Baboon Diet Example

Last updated: 2022-03-30

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Introduction

Baboons were fed different diets for two years. Adipose, liver and muscle tissue were collected. Differential expression was conducted across the diet conditions.

library(GSEABenchmarkeR)
library(EnrichmentBrowser)
library(tidyverse)
library(susieR)
library(htmltools)
library(DT)
library(kableExtra)

source('code/load_gene_sets.R')
source('code/utils.R')
source('code/logistic_susie_vb.R')
source('code/logistic_susie_veb_boost.R')
source('code/latent_logistic_susie.R')

Setup

Load Gene Sets

loadGeneSetX uniformly formats gene sets and generates the \(X\) matrix We can source any gene set from WebGestaltR::listGeneSet()

gs_list <- WebGestaltR::listGeneSet()
gobp <- loadGeneSetX('geneontology_Biological_Process', min.size=50)  # just huge number of gene sets
gobp_nr <- loadGeneSetX('geneontology_Biological_Process_noRedundant', min.size=1)
gomf <- loadGeneSetX('geneontology_Molecular_Function', min.size=1)
kegg <- loadGeneSetX('pathway_KEGG', min.size=1)
reactome <- loadGeneSetX('pathway_Reactome', min.size=1)
wikipathway_cancer <- loadGeneSetX('pathway_Wikipathway_cancer', min.size=1)
wikipathway <- loadGeneSetX('pathway_Wikipathway', min.size=1)

genesets <- list(
  gobp=gobp,
  gobp_nr=gobp_nr,
  gomf=gomf,
  kegg=kegg,
  reactome=reactome,
  wikipathway_cancer=wikipathway_cancer,
  wikipathway=wikipathway
)

adipose <- read.table('data/wenhe_baboon_diet/DE_lrt_adipose.txt')
muscle <- read.table('data/wenhe_baboon_diet/DE_lrt_muscle.txt')
liver <- read.table('data/wenhe_baboon_diet/DE_lrt_liver.txt')
deseq <- list(Adipose=adipose, Muscle = muscle, Liver = liver)

convert_labels <- function(y, from='SYMBOL', to='ENTREZID'){
  hs <- org.Hs.eg.db::org.Hs.eg.db
  gene_symbols <- names(y)
  symbol2entrez <- AnnotationDbi::select(hs, keys=gene_symbols, columns=c(to, from), keytype = from)
  symbol2entrez <- symbol2entrez[!duplicated(symbol2entrez[[from]]),]
  symbol2entrez <- symbol2entrez[!is.na(symbol2entrez[[to]]),]
  symbol2entrez <- symbol2entrez[!is.na(symbol2entrez[[from]]),]
  rownames(symbol2entrez) <- symbol2entrez[[from]]
  ysub <- y[names(y) %in% symbol2entrez[[from]]]
  names(ysub) <- symbol2entrez[names(ysub),][[to]]
  return(ysub)
}

par(mfrow=c(1,1))
deseq$Adipose %>% .$PValue %>% hist(main='Adipose p-values')

Version	Author	Date
7d1a82b	karltayeb	2022-03-30

Fitting and reporting helpers

#' take gene level results
#' put into standard format
#' call the value we threshold on 'y'
#' convert gene labels to ENTREIZID
clean_gene_list = function(dat, thresh_col='padj', from='SYMBOL'){
  thresh_col = sym(thresh_col)
  dat %>%
    as.data.frame %>%
    rownames_to_column('gene') %>%
    dplyr::select(gene, !!thresh_col) %>%
    filter(!is.na(!!thresh_col)) %>%
    mutate(y = !!thresh_col) %>%
    select(gene, y) %>%
    tibble2namedlist %>%
    convert_labels(from)
}

#' modify this for different data sources
#' makes a binary list from table like data
proc_y = function(data, thresh){
  data %>%
    clean_gene_list('PValue') %>%
    {
      y <- as.integer(. < thresh)
      names(y) <- names(.)
      y
    }
}


#' fit logistic susie, and hypergeometric test
logistic_susie_driver = function(db, celltype, thresh){
  gs <- genesets[[db]]
  data <- deseq[[celltype]]

  # set up binary y
  y <- proc_y(data, thresh)
  
  u <- process_input(gs$X, y)  # subset to common genes
  vb.fit <- logistic.susie(  # fit model
    u$X, u$y, L=10, init.intercept = 0, verbose=1, maxit=100)

  #' hypergeometric test
  ora <- tibble(
    geneSet = colnames(u$X),
    geneListSize = sum(u$y),
    geneSetSize = colSums(u$X),
    overlap = (u$y %*% u$X)[1,],
    nGenes = length(u$y),
    propInList = overlap / geneListSize,
    propInSet = overlap / geneSetSize,
    oddsRatio = (overlap / (geneListSize - overlap)) / (
      (geneSetSize - overlap) / (nGenes - geneSetSize + overlap)),
    pValueHypergeometric = phyper(
      overlap-1, geneListSize, nGenes, geneSetSize, lower.tail= FALSE),
    db = db,
    celltype = celltype,
    thresh = thresh
  ) %>% 
  left_join(gs$geneSet$geneSetDes)

  return(list(
    fit = vb.fit,
    ora = ora,
    db = db, celltype = celltype, thresh = thresh))
}

credible_set_summary = function(res){
  gs <- genesets[[res$db]]
  data <- deseq[[res$celltype]]

  # set up binary y
  y <- proc_y(data, thresh)
  
  u <- process_input(gs$X, y)  # subset to common genes

  #' report top 50 elements in cs
  credible.set.summary <- t(res$fit$alpha) %>%
    data.frame() %>%
    rownames_to_column(var='geneSet') %>%
    rename_with(~str_replace(., 'X', 'L')) %>%
    pivot_longer(starts_with('L'), names_to='component', values_to = 'alpha') %>%
    arrange(component, desc(alpha)) %>%
    dplyr::group_by(component) %>%
    filter(row_number() < 50) %>%
    mutate(cumalpha = c(0, head(cumsum(alpha), -1))) %>%
    mutate(in_cs = cumalpha < 0.95) %>%
    mutate(active_cs = component %in% names(res$fit$sets$cs)) %>%
    left_join(res$ora) %>%
    left_join(gs$geneSet$geneSetDes)

  #' map each gene set to the component with top alpha
  #' report pip
  gene.set.summary <- res$fit$pip %>% 
    as_tibble(rownames='geneSet') %>%
    rename(pip=value) %>%
    left_join(res$ora) %>%
    left_join(gs$geneSet$geneSetDes)

  return(credible.set.summary)
}

gene_set_summary = function(res){
  gs <- genesets[[res$db]]
  #' map each gene set to the component with top alpha
  #' report pip
  res$fit$pip %>% 
    as_tibble(rownames='geneSet') %>%
    rename(pip=value) %>%
    left_join(res$ora) %>%
    left_join(gs$geneSet$geneSetDes)
}

Example usage

db = 'gobp'
celltype = 'Adipose'
thresh = 1e-4
  
res <- logistic_susie_driver(db, celltype, thresh)

'select()' returned 1:many mapping between keys and columns


converged

Joining, by = "geneSet"

credible_set_summary(res) %>% head()

'select()' returned 1:many mapping between keys and columns
Joining, by = "geneSet"Joining, by = c("geneSet", "description")Joining, by = "geneSet"Joining, by = c("geneSet", "description")

# A tibble: 6 × 18
# Groups:   component [1]
  geneSet   component    alpha cumalpha in_cs active_cs geneListSize geneSetSize
  <chr>     <chr>        <dbl>    <dbl> <lgl> <lgl>            <int>       <dbl>
1 GO:00723… L1        1.00e+ 0     0    TRUE  TRUE               465          72
2 GO:00069… L1        2.76e-14     1.00 FALSE TRUE               465          50
3 GO:00025… L1        2.21e-15     1.00 FALSE TRUE               465         121
4 GO:00069… L1        1.17e-18     1    FALSE TRUE               465         137
5 GO:00029… L1        1.55e-22     1    FALSE TRUE               465          49
6 GO:00026… L1        2.79e-23     1    FALSE TRUE               465          70
# … with 10 more variables: overlap <dbl>, nGenes <int>, propInList <dbl>,
#   propInSet <dbl>, oddsRatio <dbl>, pValueHypergeometric <dbl>, db <chr>,
#   celltype <chr>, thresh <dbl>, description <chr>

gene_set_summary(res) %>% head()

Joining, by = "geneSet"
Joining, by = c("geneSet", "description")

# A tibble: 6 × 14
  geneSet       pip geneListSize geneSetSize overlap nGenes propInList propInSet
  <chr>       <dbl>        <int>       <dbl>   <dbl>  <int>      <dbl>     <dbl>
1 GO:00025… 2.90e-3          465         112      23  12643     0.0495    0.205 
2 GO:00068… 4.32e-3          465        4015     204  12643     0.439     0.0508
3 GO:00068… 2.91e-3          465         748      54  12643     0.116     0.0722
4 GO:00081… 9.98e-4          465       12643     465  12643     1         0.0368
5 GO:00099… 1.22e-3          465       11696     409  12643     0.880     0.0350
6 GO:00161… 3.34e-3          465        1679      98  12643     0.211     0.0584
# … with 6 more variables: oddsRatio <dbl>, pValueHypergeometric <dbl>,
#   db <chr>, celltype <chr>, thresh <dbl>, description <chr>

Fit logistic SuSiE

For each celltype, we fit logistic SuSiE using multiple gene set sources at various threshold of padj.

celltypes <- names(deseq)
pthresh <- c(1e-2) # c(0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001)
db_name <- names(genesets)
crossed <- cross3(db_name, celltypes, pthresh)

res <- xfun::cache_rds({
  res <- purrr::map(crossed, purrr::lift_dl(logistic_susie_driver))
  for (i in 1:length(res)){  # save some space
    res[[i]]$fit$dat <- NULL
  }
  res
  }
)

u <- map(res, credible_set_summary)
cs.summary <- do.call('rbind', u)

u <- map(res, gene_set_summary)
geneset.summary <- do.call('rbind', u)

Summary functions

Just a few functions to help streamline looking at output

library(kableExtra)

#' takes a tibble
#' organize by database and component
#' report credible set, descriptions, pips, and hypergeometric pvalue
#' in one row, with cs ordered by pip
db_component_kable = function(tbl, min_alpha=0, max_sets=10){
  tbl_filtered <-
    tbl %>%
    group_by(celltype, db, component) %>%
    arrange(celltype, db, component, desc(alpha)) %>%
    filter(alpha > min_alpha, row_number() <= max_sets)

  tbl_filtered %>%
    select(geneSet, description, alpha, pValueHypergeometric) %>%
    dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
    kbl() %>%
    column_spec(c(4, 5, 6), color=ifelse(tbl_filtered$in_cs, 'green', 'red')) %>%
    collapse_rows(columns = c(1, 2), valign = 'top') %>%
    kableExtra::kable_styling()
}

Results

Gene set results for each tissue, across multiple gene set sources.

