.3.10                            
 [41] carData_3.0-5                          
 [42] SummarizedExperiment_1.34.0            
 [43] gplots_3.1.3.1                         
 [44] qvalue_2.36.0                          
 [45] SparseArray_1.4.8                      
 [46] BiocFileCache_2.12.0                   
 [47] blob_1.2.4                             
 [48] promises_1.3.0                         
 [49] crayon_1.5.3                           
 [50] lattice_0.22-6                         
 [51] cowplot_1.1.3                          
 [52] KEGGREST_1.44.1                        
 [53] pillar_1.9.0                           
 [54] knitr_1.48                             
 [55] fgsea_1.30.0                           
 [56] rjson_0.2.21                           
 [57] boot_1.3-30                            
 [58] codetools_0.2-20                       
 [59] fastmatch_1.1-4                        
 [60] glue_1.7.0                             
 [61] getPass_0.2-4                          
 [62] ggfun_0.1.5                            
 [63] data.table_1.15.4                      
 [64] vctrs_0.6.5                            
 [65] png_0.1-8                              
 [66] treeio_1.28.0                          
 [67] gtable_0.3.5                           
 [68] cachem_1.1.0                           
 [69] xfun_0.46                              
 [70] S4Arrays_1.4.1                         
 [71] tidygraph_1.3.1                        
 [72] statmod_1.5.0                          
 [73] nlme_3.1-165                           
 [74] ggtree_3.12.0                          
 [75] bit64_4.0.5                            
 [76] progress_1.2.3                         
 [77] filelock_1.0.3                         
 [78] rprojroot_2.0.4                        
 [79] bslib_0.7.0                            
 [80] KernSmooth_2.23-24                     
 [81] colorspace_2.1-1                       
 [82] DBI_1.2.3                              
 [83] tidyselect_1.2.1                       
 [84] processx_3.8.4                         
 [85] bit_4.0.5                              
 [86] compiler_4.4.1                         
 [87] curl_5.2.1                             
 [88] git2r_0.33.0                           
 [89] httr2_1.0.2                            
 [90] xml2_1.3.6                             
 [91] DelayedArray_0.30.1                    
 [92] plotly_4.10.4                          
 [93] shadowtext_0.1.4                       
 [94] caTools_1.18.2                         
 [95] callr_3.7.6                            
 [96] rappdirs_0.3.3                         
 [97] digest_0.6.36                          
 [98] rmarkdown_2.27                         
 [99] XVector_0.44.0                         
[100] htmltools_0.5.8.1                      
[101] pkgconfig_2.0.3                        
[102] MatrixGenerics_1.16.0                  
[103] highr_0.11                             
[104] dbplyr_2.5.0                           
[105] fastmap_1.2.0                          
[106] rlang_1.1.4                            
[107] htmlwidgets_1.6.4                      
[108] UCSC.utils_1.0.0                       
[109] farver_2.1.2                           
[110] jquerylib_0.1.4                        
[111] jsonlite_1.8.8                         
[112] GOSemSim_2.30.0                        
[113] RCurl_1.98-1.16                        
[114] magrittr_2.0.3                         
[115] GenomeInfoDbData_1.2.12                
[116] ggplotify_0.1.2                        
[117] patchwork_1.2.0                        
[118] munsell_0.5.1                          
[119] Rcpp_1.0.13                            
[120] ape_5.8                                
[121] viridis_0.6.5                          
[122] stringi_1.8.4                          
[123] ggraph_2.2.1                           
[124] zlibbioc_1.50.0                        
[125] MASS_7.3-61                            
[126] plyr_1.8.9                             
[127] parallel_4.4.1                         
[128] ggrepel_0.9.5                          
[129] Biostrings_2.72.1                      
[130] graphlayouts_1.1.1                     
[131] splines_4.4.1                          
[132] hms_1.1.3                              
[133] locfit_1.5-9.10                        
[134] ps_1.7.7                               
[135] igraph_2.0.3                           
[136] ggsignif_0.6.4                         
[137] reshape2_1.4.4                         
[138] futile.options_1.0.1                   
[139] XML_3.99-0.17                          
[140] evaluate_0.24.0                        
[141] lambda.r_1.2.4                         
[142] tzdb_0.4.0                             
[143] tweenr_2.0.3                           
[144] httpuv_1.6.15                          
[145] polyclip_1.10-7                        
[146] ggforce_0.4.2                          
[147] restfulr_0.0.15                        
[148] tidytree_0.4.6                         
[149] rstatix_0.7.2                          
[150] later_1.3.2                            
[151] viridisLite_0.4.2                      
[152] aplot_0.2.3                            
[153] memoise_2.0.1                          
[154] GenomicAlignments_1.40.0               
[155] timechange_0.3.0