RNA_association_GO_analyis
Renee Matthews
2025-05-08
Last updated: 2025-05-16
Checks: 7 0
Knit directory: ATAC_learning/
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package loading
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)Loading RNA-seq data and ATAC region data
Collapsed_peaks <- read_delim("data/Final_four_data/collapsed_new_peaks.txt",
delim = "\t",
escape_double = FALSE,
trim_ws = TRUE)
Motif_list_gr <- readRDS("data/Final_four_data/re_analysis/Motif_list_granges.RDS")
##order specific
df_list <- plyr::llply(Motif_list_gr, as.data.frame)
### no change motif_list_gr names so they do not overwrite the dataframes
names(Motif_list_gr) <- paste0(names(Motif_list_gr), "_gr")
list2env(Motif_list_gr,envir= .GlobalEnv)<environment: R_GlobalEnv>list2env(df_list,envir= .GlobalEnv)<environment: R_GlobalEnv>final_peaks_gr <- Collapsed_peaks %>%
dplyr::filter(Peakid %in% mcols(all_regions_gr)$Peakid) %>%
GRanges()
final_peaks <- Collapsed_peaks %>%
dplyr::filter(Peakid %in% mcols(all_regions_gr)$Peakid)
mrc_lookup <- bind_rows(
(EAR_open %>% dplyr::select(Peakid) %>% mutate(mrc = "EAR_open")),
(EAR_close %>% dplyr::select(Peakid) %>%mutate(mrc = "EAR_close")),
(ESR_open %>% dplyr::select(Peakid) %>%mutate(mrc = "ESR_open")),
(ESR_close %>% dplyr::select(Peakid) %>%mutate(mrc = "ESR_close")),
(ESR_opcl %>% dplyr::select(Peakid) %>%mutate(mrc = "ESR_opcl")),
(ESR_clop %>% dplyr::select(Peakid) %>%mutate(mrc = "ESR_clop")),
(LR_open %>% dplyr::select(Peakid) %>%mutate(mrc = "LR_open")),
(LR_close %>% dplyr::select(Peakid) %>%mutate(mrc = "LR_close")),
(NR %>% dplyr::select(Peakid) %>%mutate(mrc = "NR"))
) %>%
distinct(Peakid, mrc)
# Collapsed_peaks %>%
# left_join(., mrc_lookup, by = c("Peakid"="Peakid"))
RNA_exp_genes <- read.csv("data/other_papers/S13Table_Matthews2024.csv") %>%
dplyr::select(ENTREZID,SYMBOL)#### HOw I assigned expressed NG TSS to new peak file
### export final peak
a4gr <- all_four_filt_counts %>%
dplyr::select(seqnames:Geneid) %>%
dplyr::rename("Peakid"=Geneid) %>%
GRanges()
###export as bedfile for analysis
export(a4gr, "data/Final_four_data/all_four_filt.bed", format = "BED")
###Import S13Table of exspressed RNA genes from Plos Genet. 2024 paper
expressed_Genes <- S13Table_Matthews2024 %>% dplyr::select(ENTREZID,SYMBOL)
###Do the same with Grab the TSS file from biomart and export as bed file
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
my_attributes <- c('chromosome_name', 'start_position', 'end_position','entrezgene_id', 'hgnc_symbol')
# searchAttributes(mart = ensembl, pattern = "refseq")
# searchDatasets(mart=ensembl,pattern="NCBI")
gene_list <- getBM(attributes=my_attributes,
filters = "hgnc_symbol",
values = expressed_Genes$SYMBOL,
mart = ensembl)
gene_list_Final <- gene_list %>%
dplyr::filter(!is.na(entrezgene_id)) %>%
mutate(chr = if_else(chromosome_name == "X", "chrX",
if_else(chromosome_name == "Y", "chrY", paste0("chr",chromosome_name)))) %>%
mutate(chromosome_name=as.numeric(chromosome_name)) %>%
mutate(chromosome_name=if_else(!is.na(chromosome_name),chr,
if_else(nchar(chr)<5,chr,"NA_character"))) %>%
dplyr::filter(chromosome_name!="NA_character")
# saveRDS(gene_list_Final,"data/other_papers/RNA_expressed_gene_list_final.RDS")
# write.csv(gene_ref,"data/gene_ref.csv")
# listFilters(ensembl)
####
# gene_ref <- read.csv("data/gene_ref.csv")
# gene_full_list <- gene_list %>%
# mutate(chromosome_name=as.numeric(chromosome_name))%>%
# # filter(!is.na(chromosome_name)) #%>%
# na.omit(.)
# dplyr::select(chromosome_name,start_position,end_position,entrezgene_id,ensembl_gene_id)
### I performed the bedtools using cli. I moved the files to the correct directory on my hardrive to do this.
# bedtools closest -a all_four_filt.bed -b All_TSS_NGs.bed -D b >assigned_newNGbyTSS.bed
#### This file only has the tss, I had to link the geneIDs and symbols and names using the lookup_table (contains TSS, Start and end, ENTREZID, ensembl_id,and SYMBOL)
## I did learn a better way later, but the information was the same so I keep using the old file
lookup_table <- read.csv("data/Final_four_data/expressedgene_lookuptable.csv", row.names = 1)
# saveRDS(lt1,"data/Final_four_data/updated_RNA_gene_lookuptable")
lt1<- readRDS("data/Final_four_data/updated_RNA_gene_lookuptable")
# lt1 <- gene_list_Final %>%
# group_by(chromosome_name,start_position) %>%
# summarise(NG_end=paste(min(end_position)),
# ENTREZID=paste(unique(entrezgene_id),collapse=":"),
# SYMBOL=paste(unique(hgnc_symbol),collapse=":"),.groups="drop") %>% #add_row(chromosome_name="chr11",start_position=1995165,NG_end="2004552",ENTREZID="283120",SYMBOL="H19") %>%
# add_row(chromosome_name="chr16",start_position=18571161,NG_end="18571162",ENTREZID="653190",SYMBOL="ABCC6P1") %>%
# add_row(chromosome_name="chr1",start_position=69217759,NG_end="69217760",ENTREZID="64946",SYMBOL="CENPH")
NG_assigned_table <- read_delim("data/Final_four_data/assigned_newNGbyTSS.bed", col_names = FALSE)
lt1_gr <- lt1 %>%
dplyr::rename("seqnames"="chromosome_name", "start"="start_position", "end"= "NG_end") %>% GRanges()
TSS_NG_table <- NG_assigned_table %>%
dplyr::rename("chr"=X1,
"start"=X2,
"end"= X3,
"Peakid"=X6,
"NG_chr"=X7,
"NG_start"=X8 ,
"NG_end"=X9 ,
"dist_to_NG"=X13) %>%
##dropping the other columns
dplyr::select(chr:end,Peakid:NG_end,dist_to_NG) %>%
###removing a doubling of a Peakid and choosing the row with the smallest distance
group_by(Peakid) %>%
slice_min(dist_to_NG)