We show the top 10 gene sets per credible set, green indicates that the gene set is in the 95% credible set. Red indicates it’s not in the 95% credible set, but still ranked highly for SuSiE that component, to help get a sense of what’s getting lumped in with the enrichments reported by SuSiE.

gen.table = function(ct, g){
  cs.summary %>%
        filter(celltype == ct, db == g, active_cs) %>%
        db_component_kable() %>%
        htmltools::HTML()
}
possibly.gen.table = possibly(gen.table, otherwise="nothing to report...")

for(ct in celltypes){
  cat("\n") 
  cat("##", ct, "\n") # Create second level headings with the names.
  
  for(g in names(genesets)){
    cat("###", g, "\n") # Create second level headings with the names.
    possibly.gen.table(ct, g) %>% print()
    cat("\n")
  }
}

Adipose

gobp

Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Adipose	gobp	L1	GO:0072376	protein activation cascade	1	7.82e-17
Adipose	gobp	L1	GO:0002526	acute inflammatory response	3.38e-06	4.28e-16
Adipose	gobp	L1	GO:0006959	humoral immune response	2.48e-06	1.55e-14
Adipose	gobp	L1	GO:0006956	complement activation	2.51e-07	9.74e-10
Adipose	gobp	L1	GO:0002920	regulation of humoral immune response	1.15e-09	2.97e-08
Adipose	gobp	L1	GO:0016485	protein processing	7.01e-10	7.07e-11
Adipose	gobp	L1	GO:0002673	regulation of acute inflammatory response	2.47e-10	8.19e-09
Adipose	gobp	L1	GO:1903317	regulation of protein maturation	8.54e-11	5.05e-08
Adipose	gobp	L1	GO:0030195	negative regulation of blood coagulation	6.43e-11	1.16e-09
Adipose	gobp	L1	GO:0070613	regulation of protein processing	4.98e-11	1.29e-07
Adipose	gobp	L2	GO:0006082	organic acid metabolic process	0.731	9.92e-19
Adipose	gobp	L2	GO:0043436	oxoacid metabolic process	0.263	3.08e-18
Adipose	gobp	L2	GO:0019752	carboxylic acid metabolic process	0.00523	6.13e-17
Adipose	gobp	L2	GO:0044281	small molecule metabolic process	0.000615	5.86e-22
Adipose	gobp	L2	GO:0032787	monocarboxylic acid metabolic process	7.92e-11	2.22e-11
Adipose	gobp	L2	GO:0006629	lipid metabolic process	5.79e-11	6.03e-20
Adipose	gobp	L2	GO:0016054	organic acid catabolic process	2.23e-12	7.63e-11
Adipose	gobp	L2	GO:0046395	carboxylic acid catabolic process	2.23e-12	7.63e-11
Adipose	gobp	L2	GO:1901605	alpha-amino acid metabolic process	4.49e-13	4.38e-10
Adipose	gobp	L2	GO:0006520	cellular amino acid metabolic process	5.62e-14	7.42e-08
Adipose	gobp	L3	GO:0032940	secretion by cell	0.627	2.79e-17
Adipose	gobp	L3	GO:0046903	secretion	0.373	1.09e-17
Adipose	gobp	L3	GO:0006887	exocytosis	5.23e-05	9.92e-14
Adipose	gobp	L3	GO:0045055	regulated exocytosis	1.31e-06	1.34e-12
Adipose	gobp	L3	GO:0002446	neutrophil mediated immunity	1.61e-07	2.04e-12
Adipose	gobp	L3	GO:0042119	neutrophil activation	1.3e-07	4.08e-12
Adipose	gobp	L3	GO:0036230	granulocyte activation	8.65e-08	6.95e-12
Adipose	gobp	L3	GO:0043312	neutrophil degranulation	8.54e-08	7.25e-12
Adipose	gobp	L3	GO:0002283	neutrophil activation involved in immune response	6.9e-08	9.48e-12
Adipose	gobp	L3	GO:0002274	myeloid leukocyte activation	4.6e-08	1.44e-11

gobp_nr

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Adipose	gobp_nr	L1	GO:0072376	protein activation cascade	1	1.8e-16
Adipose	gobp_nr	L1	GO:0002526	acute inflammatory response	5.21e-06	1.16e-15
Adipose	gobp_nr	L1	GO:0006959	humoral immune response	1.61e-06	4.14e-14
Adipose	gobp_nr	L1	GO:0019835	cytolysis	2.4e-10	5.09e-08
Adipose	gobp_nr	L1	GO:0051604	protein maturation	1.32e-11	8.96e-09
Adipose	gobp_nr	L1	GO:0050817	coagulation	6.47e-12	1.51e-09
Adipose	gobp_nr	L1	GO:0002576	platelet degranulation	3.07e-12	9.94e-09
Adipose	gobp_nr	L1	GO:0045861	negative regulation of proteolysis	8.57e-13	1.16e-09
Adipose	gobp_nr	L1	GO:0050878	regulation of body fluid levels	5.3e-13	9.71e-09
Adipose	gobp_nr	L1	GO:0007586	digestion	1.97e-13	2.2e-07
Adipose	gobp_nr	L2	GO:0008202	steroid metabolic process	1	4.68e-11
Adipose	gobp_nr	L2	GO:1901615	organic hydroxy compound metabolic process	2.01e-05	1.06e-10
Adipose	gobp_nr	L2	GO:0042445	hormone metabolic process	9.74e-06	2.6e-09
Adipose	gobp_nr	L2	GO:0019216	regulation of lipid metabolic process	6.94e-07	8.58e-09
Adipose	gobp_nr	L2	GO:0007586	digestion	8.03e-08	2.2e-07
Adipose	gobp_nr	L2	GO:0034367	protein-containing complex remodeling	4.63e-08	7.73e-06
Adipose	gobp_nr	L2	GO:0097006	regulation of plasma lipoprotein particle levels	2.85e-08	4.82e-06
Adipose	gobp_nr	L2	GO:0055088	lipid homeostasis	2.4e-08	5.64e-06
Adipose	gobp_nr	L2	GO:0015711	organic anion transport	1.57e-08	7.07e-10
Adipose	gobp_nr	L2	GO:0016042	lipid catabolic process	1.54e-08	7.43e-07
Adipose	gobp_nr	L3	GO:0002446	neutrophil mediated immunity	0.678	8.38e-12
Adipose	gobp_nr	L3	GO:0036230	granulocyte activation	0.322	2.77e-11
Adipose	gobp_nr	L3	GO:0002576	platelet degranulation	1.32e-08	9.94e-09
Adipose	gobp_nr	L3	GO:0007586	digestion	8.55e-09	2.2e-07
Adipose	gobp_nr	L3	GO:0045861	negative regulation of proteolysis	6.79e-09	1.16e-09
Adipose	gobp_nr	L3	GO:0015711	organic anion transport	4.16e-09	7.07e-10
Adipose	gobp_nr	L3	GO:0035821	modification of morphology or physiology of other organism	3.25e-09	1.72e-06
Adipose	gobp_nr	L3	GO:0005996	monosaccharide metabolic process	2.72e-09	4.45e-07
Adipose	gobp_nr	L3	GO:0019835	cytolysis	2.58e-09	5.09e-08
Adipose	gobp_nr	L3	GO:0002526	acute inflammatory response	2.42e-09	1.16e-15
Adipose	gobp_nr	L4	GO:0009308	amine metabolic process	0.998	6.97e-08
Adipose	gobp_nr	L4	GO:0006520	cellular amino acid metabolic process	0.000562	1.84e-07
Adipose	gobp_nr	L4	GO:0097164	ammonium ion metabolic process	0.000359	7.88e-07
Adipose	gobp_nr	L4	GO:0007586	digestion	9.13e-05	2.2e-07
Adipose	gobp_nr	L4	GO:0042430	indole-containing compound metabolic process	4.7e-05	0.00133
Adipose	gobp_nr	L4	GO:0015711	organic anion transport	4.6e-05	7.07e-10
Adipose	gobp_nr	L4	GO:0044282	small molecule catabolic process	4.57e-05	1.93e-08
Adipose	gobp_nr	L4	GO:0019835	cytolysis	4.35e-05	5.09e-08
Adipose	gobp_nr	L4	GO:0002576	platelet degranulation	3.28e-05	9.94e-09
Adipose	gobp_nr	L4	GO:0042537	benzene-containing compound metabolic process	3.09e-05	0.000312

