Last updated: 2024-08-02

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    Modified:   analysis/TSS_ATAC_MRC_DAR_FC_RNA.Rmd

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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

Version Author Date
bd33175 reneeisnowhere 2024-06-07

Version Author Date
bd33175 reneeisnowhere 2024-06-07

Version Author Date
bd33175 reneeisnowhere 2024-06-07 

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("EAR_hyper accessible GO:BP terms")

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("EAR_hyper accessible KEGG pathways")

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("EAR_hypo accessible GO:BP terms")

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("EAR_hypo accessible KEGG pathways")

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("EAR_hyper accessible GO:BP terms")

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("EAR_hyper accessible KEGG pathways")

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("EAR_hypo accessible GO:BP terms")

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("EAR_hypo accessible KEGG pathways")

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("ESR_hyper accessible GO:BP terms")

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("ESR_hyper accessible KEGG pathways")

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("ESR_hypo accessible GO:BP terms")

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("ESR_hypo accessible KEGG pathways")

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("ESR_hyper accessible GO:BP terms")

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("ESR_hyper accessible KEGG pathways")

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("ESR_hypo accessible GO:BP terms")

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("ESR_hypo accessible KEGG pathways")

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("LR_hyper accessible GO:BP terms")

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("LR_hyper accessible KEGG pathways")

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("LR_hypo accessible GO:BP terms")

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("LR_hypo accessible KEGG pathways")

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("LR_hyper accessible GO:BP terms")

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("LR_hyper accessible KEGG pathways")

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("LR_hypo accessible GO:BP terms")

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("LR_hypo accessible KEGG pathways")

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("NR_hyper accessible GO:BP terms")

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("NR_hyper accessible KEGG pathways")

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("NR_hypo accessible GO:BP terms")

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("NR_hypo accessible KEGG pathways")

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("NR_hyper accessible GO:BP terms")

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("NR_hyper accessible KEGG pathways")

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("NR_hypo accessible GO:BP terms")

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("NR_hypo accessible KEGG pathways")

experimental GO


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