# anti_table <- lookup_table %>% ###56 ENTREZGENEIDS
# mutate(ENTREZID=as.numeric(ENTREZID)) %>%
# dplyr::filter(!ENTREZID %in%gene_list_Final$entrezgene_id)
# anti_join(gene_list_Final, by=c("NG_chr"="chromosome_name", "NG_start"="start_position", 'NG_end'= "end_position", "ENTREZID"="entrezgene_id")) #%>%
# dplyr::select(NG_chr:SYMBOL)
# dplyr::filter(ENTREZID!=entrezgene_id)
# rbind(lookup_table %>% mutate(ENTREZID=as.numeric(ENTREZID)) %>%
# anti_join(gene_list_Final, by=c("NG_chr"="chromosome_name", "NG_start"="start_position", 'NG_end'= "end_position", "ENTREZID"="entrezgene_id")))
collapsed_lookup_table <- lookup_table %>% group_by(NG_chr,NG_start,SYMBOL) %>%
summarize(NG_end=min(NG_end),
ENTREZID=paste(unique(ENTREZID),collapse=":"),
SYMBOL=paste(unique(SYMBOL),collapse=":"), .groups="drop")
not_matched <- TSS_NG_table %>%
GRanges()
# left_join(., lt1, by= c("NG_chr"="chromosome_name","NG_end"="start_position")) %>%
# dplyr::filter(is.na(SYMBOL))
retest <- join_overlap_intersect(not_matched,lt1_gr)
# lookup_table_match <-
test <- not_matched %>%
dplyr::select(chr:dist_to_NG) %>%
ungroup() %>%
# dplyr::filter(NG_start %in% lt1$start_position) %>%
left_join(., collapsed_lookup_table, by=c("NG_chr"="NG_chr","NG_start"="NG_start"))
retest %>%
as.data.frame %>%
group_by(Peakid) %>%
tally %>%
filter(n>1)
matched_up <- TSS_NG_table %>%
left_join(., lt1, by= c("NG_chr"="chromosome_name","NG_end"="start_position")) %>%
left_join(., collapsed_lookup_table,by=c("NG_chr"="NG_chr", "NG_start"="NG_end"))
TSS_NG_table <- matched_up %>%
dplyr::rename("NG_end"="NG_end.y", "NG_TSS"=NG_end) %>% ungroup() %>%
mutate(SYMBOL= if_else(!is.na(SYMBOL.x)&!is.na(SYMBOL.y),paste0(SYMBOL.x,":",SYMBOL.y), if_else(!is.na(SYMBOL.x) & is.na(SYMBOL.y),SYMBOL.x,if_else(is.na(SYMBOL.x)&!is.na(SYMBOL.y),SYMBOL.x,SYMBOL.y)))) %>%
mutate(ENTREZID= if_else(!is.na(ENTREZID.x)&!is.na(ENTREZID.y),paste0(ENTREZID.x,":",ENTREZID.y), if_else(!is.na(ENTREZID.x) & is.na(ENTREZID.y),ENTREZID.x,if_else(is.na(ENTREZID.x)&!is.na(ENTREZID.y),ENTREZID.x,ENTREZID.y)))) %>%
dplyr::select(chr:NG_start,NG_end,NG_TSS,ENTREZID,SYMBOL,dist_to_NG) #%>%
# write_delim(.,"data/Final_four_data/TSS_assigned_NG.txt",delim = "\t",col_names = TRUE)
### Collapsing the table to only one entry per region (some regions have more than one gene assigned)
Collapsed_new_peaks <- TSS_NG_table %>%
group_by(chr, start, end, Peakid) %>%
summarise(chr=paste(unique(chr)),
start=paste(unique(start)),
end=paste(unique(end)),
NG_chr=paste(NG_chr,collapse=":"),
NG_start=paste(NG_start,collapse=":"),
NG_end=paste(NG_end,collapse=":"),
NG_TSS=paste(NG_TSS,collapse=":"),
NCBI_gene = paste(unique(ENTREZID),collapse=","),
# ensembl_ID= paste(unique(ensembl_id),collapse = ","),
SYMBOL= paste(unique(SYMBOL),collapse = ",") ,
dist_to_NG =min(dist_to_NG))
write_delim(Collapsed_new_peaks,"data/Final_four_data/collapsed_new_peaks.txt",delim = "\t",col_names = TRUE)First step was to get an idea if response clusters had a pattern or enrichments of GO:Biological Processes that are interesting for us.
near_Genes <- final_peaks %>%
left_join(., mrc_lookup, by = c("Peakid"="Peakid"))
EAR_open_genes <- near_Genes %>%
dplyr::filter(mrc=="EAR_open") %>%
dplyr::filter(dist_to_NG >-2000 & dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
EAR_close_genes <- near_Genes %>%
dplyr::filter(mrc=="EAR_close") %>%
dplyr::filter(dist_to_NG >-2000 & dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
ESR_open_genes <- near_Genes %>%
dplyr::filter(mrc=="ESR_open") %>%
dplyr::filter(dist_to_NG >-2000 & dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
ESR_close_genes <- near_Genes %>%
dplyr::filter(mrc=="ESR_close") %>%
dplyr::filter(dist_to_NG >-2000 & dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
ESR_clop_genes <- near_Genes %>%
dplyr::filter(mrc=="ESR_clop") %>%
dplyr::filter(dist_to_NG >-2000 & dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
ESR_opcl_genes <- near_Genes %>%
dplyr::filter(mrc=="ESR_opcl") %>%
dplyr::filter(dist_to_NG >-2000 & dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
LR_open_genes <- near_Genes %>%
dplyr::filter(mrc=="LR_open") %>%
dplyr::filter(dist_to_NG >-2000&dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
LR_close_genes <- near_Genes %>%
dplyr::filter(mrc=="LR_close") %>%
dplyr::filter(dist_to_NG >-2000&dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()
NR_genes <- near_Genes %>%
dplyr::filter(mrc=="NR") %>%
dplyr::filter(dist_to_NG >-2000&dist_to_NG<2000) %>%
distinct(NCBI_gene) %>%
separate_rows(NCBI_gene, sep=",")%>%
separate_rows(NCBI_gene, sep=":")%>%
distinct()gprofiler2
GO:BP and KEGG pathway analysis of expressed RNA-seq genes within 2 kb of a response region. (region is 2 kb +/- TSS of gene)
LR_close_2kresgenes <- gost(query = LR_close_genes$NCBI_gene,
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 = RNA_exp_genes$ENTREZID,
sources=c("GO:BP","KEGG"))
saveRDS(LR_close_2kresgenes,"data/Final_four_data/re_analysis/GO_analysis/LR_close_2kresgenes.RDS")EAR_open_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/EAR_open_2kresgenes.RDS")
ESR_open_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/ESR_open_2kresgenes.RDS")
LR_open_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/LR_open_2kresgenes.RDS")
EAR_close_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/EAR_close_2kresgenes.RDS")
ESR_close_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/ESR_close_2kresgenes.RDS")
LR_close_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/LR_close_2kresgenes.RDS")
ESR_clop_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/ESR_clop_2kresgenes.RDS")
ESR_opcl_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/ESR_opcl_2kresgenes.RDS")
NR_2kresgenes <- readRDS("data/Final_four_data/re_analysis/GO_analysis/NR_2kresgenes.RDS")Function for showing GO or KEGG results
GO_KEGG_analysis <- function(df,type, setp_value=1){
# Extract the name of the dataframe
a <- deparse(substitute(df)) %>%
gsub("_2kresgenes","",.)