gomf

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Adipose	gomf	L1	GO:0004867	serine-type endopeptidase inhibitor activity	0.964	2.04e-10
Adipose	gomf	L1	GO:0030414	peptidase inhibitor activity	0.0226	2.74e-10
Adipose	gomf	L1	GO:0004866	endopeptidase inhibitor activity	0.0112	7.02e-10
Adipose	gomf	L1	GO:0061135	endopeptidase regulator activity	0.00194	4.1e-09
Adipose	gomf	L1	GO:0061134	peptidase regulator activity	7.66e-05	6.17e-08
Adipose	gomf	L1	GO:0004022	alcohol dehydrogenase (NAD) activity	3.4e-07	4.08e-05
Adipose	gomf	L1	GO:0004857	enzyme inhibitor activity	1.38e-07	1e-05
Adipose	gomf	L1	GO:0046790	virion binding	9.33e-08	0.000324
Adipose	gomf	L1	GO:0001848	complement binding	7.53e-08	0.000123
Adipose	gomf	L1	GO:0004252	serine-type endopeptidase activity	7.03e-08	1.14e-07
Adipose	gomf	L2	GO:0043177	organic acid binding	0.922	2.69e-10
Adipose	gomf	L2	GO:0031406	carboxylic acid binding	0.0781	4.15e-09
Adipose	gomf	L2	GO:0033293	monocarboxylic acid binding	1.92e-05	7.98e-07
Adipose	gomf	L2	GO:0019842	vitamin binding	2.13e-06	9.34e-07
Adipose	gomf	L2	GO:0016597	amino acid binding	7.31e-07	5.4e-05
Adipose	gomf	L2	GO:0048037	cofactor binding	2.66e-07	9.67e-08
Adipose	gomf	L2	GO:0019825	oxygen binding	2.64e-07	1.52e-05
Adipose	gomf	L2	GO:0001972	retinoic acid binding	2.16e-07	2.14e-05
Adipose	gomf	L2	GO:0005501	retinoid binding	1.35e-07	3.04e-05
Adipose	gomf	L2	GO:0016209	antioxidant activity	1.05e-07	3.97e-06

kegg

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Adipose	kegg	L1	hsa04610	Complement and coagulation cascades	1	1.32e-20
Adipose	kegg	L1	hsa00511	Other glycan degradation	1.27e-18	0.000344
Adipose	kegg	L1	hsa04614	Renin-angiotensin system	6.81e-19	0.000938
Adipose	kegg	L1	hsa05150	Staphylococcus aureus infection	6.09e-19	0.00405
Adipose	kegg	L1	hsa04979	Cholesterol metabolism	5.96e-19	5.37e-06
Adipose	kegg	L1	hsa00830	Retinol metabolism	3.98e-19	7.07e-06
Adipose	kegg	L1	hsa04142	Lysosome	3.82e-19	8.16e-06
Adipose	kegg	L1	hsa00220	Arginine biosynthesis	2.01e-19	0.000583
Adipose	kegg	L1	hsa04145	Phagosome	1.77e-19	0.000336
Adipose	kegg	L1	hsa00590	Arachidonic acid metabolism	1.33e-19	0.0021
Adipose	kegg	L2	hsa04976	Bile secretion	1	4.59e-09
Adipose	kegg	L2	hsa04979	Cholesterol metabolism	1.8e-06	5.37e-06
Adipose	kegg	L2	hsa00511	Other glycan degradation	1.94e-07	0.000344
Adipose	kegg	L2	hsa04614	Renin-angiotensin system	1.09e-07	0.000938
Adipose	kegg	L2	hsa04142	Lysosome	7.24e-08	8.16e-06
Adipose	kegg	L2	hsa00830	Retinol metabolism	6.96e-08	7.07e-06
Adipose	kegg	L2	hsa00910	Nitrogen metabolism	3.4e-08	0.00676
Adipose	kegg	L2	hsa00220	Arginine biosynthesis	3.38e-08	0.000583
Adipose	kegg	L2	hsa04975	Fat digestion and absorption	3.32e-08	0.00133
Adipose	kegg	L2	hsa00590	Arachidonic acid metabolism	2.44e-08	0.0021
Adipose	kegg	L3	hsa04950	Maturity onset diabetes of the young	0.997	1.15e-06
Adipose	kegg	L3	hsa00511	Other glycan degradation	0.00052	0.000344
Adipose	kegg	L3	hsa04614	Renin-angiotensin system	0.000275	0.000938
Adipose	kegg	L3	hsa04979	Cholesterol metabolism	0.000236	5.37e-06
Adipose	kegg	L3	hsa00830	Retinol metabolism	0.000158	7.07e-06
Adipose	kegg	L3	hsa04142	Lysosome	0.00015	8.16e-06
Adipose	kegg	L3	hsa00220	Arginine biosynthesis	8.04e-05	0.000583
Adipose	kegg	L3	hsa00590	Arachidonic acid metabolism	5.24e-05	0.0021
Adipose	kegg	L3	hsa00910	Nitrogen metabolism	4.55e-05	0.00676
Adipose	kegg	L3	hsa04960	Aldosterone-regulated sodium reabsorption	4.41e-05	1
Adipose	kegg	L4	hsa00360	Phenylalanine metabolism	0.973	2.92e-06
Adipose	kegg	L4	hsa00400	Phenylalanine, tyrosine and tryptophan biosynthesis	0.00731	0.000688
Adipose	kegg	L4	hsa00350	Tyrosine metabolism	0.004	7.15e-05
Adipose	kegg	L4	hsa00511	Other glycan degradation	0.00198	0.000344
Adipose	kegg	L4	hsa00220	Arginine biosynthesis	0.00196	0.000583
Adipose	kegg	L4	hsa00982	Drug metabolism	0.00137	4.36e-06
Adipose	kegg	L4	hsa04614	Renin-angiotensin system	0.00104	0.000938
Adipose	kegg	L4	hsa04979	Cholesterol metabolism	0.000889	5.37e-06
Adipose	kegg	L4	hsa00830	Retinol metabolism	0.000603	7.07e-06
Adipose	kegg	L4	hsa04142	Lysosome	0.000565	8.16e-06
Adipose	kegg	L5	hsa00140	Steroid hormone biosynthesis	0.95	2.45e-06
Adipose	kegg	L5	hsa00830	Retinol metabolism	0.0353	7.07e-06
Adipose	kegg	L5	hsa00982	Drug metabolism	0.00193	4.36e-06
Adipose	kegg	L5	hsa00860	Porphyrin and chlorophyll metabolism	0.00167	0.00027
Adipose	kegg	L5	hsa00040	Pentose and glucuronate interconversions	0.00135	0.000548
Adipose	kegg	L5	hsa00511	Other glycan degradation	0.00124	0.000344
Adipose	kegg	L5	hsa05204	Chemical carcinogenesis	0.001	9.48e-06
Adipose	kegg	L5	hsa04614	Renin-angiotensin system	0.000678	0.000938
Adipose	kegg	L5	hsa04979	Cholesterol metabolism	0.000636	5.37e-06
Adipose	kegg	L5	hsa00980	Metabolism of xenobiotics by cytochrome P450	0.00051	2.77e-05

reactome

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Adipose	reactome	L1	R-HSA-166658	Complement cascade	0.988	7.67e-11
Adipose	reactome	L1	R-HSA-977606	Regulation of Complement cascade	0.0115	2.79e-09
Adipose	reactome	L1	R-HSA-166665	Terminal pathway of complement	5.73e-05	6.97e-06
Adipose	reactome	L1	R-HSA-168249	Innate Immune System	8.57e-07	2.26e-11
Adipose	reactome	L1	R-HSA-8963899	Plasma lipoprotein remodeling	4.84e-07	1.18e-07
Adipose	reactome	L1	R-HSA-2168880	Scavenging of heme from plasma	4.26e-07	2.55e-05
Adipose	reactome	L1	R-HSA-6798695	Neutrophil degranulation	4.19e-07	1.06e-10
Adipose	reactome	L1	R-HSA-8935690	Digestion	3.44e-07	0.000489
Adipose	reactome	L1	R-HSA-8963743	Digestion and absorption	3.22e-07	6.98e-05
Adipose	reactome	L1	R-HSA-189085	Digestion of dietary carbohydrate	2.17e-07	0.00105
Adipose	reactome	L2	R-HSA-140877	Formation of Fibrin Clot (Clotting Cascade)	0.915	5.24e-10
Adipose	reactome	L2	R-HSA-140875	Common Pathway of Fibrin Clot Formation	0.0752	4.51e-09
Adipose	reactome	L2	R-HSA-140837	Intrinsic Pathway of Fibrin Clot Formation	0.00568	3.98e-07
Adipose	reactome	L2	R-HSA-114608	Platelet degranulation	0.000559	3.98e-09
Adipose	reactome	L2	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	0.00026	1.34e-08
Adipose	reactome	L2	R-HSA-8963899	Plasma lipoprotein remodeling	0.000169	1.18e-07
Adipose	reactome	L2	R-HSA-2168880	Scavenging of heme from plasma	0.000143	2.55e-05
Adipose	reactome	L2	R-HSA-8935690	Digestion	0.000112	0.000489
Adipose	reactome	L2	R-HSA-8963743	Digestion and absorption	0.000108	6.98e-05
Adipose	reactome	L2	R-HSA-109582	Hemostasis	0.000105	1.04e-08
Adipose	reactome	L3	R-HSA-1430728	Metabolism	1	6.64e-16
Adipose	reactome	L3	R-HSA-556833	Metabolism of lipids	3.2e-13	5.38e-10
Adipose	reactome	L3	R-HSA-211859	Biological oxidations	1.07e-19	8.38e-07
Adipose	reactome	L3	R-HSA-71291	Metabolism of amino acids and derivatives	1.68e-20	0.00361
Adipose	reactome	L3	R-HSA-6798695	Neutrophil degranulation	1.16e-20	1.06e-10
Adipose	reactome	L3	R-HSA-6788656	Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism	1.2e-21	1.55e-05
Adipose	reactome	L3	R-HSA-211945	Phase I - Functionalization of compounds	4.76e-22	5.34e-05
Adipose	reactome	L3	R-HSA-168249	Innate Immune System	4.61e-22	2.26e-11
Adipose	reactome	L3	R-HSA-8963899	Plasma lipoprotein remodeling	4.48e-22	1.18e-07
Adipose	reactome	L3	R-HSA-196854	Metabolism of vitamins and cofactors	3.54e-22	0.000737
Adipose	reactome	L4	R-HSA-2022377	Metabolism of Angiotensinogen to Angiotensins	0.985	1.86e-07
Adipose	reactome	L4	R-HSA-8935690	Digestion	0.00102	0.000489
Adipose	reactome	L4	R-HSA-2168880	Scavenging of heme from plasma	0.000955	2.55e-05
Adipose	reactome	L4	R-HSA-189085	Digestion of dietary carbohydrate	0.000848	0.00105
Adipose	reactome	L4	R-HSA-8963899	Plasma lipoprotein remodeling	0.000781	1.18e-07
Adipose	reactome	L4	R-HSA-8963743	Digestion and absorption	0.000695	6.98e-05
Adipose	reactome	L4	R-HSA-6798695	Neutrophil degranulation	0.000588	1.06e-10
Adipose	reactome	L4	R-HSA-2980736	Peptide hormone metabolism	0.000425	5.13e-05
Adipose	reactome	L4	R-HSA-391160	Signal regulatory protein family interactions	0.000203	0.000996
Adipose	reactome	L4	R-HSA-159418	Recycling of bile acids and salts	0.00019	5.5e-05
Adipose	reactome	L6	R-HSA-8957275	Post-translational protein phosphorylation	0.738	9.51e-10
Adipose	reactome	L6	R-HSA-381426	Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)	0.261	1.22e-09
Adipose	reactome	L6	R-HSA-8963899	Plasma lipoprotein remodeling	0.000463	1.18e-07
Adipose	reactome	L6	R-HSA-114608	Platelet degranulation	0.000141	3.98e-09
Adipose	reactome	L6	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	6.38e-05	1.34e-08
Adipose	reactome	L6	R-HSA-2168880	Scavenging of heme from plasma	3.04e-05	2.55e-05
Adipose	reactome	L6	R-HSA-174824	Plasma lipoprotein assembly, remodeling, and clearance	2.66e-05	2.18e-06
Adipose	reactome	L6	R-HSA-6798695	Neutrophil degranulation	1.32e-05	1.06e-10
Adipose	reactome	L6	R-HSA-8963888	Chylomicron assembly	9.4e-06	6.98e-05
Adipose	reactome	L6	R-HSA-8963743	Digestion and absorption	6.64e-06	6.98e-05

wikipathway_cancer

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[1] “nothing to report…”

wikipathway

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Adipose	wikipathway	L1	WP558	Complement and Coagulation Cascades	1	2.38e-12
Adipose	wikipathway	L1	WP2806	Human Complement System	3.65e-06	8.81e-09
Adipose	wikipathway	L1	WP272	Blood Clotting Cascade	2.32e-06	5.45e-07
Adipose	wikipathway	L1	WP545	Complement Activation	3.31e-08	0.00018
Adipose	wikipathway	L1	WP4146	Macrophage markers	2.4e-08	9.92e-05
Adipose	wikipathway	L1	WP4583	Biomarkers for urea cycle disorders	2.11e-08	3.77e-05
Adipose	wikipathway	L1	WP15	Selenium Micronutrient Network	1.19e-08	1.7e-07
Adipose	wikipathway	L1	WP4571	Urea cycle and related diseases	1.03e-08	9.92e-05
Adipose	wikipathway	L1	WP1604	Codeine and Morphine Metabolism	8.54e-09	0.000255
Adipose	wikipathway	L1	WP430	Statin Pathway	3.57e-09	3.69e-05
Adipose	wikipathway	L2	WP2879	Farnesoid X Receptor Pathway	0.991	1.38e-07
Adipose	wikipathway	L2	WP2289	Drug Induction of Bile Acid Pathway	0.005	1.42e-05
Adipose	wikipathway	L2	WP4571	Urea cycle and related diseases	0.000443	9.92e-05
Adipose	wikipathway	L2	WP1604	Codeine and Morphine Metabolism	0.000404	0.000255
Adipose	wikipathway	L2	WP691	Tamoxifen metabolism	0.000402	0.000622
Adipose	wikipathway	L2	WP4146	Macrophage markers	0.000335	9.92e-05
Adipose	wikipathway	L2	WP4583	Biomarkers for urea cycle disorders	0.00012	3.77e-05
Adipose	wikipathway	L2	WP4389	Bile Acids synthesis and enterohepatic circulation	0.00012	0.00127
Adipose	wikipathway	L2	WP430	Statin Pathway	0.000119	3.69e-05
Adipose	wikipathway	L2	WP4506	Tyrosine Metabolism	0.000111	0.00464

Muscle

gobp

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Muscle	gobp	L1	GO:0072376	protein activation cascade	1	1.33e-23
Muscle	gobp	L1	GO:0002526	acute inflammatory response	1.07e-06	1.13e-20
Muscle	gobp	L1	GO:0006956	complement activation	2.29e-09	8.67e-14
Muscle	gobp	L1	GO:0006959	humoral immune response	1.79e-11	4.03e-14
Muscle	gobp	L1	GO:0002673	regulation of acute inflammatory response	3.17e-12	4.21e-12
Muscle	gobp	L1	GO:0002920	regulation of humoral immune response	1e-13	1.34e-09
Muscle	gobp	L1	GO:0016485	protein processing	3.76e-14	3.42e-12
Muscle	gobp	L1	GO:0006954	inflammatory response	1.6e-14	9.43e-18
Muscle	gobp	L1	GO:1903317	regulation of protein maturation	3.46e-15	1.87e-08
Muscle	gobp	L1	GO:0070613	regulation of protein processing	2.04e-15	3.92e-08
Muscle	gobp	L2	GO:0009063	cellular amino acid catabolic process	0.94	7.93e-20
Muscle	gobp	L2	GO:1901606	alpha-amino acid catabolic process	0.0595	2.44e-18
Muscle	gobp	L2	GO:0016054	organic acid catabolic process	9.29e-05	5.88e-22
Muscle	gobp	L2	GO:0046395	carboxylic acid catabolic process	9.29e-05	5.88e-22
Muscle	gobp	L2	GO:1901605	alpha-amino acid metabolic process	2.7e-07	3.15e-15
Muscle	gobp	L2	GO:0044282	small molecule catabolic process	1.81e-07	3.11e-21
Muscle	gobp	L2	GO:0006520	cellular amino acid metabolic process	2.8e-09	8.03e-13
Muscle	gobp	L2	GO:0006082	organic acid metabolic process	9.77e-10	6.82e-27
Muscle	gobp	L2	GO:0019752	carboxylic acid metabolic process	3.2e-10	7.62e-25
Muscle	gobp	L2	GO:0043436	oxoacid metabolic process	1.88e-10	4.61e-25
Muscle	gobp	L3	GO:0090304	nucleic acid metabolic process	1	1
Muscle	gobp	L3	GO:0016070	RNA metabolic process	0.000478	1
Muscle	gobp	L3	GO:0006139	nucleobase-containing compound metabolic process	3.34e-06	0.991
Muscle	gobp	L3	GO:0010467	gene expression	1.81e-06	0.99
Muscle	gobp	L3	GO:0046483	heterocycle metabolic process	2.84e-08	0.913
Muscle	gobp	L3	GO:0006725	cellular aromatic compound metabolic process	4.17e-09	0.821
Muscle	gobp	L3	GO:0034645	cellular macromolecule biosynthetic process	3.04e-09	0.999
Muscle	gobp	L3	GO:0034641	cellular nitrogen compound metabolic process	2.53e-09	0.816
Muscle	gobp	L3	GO:0009059	macromolecule biosynthetic process	1.82e-10	0.995
Muscle	gobp	L3	GO:0044260	cellular macromolecule metabolic process	8.24e-11	0.932
Muscle	gobp	L4	GO:0008202	steroid metabolic process	0.904	1.14e-13
Muscle	gobp	L4	GO:0016125	sterol metabolic process	0.0522	2.29e-11
Muscle	gobp	L4	GO:0008203	cholesterol metabolic process	0.0263	5.25e-11
Muscle	gobp	L4	GO:1902652	secondary alcohol metabolic process	0.0153	9.99e-11
Muscle	gobp	L4	GO:0006694	steroid biosynthetic process	0.000492	2.03e-08
Muscle	gobp	L4	GO:0016126	sterol biosynthetic process	0.000463	5.52e-08
Muscle	gobp	L4	GO:0006695	cholesterol biosynthetic process	0.000448	5.6e-08
Muscle	gobp	L4	GO:1902653	secondary alcohol biosynthetic process	0.000336	8.22e-08
Muscle	gobp	L4	GO:1901615	organic hydroxy compound metabolic process	0.000111	3.74e-14
Muscle	gobp	L4	GO:0019218	regulation of steroid metabolic process	5.87e-05	2.67e-07
Muscle	gobp	L5	GO:0030855	epithelial cell differentiation	1	9.95e-14
Muscle	gobp	L5	GO:0060429	epithelium development	1.27e-06	5.92e-10
Muscle	gobp	L5	GO:0048732	gland development	9.38e-07	1.21e-14
Muscle	gobp	L5	GO:0009888	tissue development	9.54e-08	1.03e-11
Muscle	gobp	L5	GO:0043588	skin development	2.06e-08	3.52e-08
Muscle	gobp	L5	GO:0009913	epidermal cell differentiation	1.03e-08	7.76e-07
Muscle	gobp	L5	GO:0055123	digestive system development	8.56e-09	7.62e-08
Muscle	gobp	L5	GO:0008544	epidermis development	8.19e-09	8.76e-08
Muscle	gobp	L5	GO:0048565	digestive tract development	7.28e-09	8.28e-08
Muscle	gobp	L5	GO:0030216	keratinocyte differentiation	4.95e-09	8.17e-07
Muscle	gobp	L6	GO:0016101	diterpenoid metabolic process	0.756	1.73e-10
Muscle	gobp	L6	GO:0001523	retinoid metabolic process	0.125	3.08e-09
Muscle	gobp	L6	GO:0006721	terpenoid metabolic process	0.109	4.78e-10
Muscle	gobp	L6	GO:0006805	xenobiotic metabolic process	0.00118	5.16e-09
Muscle	gobp	L6	GO:0071466	cellular response to xenobiotic stimulus	0.000721	1.85e-09
Muscle	gobp	L6	GO:0006641	triglyceride metabolic process	0.000715	1.58e-10
Muscle	gobp	L6	GO:0006720	isoprenoid metabolic process	0.000484	2.03e-07
Muscle	gobp	L6	GO:0009410	response to xenobiotic stimulus	0.00027	1.24e-10
Muscle	gobp	L6	GO:0048565	digestive tract development	0.000262	8.28e-08
Muscle	gobp	L6	GO:0048732	gland development	0.000259	1.21e-14
Muscle	gobp	L7	GO:0015849	organic acid transport	0.483	5.06e-12
Muscle	gobp	L7	GO:0046942	carboxylic acid transport	0.483	5.06e-12
Muscle	gobp	L7	GO:0015711	organic anion transport	0.0178	5.28e-12
Muscle	gobp	L7	GO:0006820	anion transport	0.0035	1.16e-11
Muscle	gobp	L7	GO:0006855	drug transmembrane transport	0.00188	2.09e-07
Muscle	gobp	L7	GO:0006865	amino acid transport	0.00123	7.08e-07
Muscle	gobp	L7	GO:1903825	organic acid transmembrane transport	0.00107	5.3e-07
Muscle	gobp	L7	GO:1905039	carboxylic acid transmembrane transport	0.00107	5.3e-07
Muscle	gobp	L7	GO:0032787	monocarboxylic acid metabolic process	0.000383	2.21e-19
Muscle	gobp	L7	GO:0010951	negative regulation of endopeptidase activity	0.000298	2.81e-10