# Prepare the table output
df_nomtable <- df$result %>%
dplyr::select(c(source, term_id,
term_name,intersection_size,
term_size, p_value))
# Create a color palette for different dataframe names
# You can customize this color palette as needed
mrc_palette <- c(
"EAR_open" = "#F8766D",
"EAR_close" = "#f6483c",
"ESR_open" = "#7CAE00",
"ESR_close" = "#587b00",
"ESR_opcl" = "cornflowerblue",
"ESR_clop"= "grey60",
"LR_open" = "#00BFC4",
"LR_close" = "#008d91",
"NR" = "#C77CFF"
)
# Use the dataframe name as the fill color (fallback to black if name is not in the palette)
fill_color <- mrc_palette[a] %||% "darkgrey"
table <- df_nomtable %>%
dplyr::filter(source==type) %>%
dplyr::filter(p_value < setp_value) %>%
mutate_at(.vars = 6, .funs = scientific_format()) %>%
kable(.,caption = paste0("Significant (p < ",setp_value," ) ",type," terms found in ",a," 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")
# plot the table as ggplot object
plot <- df_nomtable %>%
filter(source==type) %>%
slice_head(n=10) %>%
dplyr::filter(p_value < setp_value) %>%
mutate(log10_p=(-log(p_value, base=10))) %>%
ggplot(., aes(x=log10_p, y=reorder(term_name, log10_p)))+
geom_col(fill=fill_color)+
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"),
base_size=18)+
ggtitle(paste0("(p < ",setp_value," ) ",type," terms found in\n ",a," neargenes"))
print(table)
print(plot)
}GO:BP results q < 0.05
GO_KEGG_analysis(EAR_open_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in EAR_open neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006139 </td>
<td style="text-align:left;"> nucleobase-containing compound metabolic process </td>
<td style="text-align:right;"> 301 </td>
<td style="text-align:right;"> 4474 </td>
<td style="text-align:left;"> 6.85e-04 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0090304 </td>
<td style="text-align:left;"> nucleic acid metabolic process </td>
<td style="text-align:right;"> 272 </td>
<td style="text-align:right;"> 4031 </td>
<td style="text-align:left;"> 1.90e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0010467 </td>
<td style="text-align:left;"> gene expression </td>
<td style="text-align:right;"> 313 </td>
<td style="text-align:right;"> 4785 </td>
<td style="text-align:left;"> 1.91e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009059 </td>
<td style="text-align:left;"> macromolecule biosynthetic process </td>
<td style="text-align:right;"> 330 </td>
<td style="text-align:right;"> 5150 </td>
<td style="text-align:left;"> 4.45e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0034654 </td>
<td style="text-align:left;"> nucleobase-containing compound biosynthetic process </td>
<td style="text-align:right;"> 250 </td>
<td style="text-align:right;"> 3757 </td>
<td style="text-align:left;"> 6.79e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009987 </td>
<td style="text-align:left;"> cellular process </td>
<td style="text-align:right;"> 657 </td>
<td style="text-align:right;"> 11760 </td>
<td style="text-align:left;"> 6.79e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0016070 </td>
<td style="text-align:left;"> RNA metabolic process </td>
<td style="text-align:right;"> 240 </td>
<td style="text-align:right;"> 3580 </td>
<td style="text-align:left;"> 6.79e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0141187 </td>
<td style="text-align:left;"> nucleic acid biosynthetic process </td>
<td style="text-align:right;"> 237 </td>
<td style="text-align:right;"> 3518 </td>
<td style="text-align:left;"> 6.79e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006364 </td>
<td style="text-align:left;"> rRNA processing </td>
<td style="text-align:right;"> 28 </td>
<td style="text-align:right;"> 218 </td>
<td style="text-align:left;"> 7.56e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0008150 </td>
<td style="text-align:left;"> biological_process </td>
<td style="text-align:right;"> 669 </td>
<td style="text-align:right;"> 12052 </td>
<td style="text-align:left;"> 7.60e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0071840 </td>
<td style="text-align:left;"> cellular component organization or biogenesis </td>
<td style="text-align:right;"> 335 </td>
<td style="text-align:right;"> 5336 </td>
<td style="text-align:left;"> 9.73e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0016072 </td>
<td style="text-align:left;"> rRNA metabolic process </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:right;"> 254 </td>
<td style="text-align:left;"> 1.34e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042254 </td>
<td style="text-align:left;"> ribosome biogenesis </td>
<td style="text-align:right;"> 34 </td>
<td style="text-align:right;"> 304 </td>
<td style="text-align:left;"> 1.34e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0043170 </td>
<td style="text-align:left;"> macromolecule metabolic process </td>
<td style="text-align:right;"> 418 </td>
<td style="text-align:right;"> 6936 </td>
<td style="text-align:left;"> 1.53e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009058 </td>
<td style="text-align:left;"> biosynthetic process </td>
<td style="text-align:right;"> 363 </td>
<td style="text-align:right;"> 5923 </td>
<td style="text-align:left;"> 2.27e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0032774 </td>
<td style="text-align:left;"> RNA biosynthetic process </td>
<td style="text-align:right;"> 225 </td>
<td style="text-align:right;"> 3417 </td>
<td style="text-align:left;"> 2.33e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006325 </td>
<td style="text-align:left;"> chromatin organization </td>
<td style="text-align:right;"> 59 </td>
<td style="text-align:right;"> 669 </td>
<td style="text-align:left;"> 2.33e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0034476 </td>
<td style="text-align:left;"> U5 snRNA 3'-end processing </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:left;"> 4.53e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0034473 </td>
<td style="text-align:left;"> U1 snRNA 3'-end processing </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:left;"> 4.53e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(EAR_close_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in EAR_close neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009605 </td>
<td style="text-align:left;"> response to external stimulus </td>
<td style="text-align:right;"> 18 </td>
<td style="text-align:right;"> 1400 </td>
<td style="text-align:left;"> 3.27e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048513 </td>
<td style="text-align:left;"> animal organ development </td>
<td style="text-align:right;"> 23 </td>
<td style="text-align:right;"> 2135 </td>
<td style="text-align:left;"> 3.27e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_open_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in ESR_open neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0032502 </td>
<td style="text-align:left;"> developmental process </td>
<td style="text-align:right;"> 148 </td>
<td style="text-align:right;"> 4488 </td>
<td style="text-align:left;"> 3.15e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0050793 </td>
<td style="text-align:left;"> regulation of developmental process </td>
<td style="text-align:right;"> 73 </td>
<td style="text-align:right;"> 1800 </td>
<td style="text-align:left;"> 4.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0060425 </td>
<td style="text-align:left;"> lung morphogenesis </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 42 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0030154 </td>
<td style="text-align:left;"> cell differentiation </td>
<td style="text-align:right;"> 104 </td>
<td style="text-align:right;"> 2995 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042482 </td>
<td style="text-align:left;"> positive regulation of odontogenesis </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 7 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0008283 </td>
<td style="text-align:left;"> cell population proliferation </td>
<td style="text-align:right;"> 58 </td>
<td style="text-align:right;"> 1389 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048869 </td>
<td style="text-align:left;"> cellular developmental process </td>
<td style="text-align:right;"> 104 </td>
<td style="text-align:right;"> 2996 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048856 </td>
<td style="text-align:left;"> anatomical structure development </td>
<td style="text-align:right;"> 135 </td>
<td style="text-align:right;"> 4143 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003278 </td>
<td style="text-align:left;"> apoptotic process involved in heart morphogenesis </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 6 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:2000736 </td>
<td style="text-align:left;"> regulation of stem cell differentiation </td>
<td style="text-align:right;"> 10 </td>
<td style="text-align:right;"> 74 </td>
<td style="text-align:left;"> 5.35e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:2000026 </td>