gobp_nr

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Muscle	gobp_nr	L1	GO:0072376	protein activation cascade	1	2.84e-23
Muscle	gobp_nr	L1	GO:0002526	acute inflammatory response	1.14e-07	2.71e-20
Muscle	gobp_nr	L1	GO:0006959	humoral immune response	1.1e-11	8.41e-14
Muscle	gobp_nr	L1	GO:0019835	cytolysis	7.06e-16	2.88e-07
Muscle	gobp_nr	L1	GO:0051604	protein maturation	1.27e-17	3.89e-08
Muscle	gobp_nr	L1	GO:0002576	platelet degranulation	7.55e-18	6.72e-08
Muscle	gobp_nr	L1	GO:0050727	regulation of inflammatory response	3.01e-18	3.8e-10
Muscle	gobp_nr	L1	GO:0050817	coagulation	2.21e-18	3.33e-08
Muscle	gobp_nr	L1	GO:0050878	regulation of body fluid levels	1.43e-18	1.19e-10
Muscle	gobp_nr	L1	GO:0007588	excretion	1.05e-18	2.52e-06
Muscle	gobp_nr	L2	GO:0044282	small molecule catabolic process	1	1.27e-20
Muscle	gobp_nr	L2	GO:0006520	cellular amino acid metabolic process	5.68e-09	2.08e-12
Muscle	gobp_nr	L2	GO:0042737	drug catabolic process	3.61e-10	1.57e-09
Muscle	gobp_nr	L2	GO:0043648	dicarboxylic acid metabolic process	4.76e-12	4.06e-07
Muscle	gobp_nr	L2	GO:0009410	response to xenobiotic stimulus	1.43e-12	2.56e-10
Muscle	gobp_nr	L2	GO:0016053	organic acid biosynthetic process	1.4e-12	2.54e-10
Muscle	gobp_nr	L2	GO:0006631	fatty acid metabolic process	7.79e-13	1.12e-09
Muscle	gobp_nr	L2	GO:0006081	cellular aldehyde metabolic process	5.48e-13	1.24e-05
Muscle	gobp_nr	L2	GO:0006790	sulfur compound metabolic process	4.5e-13	1.06e-07
Muscle	gobp_nr	L2	GO:0007588	excretion	4.05e-13	2.52e-06
Muscle	gobp_nr	L3	GO:0008202	steroid metabolic process	0.999	2.79e-13
Muscle	gobp_nr	L3	GO:1901615	organic hydroxy compound metabolic process	0.000663	1.19e-13
Muscle	gobp_nr	L3	GO:0071825	protein-lipid complex subunit organization	0.000128	4.61e-07
Muscle	gobp_nr	L3	GO:0097006	regulation of plasma lipoprotein particle levels	7.03e-05	5.73e-07
Muscle	gobp_nr	L3	GO:0055088	lipid homeostasis	4.12e-05	1.53e-07
Muscle	gobp_nr	L3	GO:0019216	regulation of lipid metabolic process	3.91e-05	6.13e-11
Muscle	gobp_nr	L3	GO:0009410	response to xenobiotic stimulus	3.77e-05	2.56e-10
Muscle	gobp_nr	L3	GO:0006720	isoprenoid metabolic process	3.58e-05	3.04e-07
Muscle	gobp_nr	L3	GO:0006638	neutral lipid metabolic process	3.33e-05	8.64e-09
Muscle	gobp_nr	L3	GO:0007586	digestion	3.01e-05	4.2e-07
Muscle	gobp_nr	L4	GO:0048732	gland development	1	3.73e-14
Muscle	gobp_nr	L4	GO:0061008	hepaticobiliary system development	7.06e-05	2.17e-08
Muscle	gobp_nr	L4	GO:0055123	digestive system development	6.37e-05	1.23e-07
Muscle	gobp_nr	L4	GO:0043588	skin development	1.23e-05	6.41e-08
Muscle	gobp_nr	L4	GO:0008544	epidermis development	3.64e-06	1.64e-07
Muscle	gobp_nr	L4	GO:0009410	response to xenobiotic stimulus	3.59e-06	2.56e-10
Muscle	gobp_nr	L4	GO:0035270	endocrine system development	2.24e-06	8.03e-06
Muscle	gobp_nr	L4	GO:0030323	respiratory tube development	1.75e-06	3.99e-06
Muscle	gobp_nr	L4	GO:0002526	acute inflammatory response	1.17e-06	2.71e-20
Muscle	gobp_nr	L4	GO:0007588	excretion	1.08e-06	2.52e-06
Muscle	gobp_nr	L5	GO:0015849	organic acid transport	0.877	1.2e-11
Muscle	gobp_nr	L5	GO:0015711	organic anion transport	0.121	1.46e-11
Muscle	gobp_nr	L5	GO:0007588	excretion	0.000245	2.52e-06
Muscle	gobp_nr	L5	GO:0009410	response to xenobiotic stimulus	9.53e-05	2.56e-10
Muscle	gobp_nr	L5	GO:0007586	digestion	7.29e-05	4.2e-07
Muscle	gobp_nr	L5	GO:0071825	protein-lipid complex subunit organization	5.85e-05	4.61e-07
Muscle	gobp_nr	L5	GO:0002526	acute inflammatory response	4.74e-05	2.71e-20
Muscle	gobp_nr	L5	GO:0098656	anion transmembrane transport	4.71e-05	3.52e-05
Muscle	gobp_nr	L5	GO:0015893	drug transport	3.64e-05	4.49e-05
Muscle	gobp_nr	L5	GO:0043588	skin development	3.6e-05	6.41e-08

gomf

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Muscle	gomf	L1	GO:0004866	endopeptidase inhibitor activity	0.607	5.71e-12
Muscle	gomf	L1	GO:0030414	peptidase inhibitor activity	0.317	1.17e-11
Muscle	gomf	L1	GO:0061135	endopeptidase regulator activity	0.063	6.36e-11
Muscle	gomf	L1	GO:0004867	serine-type endopeptidase inhibitor activity	0.00777	8.39e-10
Muscle	gomf	L1	GO:0061134	peptidase regulator activity	0.00509	2.4e-10
Muscle	gomf	L1	GO:0004857	enzyme inhibitor activity	5.93e-05	5.25e-09
Muscle	gomf	L1	GO:0005539	glycosaminoglycan binding	1.33e-06	3.31e-10
Muscle	gomf	L1	GO:1901681	sulfur compound binding	8.92e-07	3.16e-10
Muscle	gomf	L1	GO:0008201	heparin binding	6.72e-07	4.33e-09
Muscle	gomf	L1	GO:0005102	signaling receptor binding	4.44e-07	8.45e-14
Muscle	gomf	L2	GO:0003723	RNA binding	1	1
Muscle	gomf	L2	GO:0003676	nucleic acid binding	2.22e-06	1
Muscle	gomf	L2	GO:1901363	heterocyclic compound binding	1.63e-12	0.599
Muscle	gomf	L2	GO:0097159	organic cyclic compound binding	1.59e-13	0.326
Muscle	gomf	L2	GO:0003735	structural constituent of ribosome	6.95e-15	1
Muscle	gomf	L2	GO:0003677	DNA binding	3.12e-16	0.97
Muscle	gomf	L2	GO:0005515	protein binding	6.79e-17	7.15e-11
Muscle	gomf	L2	GO:0140096	catalytic activity, acting on a protein	5.58e-17	0.407
Muscle	gomf	L2	GO:0015370	solute:sodium symporter activity	4.91e-17	3.4e-08
Muscle	gomf	L2	GO:0043021	ribonucleoprotein complex binding	4.59e-17	0.999
Muscle	gomf	L3	GO:0004252	serine-type endopeptidase activity	0.776	5.5e-12
Muscle	gomf	L3	GO:0017171	serine hydrolase activity	0.165	2.07e-11
Muscle	gomf	L3	GO:0008236	serine-type peptidase activity	0.0588	8.74e-11
Muscle	gomf	L3	GO:0005539	glycosaminoglycan binding	6.8e-07	3.31e-10
Muscle	gomf	L3	GO:0015370	solute:sodium symporter activity	6.27e-07	3.4e-08
Muscle	gomf	L3	GO:1901681	sulfur compound binding	5.95e-07	3.16e-10
Muscle	gomf	L3	GO:0005102	signaling receptor binding	5.38e-07	8.45e-14
Muscle	gomf	L3	GO:0016645	oxidoreductase activity, acting on the CH-NH group of donors	5.31e-07	2.62e-05
Muscle	gomf	L3	GO:0005501	retinoid binding	5.18e-07	2.11e-06
Muscle	gomf	L3	GO:0030170	pyridoxal phosphate binding	4.06e-07	2.67e-07

kegg

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Muscle	kegg	L1	hsa04610	Complement and coagulation cascades	1	2.33e-23
Muscle	kegg	L1	hsa00100	Steroid biosynthesis	8.96e-20	4.8e-07
Muscle	kegg	L1	hsa00260	Glycine, serine and threonine metabolism	4.4e-20	4.55e-08
Muscle	kegg	L1	hsa00430	Taurine and hypotaurine metabolism	3.51e-20	0.000207
Muscle	kegg	L1	hsa05150	Staphylococcus aureus infection	2.53e-20	0.00233
Muscle	kegg	L1	hsa05322	Systemic lupus erythematosus	1.61e-20	0.00315
Muscle	kegg	L1	hsa04514	Cell adhesion molecules (CAMs)	1.56e-20	0.000183
Muscle	kegg	L1	hsa00053	Ascorbate and aldarate metabolism	1.26e-20	8.03e-07
Muscle	kegg	L1	hsa03040	Spliceosome	9.85e-21	1
Muscle	kegg	L1	hsa00982	Drug metabolism	9.65e-21	1.68e-05
Muscle	kegg	L3	hsa04950	Maturity onset diabetes of the young	0.999	9.23e-08
Muscle	kegg	L3	hsa00100	Steroid biosynthesis	0.000269	4.8e-07
Muscle	kegg	L3	hsa00260	Glycine, serine and threonine metabolism	0.000128	4.55e-08
Muscle	kegg	L3	hsa00430	Taurine and hypotaurine metabolism	0.000107	0.000207
Muscle	kegg	L3	hsa00053	Ascorbate and aldarate metabolism	3.73e-05	8.03e-07
Muscle	kegg	L3	hsa03040	Spliceosome	2.82e-05	1
Muscle	kegg	L3	hsa00982	Drug metabolism	2.8e-05	1.68e-05
Muscle	kegg	L3	hsa00140	Steroid hormone biosynthesis	2.46e-05	4.39e-05
Muscle	kegg	L3	hsa00040	Pentose and glucuronate interconversions	2.45e-05	1.51e-05
Muscle	kegg	L3	hsa04514	Cell adhesion molecules (CAMs)	2.19e-05	0.000183
Muscle	kegg	L4	hsa01100	Metabolic pathways	1	7.34e-18
Muscle	kegg	L4	hsa00260	Glycine, serine and threonine metabolism	4.22e-15	4.55e-08
Muscle	kegg	L4	hsa01230	Biosynthesis of amino acids	9.48e-16	6.73e-06
Muscle	kegg	L4	hsa00380	Tryptophan metabolism	1.91e-16	2.5e-08
Muscle	kegg	L4	hsa01200	Carbon metabolism	1.78e-16	6.02e-05
Muscle	kegg	L4	hsa00100	Steroid biosynthesis	1.39e-16	4.8e-07
Muscle	kegg	L4	hsa00830	Retinol metabolism	7.88e-17	2.1e-05
Muscle	kegg	L4	hsa00040	Pentose and glucuronate interconversions	6.82e-17	1.51e-05
Muscle	kegg	L4	hsa00982	Drug metabolism	6.42e-17	1.68e-05
Muscle	kegg	L4	hsa00140	Steroid hormone biosynthesis	4.64e-17	4.39e-05
Muscle	kegg	L5	hsa03010	Ribosome	1	1
Muscle	kegg	L5	hsa00100	Steroid biosynthesis	1.49e-38	4.8e-07
Muscle	kegg	L5	hsa00260	Glycine, serine and threonine metabolism	6.56e-39	4.55e-08
Muscle	kegg	L5	hsa00430	Taurine and hypotaurine metabolism	6.38e-39	0.000207
Muscle	kegg	L5	hsa00053	Ascorbate and aldarate metabolism	2.01e-39	8.03e-07
Muscle	kegg	L5	hsa00982	Drug metabolism	1.43e-39	1.68e-05
Muscle	kegg	L5	hsa03040	Spliceosome	1.39e-39	1
Muscle	kegg	L5	hsa00040	Pentose and glucuronate interconversions	1.27e-39	1.51e-05
Muscle	kegg	L5	hsa00140	Steroid hormone biosynthesis	1.26e-39	4.39e-05
Muscle	kegg	L5	hsa04514	Cell adhesion molecules (CAMs)	1.08e-39	0.000183
Muscle	kegg	L6	hsa04979	Cholesterol metabolism	0.99	6.65e-07
Muscle	kegg	L6	hsa00100	Steroid biosynthesis	0.00482	4.8e-07
Muscle	kegg	L6	hsa04975	Fat digestion and absorption	0.000887	2.1e-05
Muscle	kegg	L6	hsa04976	Bile secretion	0.000496	0.000172
Muscle	kegg	L6	hsa00260	Glycine, serine and threonine metabolism	0.000483	4.55e-08
Muscle	kegg	L6	hsa00430	Taurine and hypotaurine metabolism	0.000257	0.000207
Muscle	kegg	L6	hsa03040	Spliceosome	0.000123	1
Muscle	kegg	L6	hsa00053	Ascorbate and aldarate metabolism	0.000121	8.03e-07
Muscle	kegg	L6	hsa00982	Drug metabolism	0.000108	1.68e-05
Muscle	kegg	L6	hsa04514	Cell adhesion molecules (CAMs)	9.56e-05	0.000183
Muscle	kegg	L7	hsa00190	Oxidative phosphorylation	1	1
Muscle	kegg	L7	hsa05010	Alzheimer disease	2.4e-08	1
Muscle	kegg	L7	hsa05012	Parkinson disease	1.88e-08	0.997
Muscle	kegg	L7	hsa05016	Huntington disease	8.43e-10	0.992
Muscle	kegg	L7	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	5.41e-10	0.998
Muscle	kegg	L7	hsa04714	Thermogenesis	5.46e-11	0.976
Muscle	kegg	L7	hsa00100	Steroid biosynthesis	2.68e-11	4.8e-07
Muscle	kegg	L7	hsa00260	Glycine, serine and threonine metabolism	1.33e-11	4.55e-08
Muscle	kegg	L7	hsa04966	Collecting duct acid secretion	1.11e-11	0.951
Muscle	kegg	L7	hsa00430	Taurine and hypotaurine metabolism	1.04e-11	0.000207