<td style="text-align:left;"> regulation of multicellular organismal development </td>
<td style="text-align:right;"> 46 </td>
<td style="text-align:right;"> 1014 </td>
<td style="text-align:left;"> 5.85e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048568 </td>
<td style="text-align:left;"> embryonic organ development </td>
<td style="text-align:right;"> 21 </td>
<td style="text-align:right;"> 317 </td>
<td style="text-align:left;"> 6.75e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0051094 </td>
<td style="text-align:left;"> positive regulation of developmental process </td>
<td style="text-align:right;"> 44 </td>
<td style="text-align:right;"> 970 </td>
<td style="text-align:left;"> 6.75e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045892 </td>
<td style="text-align:left;"> negative regulation of DNA-templated transcription </td>
<td style="text-align:right;"> 46 </td>
<td style="text-align:right;"> 1030 </td>
<td style="text-align:left;"> 6.75e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048863 </td>
<td style="text-align:left;"> stem cell differentiation </td>
<td style="text-align:right;"> 16 </td>
<td style="text-align:right;"> 198 </td>
<td style="text-align:left;"> 6.75e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:1902679 </td>
<td style="text-align:left;"> negative regulation of RNA biosynthetic process </td>
<td style="text-align:right;"> 46 </td>
<td style="text-align:right;"> 1040 </td>
<td style="text-align:left;"> 7.61e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048732 </td>
<td style="text-align:left;"> gland development </td>
<td style="text-align:right;"> 21 </td>
<td style="text-align:right;"> 324 </td>
<td style="text-align:left;"> 7.95e-03 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0051384 </td>
<td style="text-align:left;"> response to glucocorticoid </td>
<td style="text-align:right;"> 10 </td>
<td style="text-align:right;"> 89 </td>
<td style="text-align:left;"> 1.15e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007165 </td>
<td style="text-align:left;"> signal transduction </td>
<td style="text-align:right;"> 123 </td>
<td style="text-align:right;"> 3853 </td>
<td style="text-align:left;"> 1.63e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042471 </td>
<td style="text-align:left;"> ear morphogenesis </td>
<td style="text-align:right;"> 9 </td>
<td style="text-align:right;"> 76 </td>
<td style="text-align:left;"> 1.63e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007423 </td>
<td style="text-align:left;"> sensory organ development </td>
<td style="text-align:right;"> 23 </td>
<td style="text-align:right;"> 400 </td>
<td style="text-align:left;"> 1.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048839 </td>
<td style="text-align:left;"> inner ear development </td>
<td style="text-align:right;"> 12 </td>
<td style="text-align:right;"> 135 </td>
<td style="text-align:left;"> 1.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0043583 </td>
<td style="text-align:left;"> ear development </td>
<td style="text-align:right;"> 13 </td>
<td style="text-align:right;"> 155 </td>
<td style="text-align:left;"> 1.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042481 </td>
<td style="text-align:left;"> regulation of odontogenesis </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 11 </td>
<td style="text-align:left;"> 1.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042472 </td>
<td style="text-align:left;"> inner ear morphogenesis </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 62 </td>
<td style="text-align:left;"> 1.78e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0000122 </td>
<td style="text-align:left;"> negative regulation of transcription by RNA polymerase II </td>
<td style="text-align:right;"> 35 </td>
<td style="text-align:right;"> 757 </td>
<td style="text-align:left;"> 1.85e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0008150 </td>
<td style="text-align:left;"> biological_process </td>
<td style="text-align:right;"> 305 </td>
<td style="text-align:right;"> 12052 </td>
<td style="text-align:left;"> 1.85e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007275 </td>
<td style="text-align:left;"> multicellular organism development </td>
<td style="text-align:right;"> 110 </td>
<td style="text-align:right;"> 3392 </td>
<td style="text-align:left;"> 1.85e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003431 </td>
<td style="text-align:left;"> growth plate cartilage chondrocyte development </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:left;"> 1.87e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0032808 </td>
<td style="text-align:left;"> lacrimal gland development </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:left;"> 1.87e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0060070 </td>
<td style="text-align:left;"> canonical Wnt signaling pathway </td>
<td style="text-align:right;"> 17 </td>
<td style="text-align:right;"> 257 </td>
<td style="text-align:left;"> 1.95e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0031960 </td>
<td style="text-align:left;"> response to corticosteroid </td>
<td style="text-align:right;"> 10 </td>
<td style="text-align:right;"> 103 </td>
<td style="text-align:left;"> 2.24e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045934 </td>
<td style="text-align:left;"> negative regulation of nucleobase-containing compound metabolic process </td>
<td style="text-align:right;"> 49 </td>
<td style="text-align:right;"> 1226 </td>
<td style="text-align:left;"> 2.50e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0051253 </td>
<td style="text-align:left;"> negative regulation of RNA metabolic process </td>
<td style="text-align:right;"> 46 </td>
<td style="text-align:right;"> 1130 </td>
<td style="text-align:left;"> 2.58e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009890 </td>
<td style="text-align:left;"> negative regulation of biosynthetic process </td>
<td style="text-align:right;"> 64 </td>
<td style="text-align:right;"> 1744 </td>
<td style="text-align:left;"> 2.60e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045595 </td>
<td style="text-align:left;"> regulation of cell differentiation </td>
<td style="text-align:right;"> 46 </td>
<td style="text-align:right;"> 1136 </td>
<td style="text-align:left;"> 2.75e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003433 </td>
<td style="text-align:left;"> chondrocyte development involved in endochondral bone morphogenesis </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 6 </td>
<td style="text-align:left;"> 2.97e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048468 </td>
<td style="text-align:left;"> cell development </td>
<td style="text-align:right;"> 71 </td>
<td style="text-align:right;"> 2006 </td>
<td style="text-align:left;"> 2.99e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0010558 </td>
<td style="text-align:left;"> negative regulation of macromolecule biosynthetic process </td>
<td style="text-align:right;"> 62 </td>
<td style="text-align:right;"> 1693 </td>
<td style="text-align:left;"> 3.17e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0035265 </td>
<td style="text-align:left;"> organ growth </td>
<td style="text-align:right;"> 11 </td>
<td style="text-align:right;"> 132 </td>
<td style="text-align:left;"> 3.31e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0110110 </td>
<td style="text-align:left;"> positive regulation of animal organ morphogenesis </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:right;"> 26 </td>
<td style="text-align:left;"> 3.39e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0090103 </td>
<td style="text-align:left;"> cochlea morphogenesis </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 15 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:1902036 </td>
<td style="text-align:left;"> regulation of hematopoietic stem cell differentiation </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 15 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009888 </td>
<td style="text-align:left;"> tissue development </td>
<td style="text-align:right;"> 54 </td>
<td style="text-align:right;"> 1426 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0090596 </td>
<td style="text-align:left;"> sensory organ morphogenesis </td>
<td style="text-align:right;"> 13 </td>
<td style="text-align:right;"> 181 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0022603 </td>
<td style="text-align:left;"> regulation of anatomical structure morphogenesis </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:right;"> 650 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0023052 </td>
<td style="text-align:left;"> signaling </td>
<td style="text-align:right;"> 128 </td>
<td style="text-align:right;"> 4191 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048513 </td>
<td style="text-align:left;"> animal organ development </td>
<td style="text-align:right;"> 74 </td>
<td style="text-align:right;"> 2135 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0032501 </td>
<td style="text-align:left;"> multicellular organismal process </td>
<td style="text-align:right;"> 139 </td>
<td style="text-align:right;"> 4631 </td>
<td style="text-align:left;"> 3.41e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0060429 </td>
<td style="text-align:left;"> epithelium development </td>
<td style="text-align:right;"> 36 </td>
<td style="text-align:right;"> 839 </td>
<td style="text-align:left;"> 3.48e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042487 </td>
<td style="text-align:left;"> regulation of odontogenesis of dentin-containing tooth </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 7 </td>
<td style="text-align:left;"> 3.62e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007154 </td>
<td style="text-align:left;"> cell communication </td>
<td style="text-align:right;"> 128 </td>
<td style="text-align:right;"> 4204 </td>
<td style="text-align:left;"> 3.62e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009987 </td>
<td style="text-align:left;"> cellular process </td>
<td style="text-align:right;"> 298 </td>
<td style="text-align:right;"> 11760 </td>
<td style="text-align:left;"> 3.62e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045597 </td>
<td style="text-align:left;"> positive regulation of cell differentiation </td>
<td style="text-align:right;"> 29 </td>
<td style="text-align:right;"> 628 </td>
<td style="text-align:left;"> 3.79e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0008285 </td>
<td style="text-align:left;"> negative regulation of cell population proliferation </td>
<td style="text-align:right;"> 25 </td>
<td style="text-align:right;"> 511 </td>
<td style="text-align:left;"> 3.89e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0060038 </td>
<td style="text-align:left;"> cardiac muscle cell proliferation </td>
<td style="text-align:right;"> 6 </td>
<td style="text-align:right;"> 43 </td>
<td style="text-align:left;"> 3.89e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0030855 </td>
<td style="text-align:left;"> epithelial cell differentiation </td>
<td style="text-align:right;"> 23 </td>
<td style="text-align:right;"> 453 </td>
<td style="text-align:left;"> 3.89e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:2000738 </td>
<td style="text-align:left;"> positive regulation of stem cell differentiation </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 17 </td>
<td style="text-align:left;"> 4.38e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0030097 </td>
<td style="text-align:left;"> hemopoiesis </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:right;"> 669 </td>
<td style="text-align:left;"> 4.42e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0001837 </td>
<td style="text-align:left;"> epithelial to mesenchymal transition </td>
<td style="text-align:right;"> 11 </td>
<td style="text-align:right;"> 143 </td>
<td style="text-align:left;"> 4.42e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045823 </td>
<td style="text-align:left;"> positive regulation of heart contraction </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:left;"> 4.43e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0060218 </td>
<td style="text-align:left;"> hematopoietic stem cell differentiation </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:left;"> 4.43e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:1903524 </td>
<td style="text-align:left;"> positive regulation of blood circulation </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:left;"> 4.43e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003418 </td>
<td style="text-align:left;"> growth plate cartilage chondrocyte differentiation </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:left;"> 4.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045637 </td>
<td style="text-align:left;"> regulation of myeloid cell differentiation </td>
<td style="text-align:right;"> 11 </td>
<td style="text-align:right;"> 146 </td>
<td style="text-align:left;"> 4.81e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048523 </td>
<td style="text-align:left;"> negative regulation of cellular process </td>
<td style="text-align:right;"> 119 </td>
<td style="text-align:right;"> 3901 </td>
<td style="text-align:left;"> 4.88e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0016055 </td>
<td style="text-align:left;"> Wnt signaling pathway </td>
<td style="text-align:right;"> 20 </td>
<td style="text-align:right;"> 380 </td>
<td style="text-align:left;"> 4.90e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042476 </td>
<td style="text-align:left;"> odontogenesis </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 83 </td>
<td style="text-align:left;"> 4.97e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_close_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in ESR_close neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0032501 </td>
<td style="text-align:left;"> multicellular organismal process </td>
<td style="text-align:right;"> 139 </td>
<td style="text-align:right;"> 4631 </td>
<td style="text-align:left;"> 6.90e-04 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0030001 </td>
<td style="text-align:left;"> metal ion transport </td>
<td style="text-align:right;"> 29 </td>
<td style="text-align:right;"> 551 </td>
<td style="text-align:left;"> 1.03e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048731 </td>
<td style="text-align:left;"> system development </td>
<td style="text-align:right;"> 92 </td>
<td style="text-align:right;"> 2909 </td>
<td style="text-align:left;"> 1.03e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007275 </td>
<td style="text-align:left;"> multicellular organism development </td>
<td style="text-align:right;"> 103 </td>
<td style="text-align:right;"> 3392 </td>
<td style="text-align:left;"> 1.03e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0072359 </td>
<td style="text-align:left;"> circulatory system development </td>
<td style="text-align:right;"> 39 </td>
<td style="text-align:right;"> 899 </td>
<td style="text-align:left;"> 1.03e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0098660 </td>
<td style="text-align:left;"> inorganic ion transmembrane transport </td>
<td style="text-align:right;"> 28 </td>
<td style="text-align:right;"> 553 </td>
<td style="text-align:left;"> 1.03e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0060047 </td>
<td style="text-align:left;"> heart contraction </td>
<td style="text-align:right;"> 15 </td>
<td style="text-align:right;"> 199 </td>
<td style="text-align:left;"> 1.17e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003015 </td>
<td style="text-align:left;"> heart process </td>
<td style="text-align:right;"> 15 </td>
<td style="text-align:right;"> 209 </td>
<td style="text-align:left;"> 1.25e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0030154 </td>
<td style="text-align:left;"> cell differentiation </td>
<td style="text-align:right;"> 92 </td>
<td style="text-align:right;"> 2995 </td>
<td style="text-align:left;"> 1.25e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0045760 </td>
<td style="text-align:left;"> positive regulation of action potential </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 4 </td>
<td style="text-align:left;"> 1.25e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048869 </td>
<td style="text-align:left;"> cellular developmental process </td>
<td style="text-align:right;"> 92 </td>
<td style="text-align:right;"> 2996 </td>
<td style="text-align:left;"> 1.25e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0044057 </td>
<td style="text-align:left;"> regulation of system process </td>
<td style="text-align:right;"> 22 </td>
<td style="text-align:right;"> 399 </td>
<td style="text-align:left;"> 1.25e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006812 </td>
<td style="text-align:left;"> monoatomic cation transport </td>
<td style="text-align:right;"> 30 </td>
<td style="text-align:right;"> 650 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006813 </td>
<td style="text-align:left;"> potassium ion transport </td>
<td style="text-align:right;"> 12 </td>
<td style="text-align:right;"> 145 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0034220 </td>
<td style="text-align:left;"> monoatomic ion transmembrane transport </td>
<td style="text-align:right;"> 29 </td>
<td style="text-align:right;"> 627 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003008 </td>
<td style="text-align:left;"> system process </td>
<td style="text-align:right;"> 46 </td>
<td style="text-align:right;"> 1208 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006816 </td>
<td style="text-align:left;"> calcium ion transport </td>
<td style="text-align:right;"> 17 </td>
<td style="text-align:right;"> 267 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0008016 </td>
<td style="text-align:left;"> regulation of heart contraction </td>
<td style="text-align:right;"> 13 </td>
<td style="text-align:right;"> 169 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0098662 </td>
<td style="text-align:left;"> inorganic cation transmembrane transport </td>
<td style="text-align:right;"> 25 </td>
<td style="text-align:right;"> 508 </td>
<td style="text-align:left;"> 1.43e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006811 </td>
<td style="text-align:left;"> monoatomic ion transport </td>
<td style="text-align:right;"> 33 </td>
<td style="text-align:right;"> 767 </td>
<td style="text-align:left;"> 1.43e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048646 </td>
<td style="text-align:left;"> anatomical structure formation involved in morphogenesis </td>
<td style="text-align:right;"> 36 </td>
<td style="text-align:right;"> 874 </td>
<td style="text-align:left;"> 1.46e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0055117 </td>
<td style="text-align:left;"> regulation of cardiac muscle contraction </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 67 </td>
<td style="text-align:left;"> 1.46e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0010959 </td>
<td style="text-align:left;"> regulation of metal ion transport </td>
<td style="text-align:right;"> 16 </td>
<td style="text-align:right;"> 253 </td>
<td style="text-align:left;"> 1.59e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0098655 </td>
<td style="text-align:left;"> monoatomic cation transmembrane transport </td>
<td style="text-align:right;"> 25 </td>
<td style="text-align:right;"> 523 </td>
<td style="text-align:left;"> 1.89e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0070633 </td>
<td style="text-align:left;"> transepithelial transport </td>
<td style="text-align:right;"> 5 </td>
<td style="text-align:right;"> 24 </td>
<td style="text-align:left;"> 1.98e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0051924 </td>
<td style="text-align:left;"> regulation of calcium ion transport </td>
<td style="text-align:right;"> 12 </td>
<td style="text-align:right;"> 158 </td>
<td style="text-align:left;"> 1.98e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048856 </td>
<td style="text-align:left;"> anatomical structure development </td>
<td style="text-align:right;"> 116 </td>
<td style="text-align:right;"> 4143 </td>
<td style="text-align:left;"> 2.12e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0023052 </td>
<td style="text-align:left;"> signaling </td>
<td style="text-align:right;"> 117 </td>
<td style="text-align:right;"> 4191 </td>
<td style="text-align:left;"> 2.13e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007154 </td>
<td style="text-align:left;"> cell communication </td>
<td style="text-align:right;"> 117 </td>
<td style="text-align:right;"> 4204 </td>
<td style="text-align:left;"> 2.37e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009888 </td>
<td style="text-align:left;"> tissue development </td>
<td style="text-align:right;"> 50 </td>
<td style="text-align:right;"> 1426 </td>
<td style="text-align:left;"> 2.51e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048729 </td>
<td style="text-align:left;"> tissue morphogenesis </td>
<td style="text-align:right;"> 23 </td>
<td style="text-align:right;"> 480 </td>
<td style="text-align:left;"> 2.68e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0043269 </td>
<td style="text-align:left;"> regulation of monoatomic ion transport </td>
<td style="text-align:right;"> 17 </td>
<td style="text-align:right;"> 301 </td>
<td style="text-align:left;"> 2.73e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0003007 </td>
<td style="text-align:left;"> heart morphogenesis </td>
<td style="text-align:right;"> 14 </td>
<td style="text-align:right;"> 222 </td>
<td style="text-align:left;"> 3.11e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0042127 </td>
<td style="text-align:left;"> regulation of cell population proliferation </td>
<td style="text-align:right;"> 42 </td>
<td style="text-align:right;"> 1146 </td>
<td style="text-align:left;"> 3.11e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007165 </td>
<td style="text-align:left;"> signal transduction </td>
<td style="text-align:right;"> 108 </td>
<td style="text-align:right;"> 3853 </td>
<td style="text-align:left;"> 3.22e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:1903522 </td>
<td style="text-align:left;"> regulation of blood circulation </td>
<td style="text-align:right;"> 13 </td>
<td style="text-align:right;"> 199 </td>
<td style="text-align:left;"> 3.39e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0048513 </td>
<td style="text-align:left;"> animal organ development </td>
<td style="text-align:right;"> 67 </td>
<td style="text-align:right;"> 2135 </td>
<td style="text-align:left;"> 3.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0035725 </td>
<td style="text-align:left;"> sodium ion transmembrane transport </td>
<td style="text-align:right;"> 9 </td>
<td style="text-align:right;"> 104 </td>
<td style="text-align:left;"> 3.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006942 </td>
<td style="text-align:left;"> regulation of striated muscle contraction </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 83 </td>
<td style="text-align:left;"> 3.64e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006937 </td>
<td style="text-align:left;"> regulation of muscle contraction </td>
<td style="text-align:right;"> 10 </td>
<td style="text-align:right;"> 128 </td>
<td style="text-align:left;"> 3.74e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0051239 </td>
<td style="text-align:left;"> regulation of multicellular organismal process </td>
<td style="text-align:right;"> 64 </td>
<td style="text-align:right;"> 2028 </td>
<td style="text-align:left;"> 4.12e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009653 </td>
<td style="text-align:left;"> anatomical structure morphogenesis </td>
<td style="text-align:right;"> 62 </td>
<td style="text-align:right;"> 1957 </td>
<td style="text-align:left;"> 4.57e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0030239 </td>
<td style="text-align:left;"> myofibril assembly </td>
<td style="text-align:right;"> 7 </td>
<td style="text-align:right;"> 67 </td>
<td style="text-align:left;"> 4.63e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0032502 </td>
<td style="text-align:left;"> developmental process </td>
<td style="text-align:right;"> 121 </td>
<td style="text-align:right;"> 4488 </td>
<td style="text-align:left;"> 4.63e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0006936 </td>
<td style="text-align:left;"> muscle contraction </td>
<td style="text-align:right;"> 15 </td>
<td style="text-align:right;"> 268 </td>
<td style="text-align:left;"> 4.79e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0001738 </td>
<td style="text-align:left;"> morphogenesis of a polarized epithelium </td>
<td style="text-align:right;"> 6 </td>
<td style="text-align:right;"> 49 </td>
<td style="text-align:left;"> 4.79e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0070588 </td>
<td style="text-align:left;"> calcium ion transmembrane transport </td>
<td style="text-align:right;"> 13 </td>
<td style="text-align:right;"> 212 </td>
<td style="text-align:left;"> 4.79e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0007507 </td>
<td style="text-align:left;"> heart development </td>
<td style="text-align:right;"> 23 </td>
<td style="text-align:right;"> 516 </td>
<td style="text-align:left;"> 4.81e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_opcl_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in ESR_opcl neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_clop_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in ESR_clop neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(LR_open_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in LR_open neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(LR_close_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in LR_close neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(NR_2kresgenes,"GO:BP", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) GO:BP terms found in NR neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0008150 </td>
<td style="text-align:left;"> biological_process </td>
<td style="text-align:right;"> 5425 </td>
<td style="text-align:right;"> 12052 </td>
<td style="text-align:left;"> 8.35e-17 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0009987 </td>
<td style="text-align:left;"> cellular process </td>
<td style="text-align:right;"> 5295 </td>
<td style="text-align:right;"> 11760 </td>
<td style="text-align:left;"> 7.32e-14 </td>
</tr>
<tr>
<td style="text-align:left;"> GO:BP </td>
<td style="text-align:left;"> GO:0050794 </td>
<td style="text-align:left;"> regulation of cellular process </td>
<td style="text-align:right;"> 3519 </td>
<td style="text-align:right;"> 7763 </td>
<td style="text-align:left;"> 6.73e-03 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
KEGG results q < 0.05
GO_KEGG_analysis(EAR_open_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in EAR_open neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(EAR_close_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in EAR_close neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_open_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in ESR_open neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:05206 </td>
<td style="text-align:left;"> MicroRNAs in cancer </td>
<td style="text-align:right;"> 13 </td>
<td style="text-align:right;"> 149 </td>
<td style="text-align:left;"> 1.32e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:05216 </td>
<td style="text-align:left;"> Thyroid cancer </td>
<td style="text-align:right;"> 6 </td>
<td style="text-align:right;"> 35 </td>
<td style="text-align:left;"> 1.88e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04934 </td>
<td style="text-align:left;"> Cushing syndrome </td>
<td style="text-align:right;"> 10 </td>
<td style="text-align:right;"> 120 </td>
<td style="text-align:left;"> 4.60e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04024 </td>
<td style="text-align:left;"> cAMP signaling pathway </td>
<td style="text-align:right;"> 11 </td>
<td style="text-align:right;"> 150 </td>
<td style="text-align:left;"> 4.91e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:05217 </td>
<td style="text-align:left;"> Basal cell carcinoma </td>
<td style="text-align:right;"> 6 </td>
<td style="text-align:right;"> 49 </td>
<td style="text-align:left;"> 4.91e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_close_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in ESR_close neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:05414 </td>
<td style="text-align:left;"> Dilated cardiomyopathy </td>
<td style="text-align:right;"> 9 </td>
<td style="text-align:right;"> 84 </td>
<td style="text-align:left;"> 1.56e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04814 </td>
<td style="text-align:left;"> Motor proteins </td>
<td style="text-align:right;"> 11 </td>
<td style="text-align:right;"> 149 </td>
<td style="text-align:left;"> 2.45e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:05410 </td>
<td style="text-align:left;"> Hypertrophic cardiomyopathy </td>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 79 </td>
<td style="text-align:left;"> 2.45e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_opcl_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in ESR_opcl neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04152 </td>
<td style="text-align:left;"> AMPK signaling pathway </td>
<td style="text-align:right;"> 2 </td>
<td style="text-align:right;"> 102 </td>
<td style="text-align:left;"> 2.4e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04936 </td>
<td style="text-align:left;"> Alcoholic liver disease </td>
<td style="text-align:right;"> 2 </td>
<td style="text-align:right;"> 97 </td>
<td style="text-align:left;"> 2.4e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(ESR_clop_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in ESR_clop neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:00051 </td>
<td style="text-align:left;"> Fructose and mannose metabolism </td>
<td style="text-align:right;"> 1 </td>
<td style="text-align:right;"> 27 </td>
<td style="text-align:left;"> 4.75e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04115 </td>
<td style="text-align:left;"> p53 signaling pathway </td>
<td style="text-align:right;"> 1 </td>
<td style="text-align:right;"> 66 </td>
<td style="text-align:left;"> 4.88e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04152 </td>
<td style="text-align:left;"> AMPK signaling pathway </td>
<td style="text-align:right;"> 1 </td>
<td style="text-align:right;"> 102 </td>
<td style="text-align:left;"> 4.88e-02 </td>
</tr>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:04919 </td>
<td style="text-align:left;"> Thyroid hormone signaling pathway </td>
<td style="text-align:right;"> 1 </td>
<td style="text-align:right;"> 112 </td>
<td style="text-align:left;"> 4.88e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(LR_open_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in LR_open neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(LR_close_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in LR_close neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:left;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:right;"> NA </td>
<td style="text-align:left;"> NA </td>
</tr>
<tr>
<td style="text-align:left;"> :------ </td>
<td style="text-align:left;"> :------- </td>
<td style="text-align:left;"> :--------- </td>
<td style="text-align:right;"> -----------------: </td>
<td style="text-align:right;"> ---------: </td>
<td style="text-align:left;"> :------- </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
GO_KEGG_analysis(NR_2kresgenes,"KEGG", setp_value=0.05)<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%; "><table class=" lightable-paper lightable-striped table table-striped table-hover" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto; width: auto !important; '>
<caption>Significant (p < 0.05 ) KEGG terms found in NR neargenes</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> source </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_id </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> term_name </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> intersection_size </th>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> term_size </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> p_value </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> KEGG </td>
<td style="text-align:left;"> KEGG:00000 </td>
<td style="text-align:left;"> KEGG root term </td>
<td style="text-align:right;"> 2636 </td>
<td style="text-align:right;"> 5801 </td>
<td style="text-align:left;"> 3.95e-02 </td>
</tr>
</tbody>
</table></div>
| Version | Author | Date |
|---|---|---|
| 1a216ba | reneeisnowhere | 2025-05-08 |
RNA-seq genes and ATAC data
after assigning expressed genes to nearest peaks and collecting differences, I also wanted to look at LFC between associated ATAC peaks and nearby expressed genes.
toplistall_RNA <- readRDS("data/other_papers/toplistall_RNA.RDS") %>%
mutate(logFC = logFC*(-1))
ATAC_toptable_results <- readRDS("data/Final_four_data/re_analysis/Toptable_results.RDS")
ATAC_toptable_list <- bind_rows(ATAC_toptable_results, .id = "group")
hr3_RNA <- toplistall_RNA %>%
dplyr::select(time:logFC) %>%
dplyr::filter(time=="3_hours") %>%
pivot_wider(., id_cols=c(ENTREZID,SYMBOL), names_from = id, values_from = logFC) %>%
dplyr::rename(DOX_3_RNA=DOX, DNR_3_RNA=DNR,EPI_3_RNA=EPI,MTX_3_RNA=MTX, TRZ_3_RNA=TRZ)
hr24_RNA <- toplistall_RNA %>%
dplyr::select(time:logFC) %>%
dplyr::filter(time=="24_hours") %>%
pivot_wider(., id_cols=c(ENTREZID,SYMBOL), names_from = id, values_from = logFC) %>%
dplyr::rename(DOX_24_RNA=DOX, DNR_24_RNA=DNR,EPI_24_RNA=EPI,MTX_24_RNA=MTX, TRZ_24_RNA=TRZ)
RNA_LFC_df <- hr3_RNA %>%
left_join(., hr24_RNA, by=c("SYMBOL"="SYMBOL","ENTREZID"="ENTREZID"))
hr3_ATAC <- ATAC_toptable_list %>%
dplyr::select(group:logFC) %>%
separate_wider_delim(., group, names=c("trt","time"), delim="_") %>%
dplyr::filter(time=="3") %>%
pivot_wider(., id_cols=c(time, genes), names_from = trt, values_from = logFC) %>%
dplyr::rename(DOX_3_ATAC=DOX, DNR_3_ATAC=DNR,EPI_3_ATAC=EPI,MTX_3_ATAC=MTX, TRZ_3_ATAC=TRZ) %>%
dplyr::rename("peak"=genes)
hr24_ATAC <- ATAC_toptable_list %>%
dplyr::select(group:logFC) %>%
separate_wider_delim(., group, names=c("trt","time"), delim="_") %>%
dplyr::filter(time=="24") %>%
pivot_wider(., id_cols=c(time, genes), names_from = trt, values_from = logFC) %>%
dplyr::rename(DOX_24_ATAC=DOX, DNR_24_ATAC=DNR,EPI_24_ATAC=EPI,MTX_24_ATAC=MTX, TRZ_24_ATAC=TRZ) %>%
dplyr::rename("peak"=genes)
ATAC_LFC_df <- hr3_ATAC %>%
left_join(., hr24_ATAC, by=c("peak"="peak")) %>%
dplyr::select(!time.x) %>%
dplyr::select(!time.y)Combining ATAC LFC and RNA LFC by assigned expressed-near genes to peak
RNA_ATAC_mat <- final_peaks %>%
dplyr::select(Peakid, NCBI_gene,SYMBOL) %>%
separate_longer_delim(c(NCBI_gene), delim = ",") %>%
separate_longer_delim(c(NCBI_gene), delim = ":") %>%
separate_longer_delim(c(SYMBOL), delim = ",") %>%
separate_longer_delim(c(SYMBOL), delim = ":") %>%
left_join(.,ATAC_LFC_df,by=c("Peakid"="peak")) %>%
left_join(.,RNA_LFC_df, by=c("SYMBOL"="SYMBOL", "NCBI_gene"="ENTREZID")) %>%
distinct(Peakid,SYMBOL,NCBI_gene,.keep_all = TRUE) %>%
tidyr::unite(name,Peakid:SYMBOL, sep="_") %>%
column_to_rownames("name") %>%
as.matrix() Examining LFC correlation by trt and time between RNA-seq and ATAC-seq associated gene-region pairs
## do pearson correlation between matched observations of RNA and ATAC
pearson_cor_mat <- cor(RNA_ATAC_mat,method = "pearson", use = "pairwise.complete.obs")
## do spearman correlation between matched observation of RNA and ATAC
spearman_cor_mat <- cor(RNA_ATAC_mat,method = "spearman", use = "pairwise.complete.obs")
### make correlation heatmaps of both sets
ComplexHeatmap::Heatmap(pearson_cor_mat,
column_title = "Pearson RNA/ATAC LFC correlation")
ComplexHeatmap::Heatmap(spearman_cor_mat,
column_title = "Spearman RNA/ATAC LFC correlation")
What about the correlation of RNA-expression LFC with ATAC LFC region within 2kb of expressed gene TSS?
peaks_2kb <-Collapsed_peaks %>%
dplyr::select(Peakid,dist_to_NG) %>%
dplyr::filter(dist_to_NG>-2000 & dist_to_NG<2000)
RNA_ATAC_2kbmat <- final_peaks %>%
dplyr::select(Peakid, NCBI_gene,SYMBOL) %>%
separate_longer_delim(c(NCBI_gene), delim = ",") %>%
separate_longer_delim(c(NCBI_gene), delim = ":") %>%
separate_longer_delim(c(SYMBOL), delim = ",") %>%
separate_longer_delim(c(SYMBOL), delim = ":") %>%
left_join(.,ATAC_LFC_df,by=c("Peakid"="peak")) %>%
left_join(.,RNA_LFC_df, by=c("SYMBOL"="SYMBOL", "NCBI_gene"="ENTREZID")) %>%
dplyr::filter(Peakid %in% peaks_2kb$Peakid) %>%
distinct(Peakid,SYMBOL,NCBI_gene,.keep_all = TRUE) %>%
tidyr::unite(name,Peakid:SYMBOL, sep="_") %>%
column_to_rownames("name") %>%
as.matrix()
## do pearson correlation between matched observations of RNA and ATAC
pearson_cor_2kbmat <- cor(RNA_ATAC_2kbmat,method = "pearson", use = "pairwise.complete.obs")
## do spearman correlation between matched observation of RNA and ATAC
spearman_cor_2kbmat <- cor(RNA_ATAC_2kbmat,method = "spearman", use = "pairwise.complete.obs")
### make correlation heatmaps of both sets
ComplexHeatmap::Heatmap(pearson_cor_2kbmat,
column_title = "Pearson RNA/ATAC LFC correlation within 2kb")
ComplexHeatmap::Heatmap(spearman_cor_2kbmat,
column_title = "Spearman RNA/ATAC LFC correlation within 2kb")
sessionInfo()R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)
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_2.62.1
[2] ggpubr_0.6.0
[3] BiocParallel_1.40.0
[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_4.4.2
[11] limma_3.62.2
[12] rtracklayer_1.66.0
[13] org.Hs.eg.db_3.20.0
[14] TxDb.Hsapiens.UCSC.hg38.knownGene_3.20.0
[15] GenomicFeatures_1.58.0
[16] AnnotationDbi_1.68.0
[17] Biobase_2.66.0
[18] GenomicRanges_1.58.0
[19] GenomeInfoDb_1.42.3
[20] IRanges_2.40.1
[21] S4Vectors_0.44.0
[22] BiocGenerics_0.52.0
[23] ChIPseeker_1.42.1
[24] gprofiler2_0.2.3
[25] RColorBrewer_1.1-3
[26] broom_1.0.7
[27] kableExtra_1.4.0
[28] lubridate_1.9.4
[29] forcats_1.0.0
[30] stringr_1.5.1
[31] dplyr_1.1.4
[32] purrr_1.0.4
[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_1.6.5
[2] matrixStats_1.5.0
[3] bitops_1.0-9
[4] enrichplot_1.26.6
[5] httr_1.4.7
[6] doParallel_1.0.17
[7] tools_4.4.2
[8] backports_1.5.0
[9] R6_2.6.1
[10] lazyeval_0.2.2
[11] GetoptLong_1.0.5
[12] withr_3.0.2
[13] prettyunits_1.2.0
[14] cli_3.6.4
[15] formatR_1.14
[16] Cairo_1.6-2
[17] labeling_0.4.3
[18] sass_0.4.9
[19] Rsamtools_2.22.0
[20] systemfonts_1.2.1
[21] yulab.utils_0.2.0
[22] DOSE_4.0.0
[23] svglite_2.1.3
[24] R.utils_2.13.0
[25] plotrix_3.8-4
[26] rstudioapi_0.17.1
[27] RSQLite_2.3.9
[28] shape_1.4.6.1
[29] generics_0.1.3
[30] gridGraphics_0.5-1
[31] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[32] BiocIO_1.16.0
[33] gtools_3.9.5
[34] vroom_1.6.5
[35] car_3.1-3
[36] GO.db_3.20.0
[37] Matrix_1.7-3
[38] abind_1.4-8
[39] R.methodsS3_1.8.2
[40] lifecycle_1.0.4
[41] whisker_0.4.1
[42] yaml_2.3.10
[43] carData_3.0-5
[44] SummarizedExperiment_1.36.0
[45] gplots_3.2.0
[46] qvalue_2.38.0
[47] SparseArray_1.6.2
[48] BiocFileCache_2.14.0
[49] blob_1.2.4
[50] promises_1.3.2
[51] crayon_1.5.3
[52] ggtangle_0.0.6
[53] lattice_0.22-6
[54] cowplot_1.1.3
[55] KEGGREST_1.46.0
[56] magick_2.8.5
[57] pillar_1.10.1
[58] knitr_1.49
[59] ComplexHeatmap_2.22.0
[60] fgsea_1.32.2
[61] rjson_0.2.23
[62] boot_1.3-31
[63] codetools_0.2-20
[64] fastmatch_1.1-6
[65] glue_1.8.0
[66] getPass_0.2-4
[67] ggfun_0.1.8
[68] data.table_1.17.0
[69] vctrs_0.6.5
[70] png_0.1-8
[71] treeio_1.30.0
[72] gtable_0.3.6
[73] cachem_1.1.0
[74] xfun_0.51
[75] S4Arrays_1.6.0
[76] iterators_1.0.14
[77] statmod_1.5.0
[78] nlme_3.1-167
[79] ggtree_3.14.0
[80] bit64_4.6.0-1
[81] progress_1.2.3
[82] filelock_1.0.3
[83] rprojroot_2.0.4
[84] bslib_0.9.0
[85] KernSmooth_2.23-26
[86] colorspace_2.1-1
[87] DBI_1.2.3
[88] tidyselect_1.2.1
[89] processx_3.8.6
[90] bit_4.6.0
[91] compiler_4.4.2
[92] curl_6.2.1
[93] git2r_0.35.0
[94] httr2_1.1.1
[95] xml2_1.3.7
[96] DelayedArray_0.32.0
[97] plotly_4.10.4
[98] caTools_1.18.3
[99] callr_3.7.6
[100] rappdirs_0.3.3
[101] digest_0.6.37
[102] rmarkdown_2.29
[103] XVector_0.46.0
[104] htmltools_0.5.8.1
[105] pkgconfig_2.0.3
[106] MatrixGenerics_1.18.1
[107] dbplyr_2.5.0
[108] fastmap_1.2.0
[109] rlang_1.1.5
[110] GlobalOptions_0.1.2
[111] htmlwidgets_1.6.4
[112] UCSC.utils_1.2.0
[113] farver_2.1.2
[114] jquerylib_0.1.4
[115] jsonlite_1.9.1
[116] GOSemSim_2.32.0
[117] R.oo_1.27.0
[118] RCurl_1.98-1.16
[119] magrittr_2.0.3
[120] Formula_1.2-5
[121] GenomeInfoDbData_1.2.13
[122] ggplotify_0.1.2
[123] patchwork_1.3.0
[124] munsell_0.5.1
[125] Rcpp_1.0.14
[126] ape_5.8-1
[127] stringi_1.8.4
[128] zlibbioc_1.52.0
[129] plyr_1.8.9
[130] parallel_4.4.2
[131] ggrepel_0.9.6
[132] Biostrings_2.74.1
[133] splines_4.4.2
[134] circlize_0.4.16
[135] hms_1.1.3
[136] locfit_1.5-9.12
[137] ps_1.9.0
[138] igraph_2.1.4
[139] ggsignif_0.6.4
[140] reshape2_1.4.4
[141] futile.options_1.0.1
[142] XML_3.99-0.18
[143] evaluate_1.0.3
[144] lambda.r_1.2.4
[145] tzdb_0.4.0
[146] foreach_1.5.2
[147] httpuv_1.6.15
[148] clue_0.3-66
[149] restfulr_0.0.15
[150] tidytree_0.4.6
[151] rstatix_0.7.2
[152] later_1.4.1
[153] viridisLite_0.4.2
[154] aplot_0.2.5
[155] memoise_2.0.1
[156] GenomicAlignments_1.42.0
[157] cluster_2.1.8.1
[158] timechange_0.3.0