reactome

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Muscle	reactome	L1	R-HSA-166658	Complement cascade	0.997	4.78e-15
Muscle	reactome	L1	R-HSA-977606	Regulation of Complement cascade	0.00313	4.29e-12
Muscle	reactome	L1	R-HSA-166665	Terminal pathway of complement	2.07e-06	9.4e-07
Muscle	reactome	L1	R-HSA-166786	Creation of C4 and C2 activators	3.61e-08	8.69e-05
Muscle	reactome	L1	R-HSA-166663	Initial triggering of complement	3.27e-08	8.1e-05
Muscle	reactome	L1	R-HSA-5661270	Formation of xylulose-5-phosphate	3.24e-08	4.97e-05
Muscle	reactome	L1	R-HSA-70350	Fructose catabolism	2.7e-08	4.97e-05
Muscle	reactome	L1	R-HSA-5652084	Fructose metabolism	2.63e-08	4.22e-05
Muscle	reactome	L1	R-HSA-6807047	Cholesterol biosynthesis via desmosterol	1.6e-08	0.000361
Muscle	reactome	L1	R-HSA-6807062	Cholesterol biosynthesis via lathosterol	1.6e-08	0.000361
Muscle	reactome	L10	R-HSA-74160	Gene expression (Transcription)	0.887	1
Muscle	reactome	L10	R-HSA-73857	RNA Polymerase II Transcription	0.0991	1
Muscle	reactome	L10	R-HSA-212436	Generic Transcription Pathway	0.0141	1
Muscle	reactome	L10	R-HSA-3700989	Transcriptional Regulation by TP53	3.63e-09	0.999
Muscle	reactome	L10	R-HSA-8951664	Neddylation	1.33e-10	1
Muscle	reactome	L10	R-HSA-5688426	Deubiquitination	1.09e-10	1
Muscle	reactome	L10	R-HSA-2262752	Cellular responses to stress	1.05e-10	0.998
Muscle	reactome	L10	R-HSA-69481	G2/M Checkpoints	8.17e-11	1
Muscle	reactome	L10	R-HSA-6807070	PTEN Regulation	7.54e-11	0.998
Muscle	reactome	L10	R-HSA-8953897	Cellular responses to external stimuli	7.29e-11	0.996
Muscle	reactome	L2	R-HSA-71291	Metabolism of amino acids and derivatives	1	9.89e-10
Muscle	reactome	L2	R-HSA-6788656	Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism	1.55e-12	2.05e-10
Muscle	reactome	L2	R-HSA-1430728	Metabolism	6.21e-14	5.39e-20
Muscle	reactome	L2	R-HSA-70635	Urea cycle	1.14e-15	1.02e-06
Muscle	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	1.54e-16	0.983
Muscle	reactome	L2	R-HSA-1614558	Degradation of cysteine and homocysteine	3.78e-17	0.000178
Muscle	reactome	L2	R-HSA-71240	Tryptophan catabolism	3.78e-17	0.000178
Muscle	reactome	L2	R-HSA-8957322	Metabolism of steroids	2.92e-17	4.06e-07
Muscle	reactome	L2	R-HSA-174824	Plasma lipoprotein assembly, remodeling, and clearance	2.81e-17	7.13e-08
Muscle	reactome	L2	R-HSA-5652084	Fructose metabolism	2.41e-17	4.22e-05
Muscle	reactome	L3	R-HSA-8953854	Metabolism of RNA	1	1
Muscle	reactome	L3	R-HSA-376176	Signaling by ROBO receptors	4.5e-10	1
Muscle	reactome	L3	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	2.79e-10	1
Muscle	reactome	L3	R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol	2.07e-10	1
Muscle	reactome	L3	R-HSA-8868773	rRNA processing in the nucleus and cytosol	1.01e-10	1
Muscle	reactome	L3	R-HSA-9010553	Regulation of expression of SLITs and ROBOs	7.7e-11	1
Muscle	reactome	L3	R-HSA-72312	rRNA processing	2.14e-11	1
Muscle	reactome	L3	R-HSA-72172	mRNA Splicing	2.04e-11	1
Muscle	reactome	L3	R-HSA-72163	mRNA Splicing - Major Pathway	2.01e-11	1
Muscle	reactome	L3	R-HSA-4608870	Asymmetric localization of PCP proteins	3.1e-12	1
Muscle	reactome	L4	R-HSA-140877	Formation of Fibrin Clot (Clotting Cascade)	0.999	6.15e-14
Muscle	reactome	L4	R-HSA-140875	Common Pathway of Fibrin Clot Formation	0.000782	9.15e-10
Muscle	reactome	L4	R-HSA-140837	Intrinsic Pathway of Fibrin Clot Formation	1.88e-05	7.52e-08
Muscle	reactome	L4	R-HSA-381426	Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)	1.12e-06	8.65e-10
Muscle	reactome	L4	R-HSA-140834	Extrinsic Pathway of Fibrin Clot Formation	8.61e-07	4.97e-05
Muscle	reactome	L4	R-HSA-8957275	Post-translational protein phosphorylation	6.15e-07	5.47e-09
Muscle	reactome	L4	R-HSA-5661270	Formation of xylulose-5-phosphate	3.03e-07	4.97e-05
Muscle	reactome	L4	R-HSA-70350	Fructose catabolism	2.52e-07	4.97e-05
Muscle	reactome	L4	R-HSA-5652084	Fructose metabolism	2.38e-07	4.22e-05
Muscle	reactome	L4	R-HSA-114608	Platelet degranulation	1.61e-07	2.48e-07
Muscle	reactome	L5	R-HSA-211859	Biological oxidations	0.988	1.81e-10
Muscle	reactome	L5	R-HSA-156580	Phase II - Conjugation of compounds	0.00545	2.13e-07
Muscle	reactome	L5	R-HSA-8957322	Metabolism of steroids	0.000674	4.06e-07
Muscle	reactome	L5	R-HSA-159418	Recycling of bile acids and salts	0.000414	3.81e-05
Muscle	reactome	L5	R-HSA-211945	Phase I - Functionalization of compounds	0.000171	0.000106
Muscle	reactome	L5	R-HSA-5652084	Fructose metabolism	0.000161	4.22e-05
Muscle	reactome	L5	R-HSA-174824	Plasma lipoprotein assembly, remodeling, and clearance	0.000159	7.13e-08
Muscle	reactome	L5	R-HSA-156588	Glucuronidation	0.000157	0.000186
Muscle	reactome	L5	R-HSA-5661270	Formation of xylulose-5-phosphate	0.000131	4.97e-05
Muscle	reactome	L5	R-HSA-70350	Fructose catabolism	0.000115	4.97e-05
Muscle	reactome	L6	R-HSA-6806667	Metabolism of fat-soluble vitamins	0.733	2.74e-08
Muscle	reactome	L6	R-HSA-975634	Retinoid metabolism and transport	0.217	1.3e-07
Muscle	reactome	L6	R-HSA-174824	Plasma lipoprotein assembly, remodeling, and clearance	0.019	7.13e-08
Muscle	reactome	L6	R-HSA-8963898	Plasma lipoprotein assembly	0.00621	8.79e-06
Muscle	reactome	L6	R-HSA-8963888	Chylomicron assembly	0.00381	2.62e-05
Muscle	reactome	L6	R-HSA-8963899	Plasma lipoprotein remodeling	0.00303	5.12e-06
Muscle	reactome	L6	R-HSA-381426	Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)	0.0012	8.65e-10
Muscle	reactome	L6	R-HSA-8957275	Post-translational protein phosphorylation	0.000871	5.47e-09
Muscle	reactome	L6	R-HSA-5661270	Formation of xylulose-5-phosphate	0.000753	4.97e-05
Muscle	reactome	L6	R-HSA-5652084	Fructose metabolism	0.000728	4.22e-05
Muscle	reactome	L7	R-HSA-72766	Translation	1	1
Muscle	reactome	L7	R-HSA-72613	Eukaryotic Translation Initiation	6.11e-21	1
Muscle	reactome	L7	R-HSA-72737	Cap-dependent Translation Initiation	6.11e-21	1
Muscle	reactome	L7	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	5.7e-22	1
Muscle	reactome	L7	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	3.72e-22	1
Muscle	reactome	L7	R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	1.13e-22	1
Muscle	reactome	L7	R-HSA-72689	Formation of a pool of free 40S subunits	2.52e-23	1
Muscle	reactome	L7	R-HSA-156842	Eukaryotic Translation Elongation	2.19e-24	1
Muscle	reactome	L7	R-HSA-2408557	Selenocysteine synthesis	1.24e-24	1
Muscle	reactome	L7	R-HSA-156902	Peptide chain elongation	5.44e-25	1

wikipathway_cancer

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[1] “nothing to report…”

wikipathway

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Muscle	wikipathway	L1	WP558	Complement and Coagulation Cascades	1	3.7e-17
Muscle	wikipathway	L1	WP2806	Human Complement System	1.01e-07	1.12e-11
Muscle	wikipathway	L1	WP272	Blood Clotting Cascade	4.59e-08	1.42e-08
Muscle	wikipathway	L1	WP545	Complement Activation	4.97e-10	2.91e-06
Muscle	wikipathway	L1	WP4506	Tyrosine Metabolism	1.11e-11	0.000434
Muscle	wikipathway	L1	WP176	Folate Metabolism	7.3e-12	2.88e-06
Muscle	wikipathway	L1	WP2289	Drug Induction of Bile Acid Pathway	6.43e-12	7.17e-07
Muscle	wikipathway	L1	WP2485	NAD Biosynthesis II (from tryptophan)	6.28e-12	0.000193
Muscle	wikipathway	L1	WP4661	Amino Acid Metabolism Pathway Excerpt (Histidine catabolism extension)	4.78e-12	0.00192
Muscle	wikipathway	L1	WP1533	Vitamin B12 Metabolism	4.67e-12	1.09e-05
Muscle	wikipathway	L2	WP4571	Urea cycle and related diseases	1	2.66e-08
Muscle	wikipathway	L2	WP4506	Tyrosine Metabolism	8.07e-07	0.000434
Muscle	wikipathway	L2	WP4583	Biomarkers for urea cycle disorders	3.34e-07	2.03e-05
Muscle	wikipathway	L2	WP2485	NAD Biosynthesis II (from tryptophan)	2.67e-07	0.000193
Muscle	wikipathway	L2	WP4661	Amino Acid Metabolism Pathway Excerpt (Histidine catabolism extension)	2.52e-07	0.00192
Muscle	wikipathway	L2	WP2289	Drug Induction of Bile Acid Pathway	2.41e-07	7.17e-07
Muscle	wikipathway	L2	WP4595	Urea cycle and associated pathways	2.1e-07	0.000101
Muscle	wikipathway	L2	WP4292	Methionine metabolism leading to Sulphur Amino Acids and related disorders	1.52e-07	0.000249
Muscle	wikipathway	L2	WP430	Statin Pathway	1.43e-07	2.78e-06
Muscle	wikipathway	L2	WP465	Tryptophan metabolism	1.38e-07	1.06e-05
Muscle	wikipathway	L3	WP1604	Codeine and Morphine Metabolism	0.993	1.29e-06
Muscle	wikipathway	L3	WP2289	Drug Induction of Bile Acid Pathway	0.0056	7.17e-07
Muscle	wikipathway	L3	WP4506	Tyrosine Metabolism	0.000216	0.000434
Muscle	wikipathway	L3	WP2485	NAD Biosynthesis II (from tryptophan)	7.25e-05	0.000193
Muscle	wikipathway	L3	WP2876	Pregnane X Receptor pathway	6.88e-05	4.75e-05
Muscle	wikipathway	L3	WP691	Tamoxifen metabolism	6.85e-05	0.00192
Muscle	wikipathway	L3	WP4661	Amino Acid Metabolism Pathway Excerpt (Histidine catabolism extension)	6.8e-05	0.00192
Muscle	wikipathway	L3	WP2875	Constitutive Androstane Receptor Pathway	5.11e-05	4.75e-05
Muscle	wikipathway	L3	WP4292	Methionine metabolism leading to Sulphur Amino Acids and related disorders	4.15e-05	0.000249
Muscle	wikipathway	L3	WP430	Statin Pathway	3.92e-05	2.78e-06

Liver

gobp

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Liver	gobp	L1	GO:0001775	cell activation	0.55	1.39e-55
Liver	gobp	L1	GO:0045321	leukocyte activation	0.366	1.81e-49
Liver	gobp	L1	GO:0046649	lymphocyte activation	0.0747	1.67e-34
Liver	gobp	L1	GO:0070661	leukocyte proliferation	0.00183	7.66e-21
Liver	gobp	L1	GO:0046651	lymphocyte proliferation	0.00153	7.68e-20
Liver	gobp	L1	GO:0002376	immune system process	0.00123	1.81e-78
Liver	gobp	L1	GO:0032943	mononuclear cell proliferation	0.00112	1.35e-19
Liver	gobp	L1	GO:0042110	T cell activation	0.000598	3.18e-25
Liver	gobp	L1	GO:0030098	lymphocyte differentiation	0.000304	9.81e-20
Liver	gobp	L1	GO:0007154	cell communication	0.000247	1.5e-160
Liver	gobp	L2	GO:0006325	chromatin organization	0.874	0.243
Liver	gobp	L2	GO:0051276	chromosome organization	0.0789	0.00285
Liver	gobp	L2	GO:0006338	chromatin remodeling	0.00977	0.982
Liver	gobp	L2	GO:1901360	organic cyclic compound metabolic process	0.00671	5.68e-55
Liver	gobp	L2	GO:0090304	nucleic acid metabolic process	0.00306	8.53e-43
Liver	gobp	L2	GO:0031326	regulation of cellular biosynthetic process	0.00239	1.37e-33
Liver	gobp	L2	GO:0046483	heterocycle metabolic process	0.00167	1.66e-54
Liver	gobp	L2	GO:0010556	regulation of macromolecule biosynthetic process	0.00145	1.73e-32
Liver	gobp	L2	GO:0006725	cellular aromatic compound metabolic process	0.0014	1.59e-55
Liver	gobp	L2	GO:2000112	regulation of cellular macromolecule biosynthetic process	0.00132	1.43e-30
Liver	gobp	L4	GO:0006928	movement of cell or subcellular component	0.955	1.42e-72
Liver	gobp	L4	GO:0040011	locomotion	0.0154	1.01e-60
Liver	gobp	L4	GO:0009653	anatomical structure morphogenesis	0.00476	1.89e-72
Liver	gobp	L4	GO:0007154	cell communication	0.00388	1.5e-160
Liver	gobp	L4	GO:0023052	signaling	0.00373	1.39e-159
Liver	gobp	L4	GO:0009888	tissue development	0.00249	5.99e-53
Liver	gobp	L4	GO:0016477	cell migration	0.00214	5.11e-51
Liver	gobp	L4	GO:0048731	system development	0.00202	6.53e-117
Liver	gobp	L4	GO:0048870	cell motility	0.0017	8.04e-53
Liver	gobp	L4	GO:0051674	localization of cell	0.0017	8.04e-53

gobp_nr

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Liver	gobp_nr	L2	GO:0006338	chromatin remodeling	0.972	0.984
Liver	gobp_nr	L2	GO:0032259	methylation	0.00198	0.567
Liver	gobp_nr	L2	GO:0006638	neutral lipid metabolic process	0.0011	0.959
Liver	gobp_nr	L2	GO:0006333	chromatin assembly or disassembly	0.000815	0.801
Liver	gobp_nr	L2	GO:0006414	translational elongation	0.00078	1.99e-11
Liver	gobp_nr	L2	GO:0010257	NADH dehydrogenase complex assembly	0.00072	6.38e-08
Liver	gobp_nr	L2	GO:0007034	vacuolar transport	0.000571	0.888
Liver	gobp_nr	L2	GO:0048193	Golgi vesicle transport	0.000478	0.282
Liver	gobp_nr	L2	GO:0008037	cell recognition	0.000461	2.88e-11
Liver	gobp_nr	L2	GO:0071824	protein-DNA complex subunit organization	0.000416	0.452

gomf

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Liver	gomf	L1	GO:0004888	transmembrane signaling receptor activity	0.627	3.84e-39
Liver	gomf	L1	GO:0038023	signaling receptor activity	0.21	1.15e-42
Liver	gomf	L1	GO:0060089	molecular transducer activity	0.163	9.18e-44
Liver	gomf	L1	GO:0004930	G protein-coupled receptor activity	0.000265	1.56e-20
Liver	gomf	L1	GO:0019955	cytokine binding	2.41e-05	6.82e-14
Liver	gomf	L1	GO:0004713	protein tyrosine kinase activity	4.24e-06	9.53e-14
Liver	gomf	L1	GO:0005509	calcium ion binding	6.55e-07	1.29e-24
Liver	gomf	L1	GO:0005201	extracellular matrix structural constituent	5.61e-07	2.28e-13
Liver	gomf	L1	GO:0008092	cytoskeletal protein binding	5.03e-07	4.04e-32
Liver	gomf	L1	GO:0019956	chemokine binding	4.1e-07	6.35e-08
Liver	gomf	L2	GO:0003677	DNA binding	0.75	1.79e-09
Liver	gomf	L2	GO:0003676	nucleic acid binding	0.171	2.24e-24
Liver	gomf	L2	GO:0097159	organic cyclic compound binding	0.0325	2.82e-55
Liver	gomf	L2	GO:1901363	heterocyclic compound binding	0.0209	3.16e-54
Liver	gomf	L2	GO:0140110	transcription regulator activity	0.00721	1.25e-09
Liver	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.00395	2.42e-07
Liver	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.00147	3.41e-07
Liver	gomf	L2	GO:0042393	histone binding	0.000362	0.899
Liver	gomf	L2	GO:0003682	chromatin binding	0.000156	0.0368
Liver	gomf	L2	GO:0003824	catalytic activity	0.000147	4.62e-65

kegg

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in color does not equal to the number of rows.

[1] “nothing to report…”

reactome

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Liver	reactome	L1	R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	0.998	2.09e-21
Liver	reactome	L1	R-HSA-500792	GPCR ligand binding	0.00129	4.05e-19
Liver	reactome	L1	R-HSA-375276	Peptide ligand-binding receptors	0.000283	7.58e-13
Liver	reactome	L1	R-HSA-380108	Chemokine receptors bind chemokines	4.4e-06	6.6e-07
Liver	reactome	L1	R-HSA-6799198	Complex I biogenesis	2.39e-06	7.29e-08
Liver	reactome	L1	R-HSA-6783783	Interleukin-10 signaling	2.37e-06	6.12e-07
Liver	reactome	L1	R-HSA-418038	Nucleotide-like (purinergic) receptors	2.16e-06	1.09e-05
Liver	reactome	L1	R-HSA-5173214	O-glycosylation of TSR domain-containing proteins	1.3e-06	1.58e-06
Liver	reactome	L1	R-HSA-446203	Asparagine N-linked glycosylation	1.16e-06	0.565
Liver	reactome	L1	R-HSA-1474244	Extracellular matrix organization	1.12e-06	3.97e-16
Liver	reactome	L2	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.999	2.49e-15
Liver	reactome	L2	R-HSA-1280218	Adaptive Immune System	0.000273	9.11e-33
Liver	reactome	L2	R-HSA-1474244	Extracellular matrix organization	8.46e-05	3.97e-16
Liver	reactome	L2	R-HSA-6799198	Complex I biogenesis	3.18e-05	7.29e-08
Liver	reactome	L2	R-HSA-5173214	O-glycosylation of TSR domain-containing proteins	1.85e-05	1.58e-06
Liver	reactome	L2	R-HSA-202433	Generation of second messenger molecules	1.39e-05	1.06e-05
Liver	reactome	L2	R-HSA-392154	Nitric oxide stimulates guanylate cyclase	1.28e-05	1.06e-05
Liver	reactome	L2	R-HSA-1221632	Meiotic synapsis	1.24e-05	0.998
Liver	reactome	L2	R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	1.24e-05	0.000175
Liver	reactome	L2	R-HSA-446203	Asparagine N-linked glycosylation	1.24e-05	0.565
Liver	reactome	L3	R-HSA-397014	Muscle contraction	0.995	1.27e-19
Liver	reactome	L3	R-HSA-5576891	Cardiac conduction	0.00418	1.5e-13
Liver	reactome	L3	R-HSA-390522	Striated Muscle Contraction	0.00019	3.4e-08
Liver	reactome	L3	R-HSA-5578775	Ion homeostasis	0.00011	1.31e-08
Liver	reactome	L3	R-HSA-6799198	Complex I biogenesis	1.56e-05	7.29e-08
Liver	reactome	L3	R-HSA-5576892	Phase 0 - rapid depolarisation	1.47e-05	1.37e-06
Liver	reactome	L3	R-HSA-1474244	Extracellular matrix organization	8.94e-06	3.97e-16
Liver	reactome	L3	R-HSA-392154	Nitric oxide stimulates guanylate cyclase	8.5e-06	1.06e-05
Liver	reactome	L3	R-HSA-5173214	O-glycosylation of TSR domain-containing proteins	8.42e-06	1.58e-06
Liver	reactome	L3	R-HSA-1296071	Potassium Channels	8.35e-06	1.18e-07

wikipathway_cancer

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in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
Liver	wikipathway	L1	WP455	GPCRs, Class A Rhodopsin-like	1	3.02e-21
Liver	wikipathway	L1	WP24	Peptide GPCRs	4.93e-07	1.53e-07
Liver	wikipathway	L1	WP536	Calcium Regulation in the Cardiac Cell	1.65e-07	3.01e-14
Liver	wikipathway	L1	WP197	Cholesterol Biosynthesis Pathway	1.43e-07	1.35e-06
Liver	wikipathway	L1	WP4324	Mitochondrial complex I assembly model OXPHOS system	5.53e-08	9.64e-09
Liver	wikipathway	L1	WP183	Proteasome Degradation	5.39e-08	2.29e-08
Liver	wikipathway	L1	WP383	Striated Muscle Contraction Pathway	3.59e-08	2.12e-06
Liver	wikipathway	L1	WP4146	Macrophage markers	2.72e-08	0.000392
Liver	wikipathway	L1	WP98	Prostaglandin Synthesis and Regulation	2.68e-08	9.39e-06
Liver	wikipathway	L1	WP465	Tryptophan metabolism	2.46e-08	0.99

knitr::knit_exit()

Baboon Diet Example

karltayeb

2022-03-16

Introduction

Setup

Load Gene Sets

Fitting and reporting helpers

Example usage

Fit logistic SuSiE

Summary functions

Results

Adipose

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

Muscle

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

Liver

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway