Single-cell PBMC Example

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Last updated: 2022-04-03

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---

Introduction

Our goals here are to run Logistic SuSiE on differential expression results from TCGA. We want to assess:

1. If the resulting enrichment results look good/interpretable across multiple/concatenated gene sets
2. Assess sensitivity to a range of p-value thresholds
3. Evaluate the potential of the summary stat latent model

library(GSEABenchmarkeR)
library(EnrichmentBrowser)
library(tidyverse)
library(susieR)
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
)

load('data/pbmc-purified/deseq2-pbmc-purified.RData')
par(mfrow=c(1,1))
deseq$`CD19+ B` %>% .$padj %>% hist(main='CD19+B p-values')

Loading required package: DESeq2

Past versions of data.setup-1.png

Version	Author	Date
a2bdb56	karltayeb	2022-03-29

Fitting and reporting helpers

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)
}
convert_labels = partial(convert_labels, from='ENSEMBL')

#' take gene level results and put them in a standard format
#' a named list with ENTREZID names and gene level stats
#' target_col is the column to extract
#' from is the source gene label to convert to ENTREZID
clean_gene_list = function(data, target_col){
  target_col = sym(target_col)
  data %>%
    as.data.frame %>%
    rownames_to_column('gene') %>%
    dplyr::select(gene, !!target_col) %>%
    filter(!is.na(!!target_col)) %>%
    mutate(y = !!target_col) %>%
    select(gene, y) %>%
    tibble2namedlist %>%
    convert_labels()
}
clean_gene_list = partial(clean_gene_list, target_col='padj')

#' makes a binary list from table like data
get_y = function(data, thresh=1e-4){
  data %>%
    clean_gene_list() %>%
    {
      y <- as.integer(. < thresh)
      names(y) <- names(.)
      y
    }
}
#get_y(deseq$`CD19+ B`, 1e-40) %>% mean()

#' fit logistic susie, and hypergeometric test
do_logistic_susie = function(db, celltype, thresh, susie.args=NULL){
  gs <- genesets[[db]]
  data <- deseq[[celltype]]
  y <- get_y(data, thresh)
  u <- process_input(gs$X, y)  # subset to common genes
  
  if(is.null(susie.args)){
    susie.args = list(
      L=10, init.intercept=0, verbose=1, maxit=100, standardize=TRUE)
  }
  vb.fit <- exec(logistic.susie, u$X, u$y, !!!susie.args)

  #' 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 - geneListSize, 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))
}

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

  #' 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')) %>%
    rename(L1 = 2) %>%  # rename deals with L=1 case
    pivot_longer(starts_with('L'), names_to='component', values_to = 'alpha') %>%
    arrange(component, desc(alpha)) %>%
    dplyr::group_by(component) %>%
    filter(row_number() < 50) %>%
    mutate(alpha_rank = row_number(), 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)

  return(credible.set.summary)
}

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

Example usage

db = 'gobp_nr'
celltype = 'CD19+ B'
thresh = 1e-4
res <- do_logistic_susie(db, celltype, thresh, susie.args=list(L=1, standardize=TRUE, verbose=TRUE))

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

converged

Joining, by = "geneSet"

get_credible_set_summary(res) %>% filter(active_cs, in_cs)

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

# A tibble: 2 × 19
# Groups:   component [1]
  geneSet    component alpha alpha_rank cumalpha in_cs active_cs geneListSize
  <chr>      <chr>     <dbl>      <int>    <dbl> <lgl> <lgl>            <int>
1 GO:0002446 L1        0.514          1    0     TRUE  TRUE              6327
2 GO:0036230 L1        0.486          2    0.514 TRUE  TRUE              6327
# … with 11 more variables: geneSetSize <dbl>, overlap <dbl>, nGenes <int>,
#   propInList <dbl>, propInSet <dbl>, oddsRatio <dbl>,
#   pValueHypergeometric <dbl>, db <chr>, celltype <chr>, thresh <dbl>,
#   description <chr>

get_gene_set_summary(res) %>% head()

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

# A tibble: 6 × 15
  geneSet      pip      beta geneListSize geneSetSize overlap nGenes propInList
  <chr>      <dbl>     <dbl>        <int>       <dbl>   <dbl>  <int>      <dbl>
1 GO:0000002     0 -8.04e-20         6327          28      11  10734    0.00174
2 GO:0000041     0 -7.36e-22         6327          82      47  10734    0.00743
3 GO:0000075     0 -8.87e-22         6327         205     118  10734    0.0187 
4 GO:0000209     0 -2.10e-19         6327         236     119  10734    0.0188 
5 GO:0000726     0 -5.87e-22         6327          80      46  10734    0.00727
6 GO:0000910     0  2.06e-20         6327         134      86  10734    0.0136 
# … with 7 more variables: propInSet <dbl>, oddsRatio <dbl>,
#   pValueHypergeometric <dbl>, db <chr>, celltype <chr>, thresh <dbl>,
#   description <chr>

Fit PBMC data

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

celltypes <- names(deseq)
pthresh <- c(1e-4) # c(0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001)
db_name <- names(genesets)
crossed <- cross3(db_name, celltypes, pthresh)

run_logistic_susie = function(susie.args){
  driver = partial(do_logistic_susie, susie.args = susie.args)
  res <- xfun::cache_rds({
    res <- purrr::map(crossed, purrr::lift_dl(driver))
    for (i in 1:length(res)){  # save some space
      res[[i]]$fit$dat <- NULL
    }
    res
    }, hash = susie.args
  )
  # get summary
  cs.summary <- do.call(
    'rbind', map(res, get_credible_set_summary))
  geneset.summary <- do.call(
    'rbind',  map(res, get_gene_set_summary))

  return(list(res=res, cs.summary=cs.summary, geneset.summary=geneset.summary))
}

susie.args = list(L=10, standardize=F, verbose=T)
res.l10 = run_logistic_susie(susie.args)

# L =1
susie.args = list(L=1, standardize=F, verbose=T)
res.l1 = run_logistic_susie(susie.args)


# L=1, standardized
susie.args = list(L=1, standardize=T, verbose=T)
res.l1.standardized = run_logistic_susie(susie.args)


# L = 1, flat
susie.args = list(L=1, standardize=F, V=1000, estimate_prior_variance=F, verbose=T)
res.l1.flat = run_logistic_susie(susie.args)

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
make_susie_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()
}

make_pval_sorted_kable = function(tbl, max_sets=1000){
  tbl_filtered <-
    tbl %>%
    group_by(celltype, db) %>%
    arrange(celltype, db, pValueHypergeometric) %>%
    filter(row_number() <= max_sets)
  
  tbl_filtered %>%
    select(geneSet, description, pip, 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

A pip centerd view

Here we rank the gene sets by their hypergeometirc pvalues. The sets are green if they belong to a SuSiE credible set, red otherwise. Think about just performing the marginal test, sorting by pvalue, and then scrolling down the list.

• Which gene sets would you pick out?
• How far down would you scroll (e.g what cutoff would you pick)?
• Would you percieve gene sets high and low in the list as related to one another?

in_cs <- res.l10$cs.summary %>%
  filter(in_cs, active_cs, celltype == 'CD19+ B', db == 'gobp') %>%
  ungroup() %>%
  select(geneSet, celltype, db, in_cs) %>%
  distinct()

res.l10$geneset.summary %>%
  filter(celltype == 'CD19+ B', db == 'gobp') %>%
  left_join(in_cs) %>%
  mutate(in_cs = ifelse(is.na(in_cs), F, T)) %>%
  make_pval_sorted_kable(max_sets = 500)

Joining, by = c("geneSet", "db", "celltype")
Adding missing grouping variables: `celltype`, `db`
`mutate_if()` ignored the following grouping variables:

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	geneSet	description	pip	pValueHypergeometric
CD19+ B	gobp	GO:0002376	immune system process	1	3e-47
CD19+ B	gobp	GO:0006955	immune response	0.000507	2.03e-42
CD19+ B	gobp	GO:0001775	cell activation	0.978	1.1e-39
CD19+ B	gobp	GO:0045321	leukocyte activation	0.0219	1.65e-37
CD19+ B	gobp	GO:0002252	immune effector process	0.000371	2.96e-31
CD19+ B	gobp	GO:0002366	leukocyte activation involved in immune response	0.000596	1.23e-26
CD19+ B	gobp	GO:0002263	cell activation involved in immune response	0.000577	1.26e-26
CD19+ B	gobp	GO:0002443	leukocyte mediated immunity	0.000344	2.6e-24
CD19+ B	gobp	GO:0002682	regulation of immune system process	0.000236	7.75e-24
CD19+ B	gobp	GO:0002274	myeloid leukocyte activation	0.000439	1.15e-23
CD19+ B	gobp	GO:0050896	response to stimulus	0.00652	3.42e-22
CD19+ B	gobp	GO:0002444	myeloid leukocyte mediated immunity	0.000582	5.18e-22
CD19+ B	gobp	GO:0050776	regulation of immune response	0.000818	6.58e-22
CD19+ B	gobp	GO:0002684	positive regulation of immune system process	0.000444	8.51e-22
CD19+ B	gobp	GO:0002275	myeloid cell activation involved in immune response	0.00049	3.45e-21
CD19+ B	gobp	GO:0042119	neutrophil activation	0.000625	6.72e-21
CD19+ B	gobp	GO:0043299	leukocyte degranulation	0.000491	8.57e-21
CD19+ B	gobp	GO:0002446	neutrophil mediated immunity	0.000621	9.61e-21
CD19+ B	gobp	GO:0036230	granulocyte activation	0.000576	9.9e-21
CD19+ B	gobp	GO:0045055	regulated exocytosis	0.00139	1.45e-20
CD19+ B	gobp	GO:0002283	neutrophil activation involved in immune response	0.000592	2.38e-20
CD19+ B	gobp	GO:0043312	neutrophil degranulation	0.000557	6.27e-20
CD19+ B	gobp	GO:0046649	lymphocyte activation	0.000337	7.91e-20
CD19+ B	gobp	GO:0034097	response to cytokine	0.0502	4.54e-18
CD19+ B	gobp	GO:0045047	protein targeting to ER	0.962	8.24e-18
CD19+ B	gobp	GO:0050778	positive regulation of immune response	0.000754	1.01e-17
CD19+ B	gobp	GO:0071345	cellular response to cytokine stimulus	0.0562	1.62e-17
CD19+ B	gobp	GO:0006613	cotranslational protein targeting to membrane	0.0217	3.93e-17
CD19+ B	gobp	GO:0006950	response to stress	0.00331	1.01e-16
CD19+ B	gobp	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0145	1.96e-16
CD19+ B	gobp	GO:0006887	exocytosis	0.000574	2.73e-16
CD19+ B	gobp	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.0041	3.03e-16
CD19+ B	gobp	GO:0048534	hematopoietic or lymphoid organ development	0.000309	3.79e-16
CD19+ B	gobp	GO:0002520	immune system development	0.00029	7.75e-16
CD19+ B	gobp	GO:0030097	hemopoiesis	0.000306	2.93e-15
CD19+ B	gobp	GO:0019221	cytokine-mediated signaling pathway	0.029	2.97e-15
CD19+ B	gobp	GO:0070887	cellular response to chemical stimulus	0.0146	4.74e-15
CD19+ B	gobp	GO:0006952	defense response	0.000248	1.12e-14
CD19+ B	gobp	GO:0010033	response to organic substance	0.00577	2.58e-14
CD19+ B	gobp	GO:0030098	lymphocyte differentiation	0.000689	2.78e-14
CD19+ B	gobp	GO:0032940	secretion by cell	0.000291	3.78e-14
CD19+ B	gobp	GO:0070972	protein localization to endoplasmic reticulum	0.000677	7.22e-14
CD19+ B	gobp	GO:0045087	innate immune response	0.000448	7.95e-14
CD19+ B	gobp	GO:0002764	immune response-regulating signaling pathway	0.00109	1.14e-13
CD19+ B	gobp	GO:0051716	cellular response to stimulus	0.00726	1.39e-13
CD19+ B	gobp	GO:0016192	vesicle-mediated transport	0.00136	1.72e-13
CD19+ B	gobp	GO:0002253	activation of immune response	0.000856	2.13e-13
CD19+ B	gobp	GO:0071310	cellular response to organic substance	0.00696	2.19e-13
CD19+ B	gobp	GO:0050865	regulation of cell activation	0.000472	3.33e-13
CD19+ B	gobp	GO:0002757	immune response-activating signal transduction	0.00105	6.88e-13
CD19+ B	gobp	GO:0002694	regulation of leukocyte activation	0.000487	7.35e-13
CD19+ B	gobp	GO:0002521	leukocyte differentiation	0.000382	9.1e-13
CD19+ B	gobp	GO:0007154	cell communication	0.00555	9.47e-13
CD19+ B	gobp	GO:0001816	cytokine production	0.000916	9.98e-13
CD19+ B	gobp	GO:0006413	translational initiation	0.00629	1.01e-12
CD19+ B	gobp	GO:0007165	signal transduction	0.0042	1.03e-12
CD19+ B	gobp	GO:0048583	regulation of response to stimulus	0.000746	1.77e-12
CD19+ B	gobp	GO:0051234	establishment of localization	0.00051	1.98e-12
CD19+ B	gobp	GO:0046903	secretion	0.000238	2.18e-12
CD19+ B	gobp	GO:0023052	signaling	0.00416	2.88e-12
CD19+ B	gobp	GO:0042110	T cell activation	0.000502	4.2e-12
CD19+ B	gobp	GO:0006810	transport	0.000391	4.96e-12
CD19+ B	gobp	GO:0042221	response to chemical	0.00115	5.23e-12
CD19+ B	gobp	GO:0006119	oxidative phosphorylation	0.0175	5.6e-12
CD19+ B	gobp	GO:0042773	ATP synthesis coupled electron transport	0.624	6.5e-12
CD19+ B	gobp	GO:0048518	positive regulation of biological process	0.00135	8.63e-12
CD19+ B	gobp	GO:0002250	adaptive immune response	0.000594	8.74e-12
CD19+ B	gobp	GO:0051179	localization	0.000372	9.85e-12
CD19+ B	gobp	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.36	1.04e-11
CD19+ B	gobp	GO:0008219	cell death	0.0252	1.25e-11
CD19+ B	gobp	GO:1901564	organonitrogen compound metabolic process	0.00734	1.55e-11
CD19+ B	gobp	GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.00153	1.6e-11
CD19+ B	gobp	GO:0048584	positive regulation of response to stimulus	0.000282	2.58e-11
CD19+ B	gobp	GO:0006915	apoptotic process	0.0223	3.35e-11
CD19+ B	gobp	GO:0012501	programmed cell death	0.0203	4.03e-11
CD19+ B	gobp	GO:0001817	regulation of cytokine production	0.000708	4.39e-11
CD19+ B	gobp	GO:0070661	leukocyte proliferation	0.000611	5.52e-11
CD19+ B	gobp	GO:0046651	lymphocyte proliferation	0.000641	6.82e-11
CD19+ B	gobp	GO:0051249	regulation of lymphocyte activation	0.000542	7.72e-11
CD19+ B	gobp	GO:0032943	mononuclear cell proliferation	0.000616	9.76e-11
CD19+ B	gobp	GO:0009123	nucleoside monophosphate metabolic process	0.00835	1.21e-10
CD19+ B	gobp	GO:0050851	antigen receptor-mediated signaling pathway	0.0042	1.54e-10
CD19+ B	gobp	GO:0002696	positive regulation of leukocyte activation	0.000478	1.67e-10
CD19+ B	gobp	GO:0002429	immune response-activating cell surface receptor signaling pathway	0.00126	1.68e-10
CD19+ B	gobp	GO:0050867	positive regulation of cell activation	0.000465	2.23e-10
CD19+ B	gobp	GO:0042113	B cell activation	0.000678	2.91e-10
CD19+ B	gobp	GO:0009126	purine nucleoside monophosphate metabolic process	0.00285	4.03e-10
CD19+ B	gobp	GO:0009167	purine ribonucleoside monophosphate metabolic process	0.00285	4.03e-10
CD19+ B	gobp	GO:0046034	ATP metabolic process	0.0018	6.84e-10
CD19+ B	gobp	GO:0051251	positive regulation of lymphocyte activation	0.000515	7.02e-10
CD19+ B	gobp	GO:0043207	response to external biotic stimulus	0.000427	9.09e-10
CD19+ B	gobp	GO:0051707	response to other organism	0.000427	9.09e-10
CD19+ B	gobp	GO:0009161	ribonucleoside monophosphate metabolic process	0.00293	9.13e-10
CD19+ B	gobp	GO:0010941	regulation of cell death	0.00614	9.65e-10
CD19+ B	gobp	GO:1903039	positive regulation of leukocyte cell-cell adhesion	0.000731	1.24e-09
CD19+ B	gobp	GO:0043067	regulation of programmed cell death	0.007	1.35e-09
CD19+ B	gobp	GO:0048522	positive regulation of cellular process	0.000978	1.47e-09
CD19+ B	gobp	GO:0009607	response to biotic stimulus	0.000386	2.55e-09
CD19+ B	gobp	GO:0050870	positive regulation of T cell activation	0.000722	2.86e-09
CD19+ B	gobp	GO:0042981	regulation of apoptotic process	0.00528	3.01e-09
CD19+ B	gobp	GO:0006518	peptide metabolic process	0.0241	3.13e-09
CD19+ B	gobp	GO:1901701	cellular response to oxygen-containing compound	0.0143	3.23e-09
CD19+ B	gobp	GO:0044419	interspecies interaction between organisms	0.00762	3.33e-09
CD19+ B	gobp	GO:0007166	cell surface receptor signaling pathway	0.000288	3.79e-09
CD19+ B	gobp	GO:0009144	purine nucleoside triphosphate metabolic process	0.00184	3.79e-09
CD19+ B	gobp	GO:0007159	leukocyte cell-cell adhesion	0.000463	4.3e-09
CD19+ B	gobp	GO:0009205	purine ribonucleoside triphosphate metabolic process	0.00161	5.16e-09
CD19+ B	gobp	GO:0045785	positive regulation of cell adhesion	0.000689	5.21e-09
CD19+ B	gobp	GO:0097190	apoptotic signaling pathway	0.0562	7.22e-09
CD19+ B	gobp	GO:0009141	nucleoside triphosphate metabolic process	0.00205	7.32e-09
CD19+ B	gobp	GO:0006612	protein targeting to membrane	0.000585	8.51e-09
CD19+ B	gobp	GO:0017144	drug metabolic process	0.00858	8.56e-09
CD19+ B	gobp	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	0.00069	9.05e-09
CD19+ B	gobp	GO:0022900	electron transport chain	0.00129	1.01e-08
CD19+ B	gobp	GO:0022904	respiratory electron transport chain	0.00081	1.04e-08
CD19+ B	gobp	GO:0051704	multi-organism process	0.000393	1.08e-08
CD19+ B	gobp	GO:0009199	ribonucleoside triphosphate metabolic process	0.00143	1.11e-08
CD19+ B	gobp	GO:1903706	regulation of hemopoiesis	0.000421	1.17e-08
CD19+ B	gobp	GO:0070665	positive regulation of leukocyte proliferation	0.00156	1.23e-08
CD19+ B	gobp	GO:0016032	viral process	0.0119	1.3e-08
CD19+ B	gobp	GO:0050863	regulation of T cell activation	0.000558	1.31e-08
CD19+ B	gobp	GO:0032946	positive regulation of mononuclear cell proliferation	0.0015	1.8e-08
CD19+ B	gobp	GO:0043604	amide biosynthetic process	0.0364	1.84e-08
CD19+ B	gobp	GO:1901700	response to oxygen-containing compound	0.00203	2.47e-08
CD19+ B	gobp	GO:0050671	positive regulation of lymphocyte proliferation	0.00143	2.62e-08
CD19+ B	gobp	GO:0043603	cellular amide metabolic process	0.0198	2.79e-08
CD19+ B	gobp	GO:0032944	regulation of mononuclear cell proliferation	0.000586	3.04e-08
CD19+ B	gobp	GO:0048870	cell motility	0.00127	3.05e-08
CD19+ B	gobp	GO:0051674	localization of cell	0.00127	3.05e-08
CD19+ B	gobp	GO:0070663	regulation of leukocyte proliferation	0.000574	3.09e-08
CD19+ B	gobp	GO:0022409	positive regulation of cell-cell adhesion	0.000578	3.22e-08
CD19+ B	gobp	GO:0046631	alpha-beta T cell activation	0.00105	3.73e-08
CD19+ B	gobp	GO:0016477	cell migration	0.000871	3.8e-08
CD19+ B	gobp	GO:0044403	symbiont process	0.00469	3.84e-08
CD19+ B	gobp	GO:0050670	regulation of lymphocyte proliferation	0.000581	4.13e-08
CD19+ B	gobp	GO:0001819	positive regulation of cytokine production	0.000474	4.2e-08
CD19+ B	gobp	GO:0080134	regulation of response to stress	0.000264	4.75e-08
CD19+ B	gobp	GO:0002683	negative regulation of immune system process	0.000418	5.04e-08
CD19+ B	gobp	GO:0048519	negative regulation of biological process	0.00031	5.36e-08
CD19+ B	gobp	GO:1903037	regulation of leukocyte cell-cell adhesion	0.000533	5.47e-08
CD19+ B	gobp	GO:0002697	regulation of immune effector process	0.000456	5.84e-08
CD19+ B	gobp	GO:0043043	peptide biosynthetic process	0.0116	6.59e-08
CD19+ B	gobp	GO:1902105	regulation of leukocyte differentiation	0.000518	6.84e-08
CD19+ B	gobp	GO:0035556	intracellular signal transduction	0.00113	7.58e-08
CD19+ B	gobp	GO:0045619	regulation of lymphocyte differentiation	0.00075	7.85e-08
CD19+ B	gobp	GO:0030155	regulation of cell adhesion	0.00035	9.37e-08
CD19+ B	gobp	GO:0030217	T cell differentiation	0.000528	9.82e-08
CD19+ B	gobp	GO:0051246	regulation of protein metabolic process	0.000903	9.89e-08
CD19+ B	gobp	GO:0022610	biological adhesion	0.000309	9.93e-08
CD19+ B	gobp	GO:0002285	lymphocyte activation involved in immune response	0.000671	1.18e-07
CD19+ B	gobp	GO:0001906	cell killing	0.00183	1.32e-07
CD19+ B	gobp	GO:0016071	mRNA metabolic process	0.00105	1.33e-07
CD19+ B	gobp	GO:0007155	cell adhesion	0.000298	1.54e-07
CD19+ B	gobp	GO:0006412	translation	0.00761	1.56e-07
CD19+ B	gobp	GO:0050853	B cell receptor signaling pathway	0.00518	1.65e-07
CD19+ B	gobp	GO:0002449	lymphocyte mediated immunity	0.00056	1.76e-07
CD19+ B	gobp	GO:0046632	alpha-beta T cell differentiation	0.00141	1.86e-07
CD19+ B	gobp	GO:1902107	positive regulation of leukocyte differentiation	0.00111	2.25e-07
CD19+ B	gobp	GO:0008283	cell proliferation	0.000391	2.25e-07
CD19+ B	gobp	GO:0031347	regulation of defense response	0.000395	2.51e-07
CD19+ B	gobp	GO:0045088	regulation of innate immune response	0.000458	3.01e-07
CD19+ B	gobp	GO:1903708	positive regulation of hemopoiesis	0.000865	3.28e-07
CD19+ B	gobp	GO:0022407	regulation of cell-cell adhesion	0.000483	3.35e-07
CD19+ B	gobp	GO:0006796	phosphate-containing compound metabolic process	0.000674	3.82e-07
CD19+ B	gobp	GO:0048872	homeostasis of number of cells	0.000687	3.92e-07
CD19+ B	gobp	GO:0031349	positive regulation of defense response	0.000422	4.25e-07
CD19+ B	gobp	GO:0045333	cellular respiration	0.000683	4.5e-07
CD19+ B	gobp	GO:0006793	phosphorus metabolic process	0.000666	4.96e-07
CD19+ B	gobp	GO:0030183	B cell differentiation	0.00109	5.02e-07
CD19+ B	gobp	GO:0010942	positive regulation of cell death	0.00373	5.78e-07
CD19+ B	gobp	GO:0002699	positive regulation of immune effector process	0.000568	5.84e-07
CD19+ B	gobp	GO:0090150	establishment of protein localization to membrane	0.000482	6.29e-07
CD19+ B	gobp	GO:0002576	platelet degranulation	0.0418	7.18e-07
CD19+ B	gobp	GO:0006091	generation of precursor metabolites and energy	0.00178	7.96e-07
CD19+ B	gobp	GO:0042100	B cell proliferation	0.0017	9.36e-07
CD19+ B	gobp	GO:0042102	positive regulation of T cell proliferation	0.0014	9.53e-07
CD19+ B	gobp	GO:1901566	organonitrogen compound biosynthetic process	0.00815	9.73e-07
CD19+ B	gobp	GO:0010605	negative regulation of macromolecule metabolic process	0.000607	1.37e-06
CD19+ B	gobp	GO:0009117	nucleotide metabolic process	0.00295	1.45e-06
CD19+ B	gobp	GO:0032268	regulation of cellular protein metabolic process	0.000617	1.51e-06
CD19+ B	gobp	GO:0001909	leukocyte mediated cytotoxicity	0.00155	1.51e-06
CD19+ B	gobp	GO:0072657	protein localization to membrane	0.000487	1.58e-06
CD19+ B	gobp	GO:0034655	nucleobase-containing compound catabolic process	0.000601	1.58e-06
CD19+ B	gobp	GO:0055086	nucleobase-containing small molecule metabolic process	0.00385	1.61e-06
CD19+ B	gobp	GO:0044270	cellular nitrogen compound catabolic process	0.000659	1.84e-06
CD19+ B	gobp	GO:0002286	T cell activation involved in immune response	0.00116	1.92e-06
CD19+ B	gobp	GO:0042098	T cell proliferation	0.000583	1.93e-06
CD19+ B	gobp	GO:0009605	response to external stimulus	0.000239	2.06e-06
CD19+ B	gobp	GO:0006753	nucleoside phosphate metabolic process	0.00262	2.11e-06
CD19+ B	gobp	GO:0034612	response to tumor necrosis factor	0.00381	2.12e-06
CD19+ B	gobp	GO:0006954	inflammatory response	0.000351	2.17e-06
CD19+ B	gobp	GO:0046700	heterocycle catabolic process	0.000623	2.18e-06
CD19+ B	gobp	GO:0097237	cellular response to toxic substance	0.0308	2.18e-06
CD19+ B	gobp	GO:0023051	regulation of signaling	0.000446	2.19e-06
CD19+ B	gobp	GO:0051239	regulation of multicellular organismal process	0.000172	2.24e-06
CD19+ B	gobp	GO:0045595	regulation of cell differentiation	0.000402	2.29e-06
CD19+ B	gobp	GO:1901361	organic cyclic compound catabolic process	0.000687	2.34e-06
CD19+ B	gobp	GO:0009892	negative regulation of metabolic process	0.000415	2.55e-06
CD19+ B	gobp	GO:0006605	protein targeting	0.000439	2.69e-06
CD19+ B	gobp	GO:0045089	positive regulation of innate immune response	0.000483	2.97e-06
CD19+ B	gobp	GO:0010035	response to inorganic substance	0.00635	3.09e-06
CD19+ B	gobp	GO:0019439	aromatic compound catabolic process	0.000604	3.1e-06
CD19+ B	gobp	GO:0045621	positive regulation of lymphocyte differentiation	0.00107	3.15e-06
CD19+ B	gobp	GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.000548	3.15e-06
CD19+ B	gobp	GO:0010646	regulation of cell communication	0.000391	3.18e-06
CD19+ B	gobp	GO:0002440	production of molecular mediator of immune response	0.000579	3.19e-06
CD19+ B	gobp	GO:0019637	organophosphate metabolic process	0.00238	3.2e-06
CD19+ B	gobp	GO:0050852	T cell receptor signaling pathway	0.000977	3.44e-06
CD19+ B	gobp	GO:0006909	phagocytosis	0.000905	3.54e-06
CD19+ B	gobp	GO:0019538	protein metabolic process	0.000532	3.67e-06
CD19+ B	gobp	GO:0046677	response to antibiotic	0.00546	3.74e-06
CD19+ B	gobp	GO:0002228	natural killer cell mediated immunity	0.00262	3.76e-06
CD19+ B	gobp	GO:0009966	regulation of signal transduction	0.000374	3.77e-06
CD19+ B	gobp	GO:0052548	regulation of endopeptidase activity	0.00892	4.16e-06
CD19+ B	gobp	GO:0071236	cellular response to antibiotic	0.0174	4.38e-06
CD19+ B	gobp	GO:0030099	myeloid cell differentiation	0.000423	4.41e-06
CD19+ B	gobp	GO:0072521	purine-containing compound metabolic process	0.00135	4.44e-06
CD19+ B	gobp	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	0.0192	4.48e-06
CD19+ B	gobp	GO:0009615	response to virus	0.000749	4.58e-06
CD19+ B	gobp	GO:0042127	regulation of cell proliferation	0.000315	4.69e-06
CD19+ B	gobp	GO:0043065	positive regulation of apoptotic process	0.00242	4.84e-06
CD19+ B	gobp	GO:0033036	macromolecule localization	0.000347	4.98e-06
CD19+ B	gobp	GO:0052547	regulation of peptidase activity	0.00699	5.36e-06
CD19+ B	gobp	GO:0071356	cellular response to tumor necrosis factor	0.00301	5.37e-06
CD19+ B	gobp	GO:0032496	response to lipopolysaccharide	0.000961	5.45e-06
CD19+ B	gobp	GO:0050864	regulation of B cell activation	0.000735	5.49e-06
CD19+ B	gobp	GO:0043068	positive regulation of programmed cell death	0.00216	5.93e-06
CD19+ B	gobp	GO:0045580	regulation of T cell differentiation	0.000666	6.09e-06
CD19+ B	gobp	GO:0006163	purine nucleotide metabolic process	0.00107	6.27e-06
CD19+ B	gobp	GO:0002262	myeloid cell homeostasis	0.000919	6.27e-06
CD19+ B	gobp	GO:0046635	positive regulation of alpha-beta T cell activation	0.00156	6.72e-06
CD19+ B	gobp	GO:0033993	response to lipid	0.00122	7.32e-06
CD19+ B	gobp	GO:0098542	defense response to other organism	0.000419	7.4e-06
CD19+ B	gobp	GO:0048523	negative regulation of cellular process	0.000362	7.49e-06
CD19+ B	gobp	GO:0051641	cellular localization	0.000529	7.61e-06
CD19+ B	gobp	GO:0043933	protein-containing complex subunit organization	0.000982	7.77e-06
CD19+ B	gobp	GO:0051649	establishment of localization in cell	0.00038	7.88e-06
CD19+ B	gobp	GO:0034622	cellular protein-containing complex assembly	0.00153	8.47e-06
CD19+ B	gobp	GO:0002703	regulation of leukocyte mediated immunity	0.000572	8.62e-06
CD19+ B	gobp	GO:0019693	ribose phosphate metabolic process	0.00108	8.63e-06
CD19+ B	gobp	GO:2001233	regulation of apoptotic signaling pathway	0.00518	9.16e-06
CD19+ B	gobp	GO:0097193	intrinsic apoptotic signaling pathway	0.00649	9.36e-06
CD19+ B	gobp	GO:0050900	leukocyte migration	0.00052	9.39e-06
CD19+ B	gobp	GO:0035710	CD4-positive, alpha-beta T cell activation	0.000946	1.01e-05
CD19+ B	gobp	GO:0034341	response to interferon-gamma	0.00104	1.03e-05
CD19+ B	gobp	GO:0045184	establishment of protein localization	0.000246	1.04e-05
CD19+ B	gobp	GO:0032879	regulation of localization	0.000376	1.04e-05
CD19+ B	gobp	GO:1902531	regulation of intracellular signal transduction	0.000537	1.05e-05
CD19+ B	gobp	GO:0098609	cell-cell adhesion	0.00045	1.05e-05
CD19+ B	gobp	GO:0009150	purine ribonucleotide metabolic process	0.000906	1.09e-05
CD19+ B	gobp	GO:0006897	endocytosis	0.00114	1.1e-05
CD19+ B	gobp	GO:1901135	carbohydrate derivative metabolic process	0.00389	1.17e-05
CD19+ B	gobp	GO:0009259	ribonucleotide metabolic process	0.00095	1.26e-05
CD19+ B	gobp	GO:0044267	cellular protein metabolic process	0.000482	1.29e-05
CD19+ B	gobp	GO:0002237	response to molecule of bacterial origin	0.000708	1.3e-05
CD19+ B	gobp	GO:0060333	interferon-gamma-mediated signaling pathway	0.00354	1.32e-05
CD19+ B	gobp	GO:0008380	RNA splicing	0.823	1.35e-05
CD19+ B	gobp	GO:0015980	energy derivation by oxidation of organic compounds	0.000536	1.35e-05
CD19+ B	gobp	GO:0040011	locomotion	0.000283	1.4e-05
CD19+ B	gobp	GO:0006338	chromatin remodeling	0.119	1.46e-05
CD19+ B	gobp	GO:0046907	intracellular transport	0.000408	1.48e-05
CD19+ B	gobp	GO:0009617	response to bacterium	0.000385	1.5e-05
CD19+ B	gobp	GO:0006959	humoral immune response	0.000819	1.51e-05
CD19+ B	gobp	GO:0045582	positive regulation of T cell differentiation	0.00104	1.55e-05
CD19+ B	gobp	GO:0035690	cellular response to drug	0.00526	1.74e-05
CD19+ B	gobp	GO:0043069	negative regulation of programmed cell death	0.000631	1.76e-05
CD19+ B	gobp	GO:0071222	cellular response to lipopolysaccharide	0.0013	1.77e-05
CD19+ B	gobp	GO:0065008	regulation of biological quality	0.000322	1.78e-05
CD19+ B	gobp	GO:0002821	positive regulation of adaptive immune response	0.00087	1.79e-05
CD19+ B	gobp	GO:0070527	platelet aggregation	0.00246	1.81e-05
CD19+ B	gobp	GO:0006928	movement of cell or subcellular component	0.000351	1.84e-05
CD19+ B	gobp	GO:0042129	regulation of T cell proliferation	0.000628	1.99e-05
CD19+ B	gobp	GO:0002705	positive regulation of leukocyte mediated immunity	0.000715	2.03e-05
CD19+ B	gobp	GO:0008104	protein localization	0.000249	2.1e-05
CD19+ B	gobp	GO:0042267	natural killer cell mediated cytotoxicity	0.00189	2.1e-05
CD19+ B	gobp	GO:0051241	negative regulation of multicellular organismal process	0.000376	2.13e-05
CD19+ B	gobp	GO:0050793	regulation of developmental process	0.000213	2.19e-05
CD19+ B	gobp	GO:0034109	homotypic cell-cell adhesion	0.00269	2.54e-05
CD19+ B	gobp	GO:0051247	positive regulation of protein metabolic process	0.000294	2.55e-05
CD19+ B	gobp	GO:0007599	hemostasis	0.000752	2.62e-05
CD19+ B	gobp	GO:1902275	regulation of chromatin organization	0.0262	2.67e-05
CD19+ B	gobp	GO:0060548	negative regulation of cell death	0.000521	2.69e-05
CD19+ B	gobp	GO:0032663	regulation of interleukin-2 production	0.00243	2.73e-05
CD19+ B	gobp	GO:0051336	regulation of hydrolase activity	0.00753	2.87e-05
CD19+ B	gobp	GO:0044281	small molecule metabolic process	0.00741	2.99e-05
CD19+ B	gobp	GO:0009967	positive regulation of signal transduction	0.000267	3.07e-05
CD19+ B	gobp	GO:1905269	positive regulation of chromatin organization	0.0136	3.16e-05
CD19+ B	gobp	GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.000852	3.29e-05
CD19+ B	gobp	GO:0006979	response to oxidative stress	0.00145	3.31e-05
CD19+ B	gobp	GO:0065003	protein-containing complex assembly	0.000428	3.38e-05
CD19+ B	gobp	GO:0031056	regulation of histone modification	0.0152	3.48e-05
CD19+ B	gobp	GO:0000956	nuclear-transcribed mRNA catabolic process	0.000558	3.53e-05
CD19+ B	gobp	GO:0038093	Fc receptor signaling pathway	0.00085	3.58e-05
CD19+ B	gobp	GO:0050684	regulation of mRNA processing	0.00942	3.58e-05
CD19+ B	gobp	GO:0043484	regulation of RNA splicing	0.00722	3.65e-05
CD19+ B	gobp	GO:0015031	protein transport	0.000209	3.79e-05
CD19+ B	gobp	GO:0023056	positive regulation of signaling	0.000245	3.91e-05
CD19+ B	gobp	GO:0031058	positive regulation of histone modification	0.0114	3.98e-05
CD19+ B	gobp	GO:0016310	phosphorylation	0.000186	4.05e-05
CD19+ B	gobp	GO:0002218	activation of innate immune response	0.000517	4.21e-05
CD19+ B	gobp	GO:0031399	regulation of protein modification process	0.000369	4.23e-05
CD19+ B	gobp	GO:0010952	positive regulation of peptidase activity	0.00373	4.28e-05
CD19+ B	gobp	GO:0015833	peptide transport	0.000204	4.33e-05
CD19+ B	gobp	GO:0046634	regulation of alpha-beta T cell activation	0.000793	4.38e-05
CD19+ B	gobp	GO:1901575	organic substance catabolic process	0.000656	4.54e-05
CD19+ B	gobp	GO:0002377	immunoglobulin production	0.000797	4.67e-05
CD19+ B	gobp	GO:0032623	interleukin-2 production	0.00179	4.7e-05
CD19+ B	gobp	GO:0050866	negative regulation of cell activation	0.000632	4.77e-05
CD19+ B	gobp	GO:2000145	regulation of cell motility	0.000563	4.87e-05
CD19+ B	gobp	GO:0034101	erythrocyte homeostasis	0.00094	4.91e-05
CD19+ B	gobp	GO:0014070	response to organic cyclic compound	0.00127	4.93e-05
CD19+ B	gobp	GO:0009124	nucleoside monophosphate biosynthetic process	0.0226	5.1e-05
CD19+ B	gobp	GO:0043066	negative regulation of apoptotic process	0.000507	5.16e-05
CD19+ B	gobp	GO:0006886	intracellular protein transport	0.000322	5.38e-05
CD19+ B	gobp	GO:0010647	positive regulation of cell communication	0.000238	5.58e-05
CD19+ B	gobp	GO:0002695	negative regulation of leukocyte activation	0.000654	5.59e-05
CD19+ B	gobp	GO:0071346	cellular response to interferon-gamma	0.000957	5.74e-05
CD19+ B	gobp	GO:0034613	cellular protein localization	0.000377	5.74e-05
CD19+ B	gobp	GO:0051172	negative regulation of nitrogen compound metabolic process	0.000997	5.91e-05
CD19+ B	gobp	GO:0030888	regulation of B cell proliferation	0.00116	5.95e-05
CD19+ B	gobp	GO:0032270	positive regulation of cellular protein metabolic process	0.000292	6.03e-05
CD19+ B	gobp	GO:0007596	blood coagulation	0.000656	6.08e-05
CD19+ B	gobp	GO:0002700	regulation of production of molecular mediator of immune response	0.000645	6.27e-05
CD19+ B	gobp	GO:0048513	animal organ development	0.00017	6.93e-05
CD19+ B	gobp	GO:0043367	CD4-positive, alpha-beta T cell differentiation	0.000901	6.95e-05
CD19+ B	gobp	GO:0070727	cellular macromolecule localization	0.000346	7.04e-05
CD19+ B	gobp	GO:0051345	positive regulation of hydrolase activity	0.00578	7.11e-05
CD19+ B	gobp	GO:0006401	RNA catabolic process	0.000431	7.2e-05
CD19+ B	gobp	GO:0051607	defense response to virus	0.000623	7.31e-05
CD19+ B	gobp	GO:0071219	cellular response to molecule of bacterial origin	0.000856	7.32e-05
CD19+ B	gobp	GO:1901698	response to nitrogen compound	0.000621	7.36e-05
CD19+ B	gobp	GO:0030334	regulation of cell migration	0.000495	7.66e-05
CD19+ B	gobp	GO:0098657	import into cell	0.000704	8.04e-05
CD19+ B	gobp	GO:0009127	purine nucleoside monophosphate biosynthetic process	0.0105	8.09e-05
CD19+ B	gobp	GO:0009168	purine ribonucleoside monophosphate biosynthetic process	0.0105	8.09e-05
CD19+ B	gobp	GO:0006402	mRNA catabolic process	0.000459	8.25e-05
CD19+ B	gobp	GO:0044093	positive regulation of molecular function	0.000515	8.34e-05
CD19+ B	gobp	GO:0002292	T cell differentiation involved in immune response	0.000972	8.46e-05
CD19+ B	gobp	GO:0072594	establishment of protein localization to organelle	0.000367	8.5e-05
CD19+ B	gobp	GO:0031324	negative regulation of cellular metabolic process	0.000803	8.57e-05
CD19+ B	gobp	GO:0051270	regulation of cellular component movement	0.000485	8.62e-05
CD19+ B	gobp	GO:0050817	coagulation	0.000611	8.65e-05
CD19+ B	gobp	GO:0002181	cytoplasmic translation	0.00152	8.73e-05
CD19+ B	gobp	GO:0051248	negative regulation of protein metabolic process	0.000949	9e-05
CD19+ B	gobp	GO:0071214	cellular response to abiotic stimulus	0.00702	9.03e-05
CD19+ B	gobp	GO:0104004	cellular response to environmental stimulus	0.00702	9.03e-05
CD19+ B	gobp	GO:0050727	regulation of inflammatory response	0.000461	9.16e-05
CD19+ B	gobp	GO:0032502	developmental process	0.000148	9.21e-05
CD19+ B	gobp	GO:0032501	multicellular organismal process	0.000117	9.49e-05
CD19+ B	gobp	GO:0009636	response to toxic substance	0.00191	9.61e-05
CD19+ B	gobp	GO:0042886	amide transport	0.000194	9.78e-05
CD19+ B	gobp	GO:0001818	negative regulation of cytokine production	0.00061	0.000101
CD19+ B	gobp	GO:0002886	regulation of myeloid leukocyte mediated immunity	0.00126	0.00011
CD19+ B	gobp	GO:0043122	regulation of I-kappaB kinase/NF-kappaB signaling	0.00166	0.00012
CD19+ B	gobp	GO:0065009	regulation of molecular function	0.00028	0.000131
CD19+ B	gobp	GO:0071396	cellular response to lipid	0.00105	0.000132
CD19+ B	gobp	GO:2001242	regulation of intrinsic apoptotic signaling pathway	0.00298	0.000136
CD19+ B	gobp	GO:1903707	negative regulation of hemopoiesis	0.000782	0.000149
CD19+ B	gobp	GO:0042592	homeostatic process	0.000268	0.000151
CD19+ B	gobp	GO:0033365	protein localization to organelle	0.00031	0.000151
CD19+ B	gobp	GO:0009156	ribonucleoside monophosphate biosynthetic process	0.0101	0.000153
CD19+ B	gobp	GO:0070555	response to interleukin-1	0.00151	0.000155
CD19+ B	gobp	GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.00124	0.000158
CD19+ B	gobp	GO:0001776	leukocyte homeostasis	0.00081	0.00016
CD19+ B	gobp	GO:1902533	positive regulation of intracellular signal transduction	0.000282	0.00016
CD19+ B	gobp	GO:0010950	positive regulation of endopeptidase activity	0.00261	0.000166
CD19+ B	gobp	GO:0007249	I-kappaB kinase/NF-kappaB signaling	0.000992	0.000167
CD19+ B	gobp	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0496	0.000168
CD19+ B	gobp	GO:0000398	mRNA splicing, via spliceosome	0.0496	0.000168
CD19+ B	gobp	GO:0044248	cellular catabolic process	0.000404	0.00017
CD19+ B	gobp	GO:0033554	cellular response to stress	0.000957	0.000171
CD19+ B	gobp	GO:0045637	regulation of myeloid cell differentiation	0.000531	0.000176
CD19+ B	gobp	GO:0030335	positive regulation of cell migration	0.000587	0.000178
CD19+ B	gobp	GO:0051250	negative regulation of lymphocyte activation	0.000687	0.000181
CD19+ B	gobp	GO:0051130	positive regulation of cellular component organization	0.00108	0.000189
CD19+ B	gobp	GO:0050821	protein stabilization	0.00894	0.000193
CD19+ B	gobp	GO:0048869	cellular developmental process	0.000148	0.000196
CD19+ B	gobp	GO:0050777	negative regulation of immune response	0.000689	0.000201
CD19+ B	gobp	GO:0071705	nitrogen compound transport	0.000183	0.000206
CD19+ B	gobp	GO:0034340	response to type I interferon	0.00189	0.000206
CD19+ B	gobp	GO:0009060	aerobic respiration	0.00172	0.000211
CD19+ B	gobp	GO:0055114	oxidation-reduction process	0.00188	0.000214
CD19+ B	gobp	GO:0051272	positive regulation of cellular component movement	0.00057	0.000216
CD19+ B	gobp	GO:0030168	platelet activation	0.000667	0.00022
CD19+ B	gobp	GO:2000147	positive regulation of cell motility	0.00058	0.000224
CD19+ B	gobp	GO:0046637	regulation of alpha-beta T cell differentiation	0.000954	0.000225
CD19+ B	gobp	GO:0002287	alpha-beta T cell activation involved in immune response	0.000953	0.000225
CD19+ B	gobp	GO:0002293	alpha-beta T cell differentiation involved in immune response	0.000953	0.000225
CD19+ B	gobp	GO:2000116	regulation of cysteine-type endopeptidase activity	0.00167	0.000226
CD19+ B	gobp	GO:0009056	catabolic process	0.000365	0.000227
CD19+ B	gobp	GO:0042060	wound healing	0.000448	0.000231
CD19+ B	gobp	GO:0019884	antigen processing and presentation of exogenous antigen	0.000981	0.000235
CD19+ B	gobp	GO:0032269	negative regulation of cellular protein metabolic process	0.000863	0.000239
CD19+ B	gobp	GO:0097191	extrinsic apoptotic signaling pathway	0.00169	0.000243
CD19+ B	gobp	GO:0071216	cellular response to biotic stimulus	0.000733	0.000244
CD19+ B	gobp	GO:0045597	positive regulation of cell differentiation	0.000396	0.000246
CD19+ B	gobp	GO:0000375	RNA splicing, via transesterification reactions	0.033	0.000249
CD19+ B	gobp	GO:0000380	alternative mRNA splicing, via spliceosome	0.00294	0.000256
CD19+ B	gobp	GO:0009145	purine nucleoside triphosphate biosynthetic process	0.00609	0.000257
CD19+ B	gobp	GO:0071702	organic substance transport	0.00018	0.000258
CD19+ B	gobp	GO:0002532	production of molecular mediator involved in inflammatory response	0.00162	0.000268
CD19+ B	gobp	GO:0002819	regulation of adaptive immune response	0.000695	0.000269
CD19+ B	gobp	GO:0050708	regulation of protein secretion	0.000567	0.000271
CD19+ B	gobp	GO:0040017	positive regulation of locomotion	0.000544	0.000275
CD19+ B	gobp	GO:0050790	regulation of catalytic activity	0.000377	0.000281
CD19+ B	gobp	GO:0051049	regulation of transport	0.000288	0.000291
CD19+ B	gobp	GO:0002431	Fc receptor mediated stimulatory signaling pathway	0.000992	0.000292
CD19+ B	gobp	GO:0016043	cellular component organization	0.000434	0.000294
CD19+ B	gobp	GO:0002758	innate immune response-activating signal transduction	0.00054	0.000301
CD19+ B	gobp	GO:0034728	nucleosome organization	0.0504	0.000305
CD19+ B	gobp	GO:0030154	cell differentiation	0.000151	0.000317
CD19+ B	gobp	GO:0002294	CD4-positive, alpha-beta T cell differentiation involved in immune response	0.000931	0.000319
CD19+ B	gobp	GO:0006333	chromatin assembly or disassembly	0.058	0.000322
CD19+ B	gobp	GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.00529	0.000336
CD19+ B	gobp	GO:0031325	positive regulation of cellular metabolic process	0.000172	0.000345
CD19+ B	gobp	GO:0033209	tumor necrosis factor-mediated signaling pathway	0.00206	0.000346
CD19+ B	gobp	GO:0008285	negative regulation of cell proliferation	0.000689	0.000361
CD19+ B	gobp	GO:0010257	NADH dehydrogenase complex assembly	0.000807	0.000371
CD19+ B	gobp	GO:0032981	mitochondrial respiratory chain complex I assembly	0.000807	0.000371
CD19+ B	gobp	GO:0042493	response to drug	0.000577	0.000374
CD19+ B	gobp	GO:0050789	regulation of biological process	9.68e-05	0.000378
CD19+ B	gobp	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	0.00377	0.000389
CD19+ B	gobp	GO:0045596	negative regulation of cell differentiation	0.000662	0.000394
CD19+ B	gobp	GO:0070201	regulation of establishment of protein localization	0.000468	0.000401
CD19+ B	gobp	GO:0071840	cellular component organization or biogenesis	0.000352	0.00041
CD19+ B	gobp	GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.000721	0.000411
CD19+ B	gobp	GO:0040012	regulation of locomotion	0.000326	0.00042
CD19+ B	gobp	GO:0045576	mast cell activation	0.00096	0.000421
CD19+ B	gobp	GO:0002478	antigen processing and presentation of exogenous peptide antigen	0.000971	0.000423
CD19+ B	gobp	GO:0006397	mRNA processing	0.0172	0.000426
CD19+ B	gobp	GO:0009628	response to abiotic stimulus	0.000632	0.00044
CD19+ B	gobp	GO:2001252	positive regulation of chromosome organization	0.00714	0.000442
CD19+ B	gobp	GO:0002706	regulation of lymphocyte mediated immunity	0.000686	0.000449
CD19+ B	gobp	GO:0051128	regulation of cellular component organization	0.000867	0.00047
CD19+ B	gobp	GO:0006754	ATP biosynthetic process	0.00471	0.000479
CD19+ B	gobp	GO:0065007	biological regulation	9.72e-05	0.000484
CD19+ B	gobp	GO:0010243	response to organonitrogen compound	0.000457	0.000499
CD19+ B	gobp	GO:0002708	positive regulation of lymphocyte mediated immunity	0.00071	0.000512
CD19+ B	gobp	GO:0031341	regulation of cell killing	0.000862	0.000523
CD19+ B	gobp	GO:0002433	immune response-regulating cell surface receptor signaling pathway involved in phagocytosis	0.000991	0.000534
CD19+ B	gobp	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	0.000991	0.000534
CD19+ B	gobp	GO:0048010	vascular endothelial growth factor receptor signaling pathway	0.00177	0.000534
CD19+ B	gobp	GO:0038094	Fc-gamma receptor signaling pathway	0.000937	0.000534
CD19+ B	gobp	GO:0071407	cellular response to organic cyclic compound	0.00136	0.000542
CD19+ B	gobp	GO:0071229	cellular response to acid chemical	0.00342	0.000544
CD19+ B	gobp	GO:0009142	nucleoside triphosphate biosynthetic process	0.00567	0.000547
CD19+ B	gobp	GO:0031343	positive regulation of cell killing	0.00112	0.000554
CD19+ B	gobp	GO:1903311	regulation of mRNA metabolic process	0.0012	0.000561
CD19+ B	gobp	GO:0031497	chromatin assembly	0.0315	0.000568
CD19+ B	gobp	GO:0034614	cellular response to reactive oxygen species	0.00207	0.000572
CD19+ B	gobp	GO:0030218	erythrocyte differentiation	0.000774	0.000588
CD19+ B	gobp	GO:0032635	interleukin-6 production	0.000765	0.000588
CD19+ B	gobp	GO:0043085	positive regulation of catalytic activity	0.000456	0.00059
CD19+ B	gobp	GO:0051090	regulation of DNA-binding transcription factor activity	0.000493	0.000595
CD19+ B	gobp	GO:0002792	negative regulation of peptide secretion	0.0024	0.000627
CD19+ B	gobp	GO:0033108	mitochondrial respiratory chain complex assembly	0.00077	0.000627
CD19+ B	gobp	GO:0042093	T-helper cell differentiation	0.000899	0.000636
CD19+ B	gobp	GO:0051240	positive regulation of multicellular organismal process	0.000391	0.00064
CD19+ B	gobp	GO:0009201	ribonucleoside triphosphate biosynthetic process	0.00414	0.000652
CD19+ B	gobp	GO:0010629	negative regulation of gene expression	0.000225	0.000653
CD19+ B	gobp	GO:0019882	antigen processing and presentation	0.000603	0.000654
CD19+ B	gobp	GO:0031400	negative regulation of protein modification process	0.0012	0.000655
CD19+ B	gobp	GO:2001056	positive regulation of cysteine-type endopeptidase activity	0.00184	0.000663
CD19+ B	gobp	GO:0001836	release of cytochrome c from mitochondria	0.00455	0.000666
CD19+ B	gobp	GO:0006334	nucleosome assembly	0.0263	0.000677
CD19+ B	gobp	GO:0016575	histone deacetylation	0.0107	0.000691
CD19+ B	gobp	GO:0048024	regulation of mRNA splicing, via spliceosome	0.00184	0.000691
CD19+ B	gobp	GO:0002791	regulation of peptide secretion	0.000465	0.000715
CD19+ B	gobp	GO:0060337	type I interferon signaling pathway	0.00142	0.000721
CD19+ B	gobp	GO:0071357	cellular response to type I interferon	0.00142	0.000721
CD19+ B	gobp	GO:0071384	cellular response to corticosteroid stimulus	0.00454	0.000726
CD19+ B	gobp	GO:0006325	chromatin organization	0.0179	0.000735
CD19+ B	gobp	GO:0033044	regulation of chromosome organization	0.00857	0.000744
CD19+ B	gobp	GO:0032880	regulation of protein localization	0.000416	0.000759
CD19+ B	gobp	GO:0042542	response to hydrogen peroxide	0.00146	0.000764
CD19+ B	gobp	GO:0050709	negative regulation of protein secretion	0.00213	0.000844
CD19+ B	gobp	GO:0002221	pattern recognition receptor signaling pathway	0.000582	0.00086
CD19+ B	gobp	GO:0098732	macromolecule deacylation	0.0118	0.000873
CD19+ B	gobp	GO:0042325	regulation of phosphorylation	0.000232	0.000873
CD19+ B	gobp	GO:0034599	cellular response to oxidative stress	0.00112	0.000884
CD19+ B	gobp	GO:0019058	viral life cycle	0.000681	0.000884
CD19+ B	gobp	GO:2000514	regulation of CD4-positive, alpha-beta T cell activation	0.000886	0.000892
CD19+ B	gobp	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	0.00292	0.000892
CD19+ B	gobp	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	0.00214	0.000893
CD19+ B	gobp	GO:0048856	anatomical structure development	0.000126	0.000929
CD19+ B	gobp	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	0.00218	0.000934
CD19+ B	gobp	GO:0006457	protein folding	0.0166	0.000983
CD19+ B	gobp	GO:0050792	regulation of viral process	0.00131	0.00101
CD19+ B	gobp	GO:0031401	positive regulation of protein modification process	0.000271	0.00102
CD19+ B	gobp	GO:0042326	negative regulation of phosphorylation	0.00112	0.00104
CD19+ B	gobp	GO:0033043	regulation of organelle organization	0.00224	0.00106
CD19+ B	gobp	GO:0051224	negative regulation of protein transport	0.00257	0.00107
CD19+ B	gobp	GO:0018193	peptidyl-amino acid modification	0.000631	0.00108
CD19+ B	gobp	GO:2001234	negative regulation of apoptotic signaling pathway	0.00147	0.00111
CD19+ B	gobp	GO:0035601	protein deacylation	0.01	0.00112
CD19+ B	gobp	GO:0060326	cell chemotaxis	0.000542	0.00112
CD19+ B	gobp	GO:0002367	cytokine production involved in immune response	0.000712	0.00114
CD19+ B	gobp	GO:0009306	protein secretion	0.000394	0.00116
CD19+ B	gobp	GO:0000302	response to reactive oxygen species	0.000964	0.00119
CD19+ B	gobp	GO:0002702	positive regulation of production of molecular mediator of immune response	0.000724	0.00121

A set focussed view

What if we just pick out the gene sets in the SuSiE 95% credible sets? Do we trust these? Some have relatively weak marginal enrichment.

res.l10$cs.summary %>%
  filter(in_cs, active_cs, celltype == 'CD19+ B', db == 'gobp') %>%
  left_join(in_cs) %>%
  mutate(in_cs = ifelse(is.na(in_cs), F, T)) %>%
  make_susie_component_kable()

Joining, by = c("geneSet", "in_cs", "db", "celltype")
Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	gobp	L1	GO:0002376	immune system process	1	3e-47
CD19+ B	gobp	L2	GO:0045047	protein targeting to ER	0.962	8.24e-18
CD19+ B	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.624	6.5e-12
CD19+ B	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.36	1.04e-11
CD19+ B	gobp	L5	GO:0001775	cell activation	0.978	1.1e-39
CD19+ B	gobp	L6	GO:0008380	RNA splicing	0.823	1.35e-05
CD19+ B	gobp	L6	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0492	0.000168
CD19+ B	gobp	L6	GO:0000398	mRNA splicing, via spliceosome	0.0492	0.000168
CD19+ B	gobp	L6	GO:0000375	RNA splicing, via transesterification reactions	0.0326	0.000249

Credible set sizes

res.l10$cs.summary %>%
  filter(in_cs, active_cs) %>%
  count(celltype, db) %>%
  ggplot(aes(x=n, fill=celltype)) + geom_bar() + facet_wrap(vars(db), ncol = 1)

Past versions of unnamed-chunk-4-1.png

Version	Author	Date
2f395f0	karltayeb	2022-04-03

CS vs pValues

do.or.plot = function(res, 
                      ct=NULL, 
                      g=NULL, 
                      x='oddsRatio', 
                      s='geneSetSize', 
                      c='in_cs'){
  col_sym = sym(x)
  gene.set.order <- res$geneset.summary %>% 
    filter(if(!is.null(ct)) celltype == ct else TRUE) %>%
    filter(if(!is.null(g)) db == g else TRUE) %>%
    arrange(db, !!col_sym) %>%
    .$geneSet %>% unique()
  
  size_sym = sym(s)
  color_sym = sym(c)
  plot <- res$cs.summary %>%
    filter(if(!is.null(ct)) celltype == ct else TRUE) %>%
    filter(if(!is.null(g)) db == g else TRUE) %>%
    filter(active_cs, alpha_rank <= 10) %>%
    mutate(geneSet=factor(geneSet, levels=gene.set.order)) %>%
    ggplot(aes(x=!!col_sym, y=geneSet, color=!!color_sym, size=!!size_sym)) +
    geom_point() +
    facet_wrap(vars(component), scale='free', nrow = 1)
  return(plot)
}


res.l10$cs.summary <-
  res.l10$cs.summary %>%
  mutate(nl10p = -log10(pValueHypergeometric))
res.l10$geneset.summary <-
  res.l10$geneset.summary %>%
  mutate(nl10p = -log10(pValueHypergeometric))

celltype <- celltypes[1]
geneset_sources <- names(genesets)

plots <- purrr::map(geneset_sources, ~do.or.plot(
  res.l10, ct=celltype, g=.x, x='nl10p'))

for(i in 1:length(plot)){
  cat('###', geneset_sources[[i]])
  print(plots[[i]])
  cat('\n')
}

gobp

A long list of results

Here for each cell type and gene set database, we look at the top 10 gene sets per SuSiE component. Gene sets are colored green if they’re in the credible set and red otherwise.

There tables are a lot to look at, so I’ll have to come back and summarise results somehow.

General obseravtion: * Virtually ALL of these gene sets report as highly significant by hypergeometric test * For “dense” gene set sources like GO-BP the top 10 gene sets in a component are often closely related, but outside of the credible set often have vanishingly small alpha. So although they are marginally enriched, logistic SuSiE thinks that other gene sets provide a much better explaination for the observed gene list. I think this is the type of result we want to see– credible sets capture related gene sets and nominate one/a few of them * Sometime we see a mix of topics within a component.

library(htmltools)

make_susie_html_table = function(ct, g){
  res.l10$cs.summary %>%
        filter(celltype == ct, db == g, active_cs) %>%
        make_susie_component_kable() %>%
        htmltools::HTML()
}
possibly_make_susie_html_table = possibly(make_susie_html_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_make_susie_html_table(ct, g) %>% print()
    cat("\n")
  }
}

CD19+ B

gobp

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	gobp	L1	GO:0002376	immune system process	1	3e-47
CD19+ B	gobp	L1	GO:0006955	immune response	4.25e-05	2.03e-42
CD19+ B	gobp	L1	GO:0050896	response to stimulus	2.34e-12	3.42e-22
CD19+ B	gobp	L1	GO:0002252	immune effector process	8.01e-15	2.96e-31
CD19+ B	gobp	L1	GO:0002682	regulation of immune system process	2.95e-15	7.75e-24
CD19+ B	gobp	L1	GO:0050776	regulation of immune response	7e-16	6.58e-22
CD19+ B	gobp	L1	GO:0051716	cellular response to stimulus	6.02e-16	1.39e-13
CD19+ B	gobp	L1	GO:0006950	response to stress	4.51e-16	1.01e-16
CD19+ B	gobp	L1	GO:0007154	cell communication	1.39e-16	9.47e-13
CD19+ B	gobp	L1	GO:0034097	response to cytokine	1.28e-16	4.54e-18
CD19+ B	gobp	L2	GO:0045047	protein targeting to ER	0.962	8.24e-18
CD19+ B	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.0208	3.93e-17
CD19+ B	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0138	1.96e-16
CD19+ B	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.00332	3.03e-16
CD19+ B	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	2.53e-07	7.22e-14
CD19+ B	gobp	L2	GO:0006413	translational initiation	2.2e-12	1.01e-12
CD19+ B	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1.77e-14	9.05e-09
CD19+ B	gobp	L2	GO:0006612	protein targeting to membrane	4.35e-15	8.51e-09
CD19+ B	gobp	L2	GO:0043604	amide biosynthetic process	2.51e-18	1.84e-08
CD19+ B	gobp	L2	GO:0006518	peptide metabolic process	2.02e-18	3.13e-09
CD19+ B	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.624	6.5e-12
CD19+ B	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.36	1.04e-11
CD19+ B	gobp	L3	GO:0006119	oxidative phosphorylation	0.0162	5.6e-12
CD19+ B	gobp	L3	GO:0022904	respiratory electron transport chain	7.59e-05	1.04e-08
CD19+ B	gobp	L3	GO:0022900	electron transport chain	4.32e-06	1.01e-08
CD19+ B	gobp	L3	GO:0009123	nucleoside monophosphate metabolic process	6.14e-07	1.21e-10
CD19+ B	gobp	L3	GO:0046034	ATP metabolic process	1.52e-07	6.84e-10
CD19+ B	gobp	L3	GO:0009126	purine nucleoside monophosphate metabolic process	1.06e-07	4.03e-10
CD19+ B	gobp	L3	GO:0009167	purine ribonucleoside monophosphate metabolic process	1.06e-07	4.03e-10
CD19+ B	gobp	L3	GO:0009161	ribonucleoside monophosphate metabolic process	6.22e-08	9.13e-10
CD19+ B	gobp	L5	GO:0001775	cell activation	0.978	1.1e-39
CD19+ B	gobp	L5	GO:0045321	leukocyte activation	0.0217	1.65e-37
CD19+ B	gobp	L5	GO:0002366	leukocyte activation involved in immune response	0.00012	1.23e-26
CD19+ B	gobp	L5	GO:0002263	cell activation involved in immune response	0.000112	1.26e-26
CD19+ B	gobp	L5	GO:0045055	regulated exocytosis	1.89e-05	1.45e-20
CD19+ B	gobp	L5	GO:0006955	immune response	1.46e-05	2.03e-42
CD19+ B	gobp	L5	GO:0002252	immune effector process	8.26e-06	2.96e-31
CD19+ B	gobp	L5	GO:0002274	myeloid leukocyte activation	8.08e-06	1.15e-23
CD19+ B	gobp	L5	GO:0002444	myeloid leukocyte mediated immunity	3.59e-06	5.18e-22
CD19+ B	gobp	L5	GO:0042119	neutrophil activation	2.34e-06	6.72e-21
CD19+ B	gobp	L6	GO:0008380	RNA splicing	0.823	1.35e-05
CD19+ B	gobp	L6	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0492	0.000168
CD19+ B	gobp	L6	GO:0000398	mRNA splicing, via spliceosome	0.0492	0.000168
CD19+ B	gobp	L6	GO:0000375	RNA splicing, via transesterification reactions	0.0326	0.000249
CD19+ B	gobp	L6	GO:0006397	mRNA processing	0.0169	0.000426
CD19+ B	gobp	L6	GO:0050684	regulation of mRNA processing	0.00633	3.58e-05
CD19+ B	gobp	L6	GO:0043484	regulation of RNA splicing	0.00555	3.65e-05
CD19+ B	gobp	L6	GO:0000380	alternative mRNA splicing, via spliceosome	0.00085	0.000256
CD19+ B	gobp	L6	GO:0016071	mRNA metabolic process	0.000744	1.33e-07
CD19+ B	gobp	L6	GO:0006338	chromatin remodeling	0.00065	1.46e-05

gobp_nr

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.515	5.55e-18
CD19+ B	gobp_nr	L1	GO:0036230	granulocyte activation	0.485	5.84e-18
CD19+ B	gobp_nr	L1	GO:0002576	platelet degranulation	2.06e-13	3.48e-06
CD19+ B	gobp_nr	L1	GO:0001906	cell killing	8.55e-14	7.55e-07
CD19+ B	gobp_nr	L1	GO:0034109	homotypic cell-cell adhesion	2.66e-14	7.54e-05
CD19+ B	gobp_nr	L1	GO:0006338	chromatin remodeling	2.38e-14	7.68e-05
CD19+ B	gobp_nr	L1	GO:0051647	nucleus localization	2.14e-14	0.000379
CD19+ B	gobp_nr	L1	GO:0034612	response to tumor necrosis factor	1.88e-14	1.75e-05
CD19+ B	gobp_nr	L1	GO:0070661	leukocyte proliferation	1.81e-14	1.35e-09
CD19+ B	gobp_nr	L1	GO:0002250	adaptive immune response	1.77e-14	4.44e-10
CD19+ B	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	1	1.1e-12
CD19+ B	gobp_nr	L2	GO:0006413	translational initiation	4.19e-05	2.25e-11
CD19+ B	gobp_nr	L2	GO:0090150	establishment of protein localization to membrane	4.11e-11	1.01e-05
CD19+ B	gobp_nr	L2	GO:0006605	protein targeting	5.27e-12	5.39e-05
CD19+ B	gobp_nr	L2	GO:0002181	cytoplasmic translation	2.48e-12	0.000293
CD19+ B	gobp_nr	L2	GO:0006401	RNA catabolic process	1.43e-12	0.000735
CD19+ B	gobp_nr	L2	GO:0051647	nucleus localization	3.73e-13	0.000379
CD19+ B	gobp_nr	L2	GO:0002576	platelet degranulation	2.84e-13	3.48e-06
CD19+ B	gobp_nr	L2	GO:0072348	sulfur compound transport	2.11e-13	1
CD19+ B	gobp_nr	L2	GO:0006338	chromatin remodeling	1.67e-13	7.68e-05
CD19+ B	gobp_nr	L4	GO:0009123	nucleoside monophosphate metabolic process	0.984	4.19e-09
CD19+ B	gobp_nr	L4	GO:0009141	nucleoside triphosphate metabolic process	0.0154	1.67e-07
CD19+ B	gobp_nr	L4	GO:0006091	generation of precursor metabolites and energy	8.64e-05	2e-05
CD19+ B	gobp_nr	L4	GO:0009259	ribonucleotide metabolic process	1.7e-05	0.000236
CD19+ B	gobp_nr	L4	GO:0002576	platelet degranulation	3.53e-06	3.48e-06
CD19+ B	gobp_nr	L4	GO:0010257	NADH dehydrogenase complex assembly	3.51e-06	0.000956
CD19+ B	gobp_nr	L4	GO:0033108	mitochondrial respiratory chain complex assembly	2.51e-06	0.0019
CD19+ B	gobp_nr	L4	GO:0006338	chromatin remodeling	1.93e-06	7.68e-05
CD19+ B	gobp_nr	L4	GO:0051647	nucleus localization	1.19e-06	0.000379
CD19+ B	gobp_nr	L4	GO:0008380	RNA splicing	1.08e-06	0.000218
CD19+ B	gobp_nr	L5	GO:0002764	immune response-regulating signaling pathway	0.996	1.51e-11
CD19+ B	gobp_nr	L5	GO:0002250	adaptive immune response	0.00109	4.44e-10
CD19+ B	gobp_nr	L5	GO:0070661	leukocyte proliferation	0.00031	1.35e-09
CD19+ B	gobp_nr	L5	GO:0002694	regulation of leukocyte activation	0.000186	8.26e-11
CD19+ B	gobp_nr	L5	GO:0045088	regulation of innate immune response	0.000112	5.37e-06
CD19+ B	gobp_nr	L5	GO:0042113	B cell activation	0.000102	5.21e-09
CD19+ B	gobp_nr	L5	GO:0050867	positive regulation of cell activation	8.82e-05	6.51e-09
CD19+ B	gobp_nr	L5	GO:0009615	response to virus	8.7e-05	5.14e-05
CD19+ B	gobp_nr	L5	GO:0002576	platelet degranulation	8.44e-05	3.48e-06
CD19+ B	gobp_nr	L5	GO:0034612	response to tumor necrosis factor	7.43e-05	1.75e-05

gomf

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	gomf	L1	GO:0003723	RNA binding	1	2.04e-13
CD19+ B	gomf	L1	GO:0005515	protein binding	0.000249	4.01e-18
CD19+ B	gomf	L1	GO:0044877	protein-containing complex binding	9.72e-07	3.93e-07
CD19+ B	gomf	L1	GO:0042802	identical protein binding	8.92e-07	3.75e-06
CD19+ B	gomf	L1	GO:0046983	protein dimerization activity	3.56e-07	3.8e-05
CD19+ B	gomf	L1	GO:0019899	enzyme binding	2.08e-07	9.92e-06
CD19+ B	gomf	L1	GO:0042803	protein homodimerization activity	1.51e-07	4.47e-05
CD19+ B	gomf	L1	GO:0003682	chromatin binding	1.09e-07	0.000226
CD19+ B	gomf	L1	GO:0019904	protein domain specific binding	4.17e-08	0.000273
CD19+ B	gomf	L1	GO:0009055	electron transfer activity	3.73e-08	4.55e-05
CD19+ B	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.995	1
CD19+ B	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.005	1
CD19+ B	gomf	L2	GO:0140110	transcription regulator activity	5.42e-08	1
CD19+ B	gomf	L2	GO:0003677	DNA binding	2.18e-10	1
CD19+ B	gomf	L2	GO:0003676	nucleic acid binding	5.54e-15	0.722
CD19+ B	gomf	L2	GO:1901363	heterocyclic compound binding	5.96e-17	0.959
CD19+ B	gomf	L2	GO:0097159	organic cyclic compound binding	2.02e-17	0.944
CD19+ B	gomf	L2	GO:0046872	metal ion binding	1.27e-19	1
CD19+ B	gomf	L2	GO:0000976	transcription regulatory region sequence-specific DNA binding	1.24e-19	0.0146
CD19+ B	gomf	L2	GO:0044212	transcription regulatory region DNA binding	9.57e-20	0.0509
CD19+ B	gomf	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.487	0.00459
CD19+ B	gomf	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	0.431	0.00538
CD19+ B	gomf	L3	GO:0000987	proximal promoter sequence-specific DNA binding	0.0364	0.000931
CD19+ B	gomf	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	0.0242	0.000898
CD19+ B	gomf	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	0.0131	0.0146
CD19+ B	gomf	L3	GO:0003690	double-stranded DNA binding	0.00581	0.00278
CD19+ B	gomf	L3	GO:1990837	sequence-specific double-stranded DNA binding	0.00128	0.0177
CD19+ B	gomf	L3	GO:0001067	regulatory region nucleic acid binding	0.000374	0.0442
CD19+ B	gomf	L3	GO:0044212	transcription regulatory region DNA binding	0.000265	0.0509
CD19+ B	gomf	L3	GO:0043565	sequence-specific DNA binding	2.39e-05	0.111
CD19+ B	gomf	L6	GO:0003735	structural constituent of ribosome	0.995	9.07e-12
CD19+ B	gomf	L6	GO:0003823	antigen binding	0.000162	1.3e-05
CD19+ B	gomf	L6	GO:0016860	intramolecular oxidoreductase activity	0.000138	2.25e-05
CD19+ B	gomf	L6	GO:0005070	SH3/SH2 adaptor activity	9.78e-05	3.21e-05
CD19+ B	gomf	L6	GO:0042287	MHC protein binding	4.95e-05	0.000155
CD19+ B	gomf	L6	GO:0009055	electron transfer activity	4.48e-05	4.55e-05
CD19+ B	gomf	L6	GO:0005515	protein binding	4.4e-05	4.01e-18
CD19+ B	gomf	L6	GO:0030276	clathrin binding	3.62e-05	0.000424
CD19+ B	gomf	L6	GO:0004842	ubiquitin-protein transferase activity	3.19e-05	1
CD19+ B	gomf	L6	GO:0061659	ubiquitin-like protein ligase activity	3e-05	1
CD19+ B	gomf	L7	GO:0003954	NADH dehydrogenase activity	0.326	2.42e-06
CD19+ B	gomf	L7	GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.218	3.8e-06
CD19+ B	gomf	L7	GO:0050136	NADH dehydrogenase (quinone) activity	0.218	3.8e-06
CD19+ B	gomf	L7	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	0.177	2.76e-06
CD19+ B	gomf	L7	GO:0016651	oxidoreductase activity, acting on NAD(P)H	0.0382	6.14e-06
CD19+ B	gomf	L7	GO:0009055	electron transfer activity	0.00115	4.55e-05
CD19+ B	gomf	L7	GO:0003823	antigen binding	0.000758	1.3e-05
CD19+ B	gomf	L7	GO:0016491	oxidoreductase activity	0.000747	4.4e-05
CD19+ B	gomf	L7	GO:0016860	intramolecular oxidoreductase activity	0.000666	2.25e-05
CD19+ B	gomf	L7	GO:0005070	SH3/SH2 adaptor activity	0.000431	3.21e-05

kegg

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	kegg	L1	hsa00190	Oxidative phosphorylation	0.998	8.69e-10
CD19+ B	kegg	L1	hsa05012	Parkinson disease	0.002	2.49e-08
CD19+ B	kegg	L1	hsa05010	Alzheimer disease	1.62e-05	3.84e-07
CD19+ B	kegg	L1	hsa05016	Huntington disease	3.95e-07	4.46e-05
CD19+ B	kegg	L1	hsa04714	Thermogenesis	4.8e-08	0.000479
CD19+ B	kegg	L1	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	6.5e-09	0.000586
CD19+ B	kegg	L1	hsa04260	Cardiac muscle contraction	1.33e-09	0.00576
CD19+ B	kegg	L1	hsa00770	Pantothenate and CoA biosynthesis	1.13e-09	1
CD19+ B	kegg	L1	hsa04512	ECM-receptor interaction	9.86e-10	0.999
CD19+ B	kegg	L1	hsa01200	Carbon metabolism	8.64e-10	0.000567
CD19+ B	kegg	L2	hsa04640	Hematopoietic cell lineage	1	1.42e-07
CD19+ B	kegg	L2	hsa05332	Graft-versus-host disease	5.54e-05	2.62e-06
CD19+ B	kegg	L2	hsa04659	Th17 cell differentiation	1.8e-05	2.14e-05
CD19+ B	kegg	L2	hsa05330	Allograft rejection	1.72e-05	1.52e-05
CD19+ B	kegg	L2	hsa04940	Type I diabetes mellitus	1.68e-05	2.73e-05
CD19+ B	kegg	L2	hsa04658	Th1 and Th2 cell differentiation	1.06e-05	3.98e-05
CD19+ B	kegg	L2	hsa04612	Antigen processing and presentation	1.05e-05	8.72e-05
CD19+ B	kegg	L2	hsa05169	Epstein-Barr virus infection	7.26e-06	3.08e-05
CD19+ B	kegg	L2	hsa05340	Primary immunodeficiency	5.98e-06	0.000397
CD19+ B	kegg	L2	hsa05320	Autoimmune thyroid disease	5.55e-06	0.00014
CD19+ B	kegg	L3	hsa03010	Ribosome	1	6.81e-10
CD19+ B	kegg	L3	hsa00770	Pantothenate and CoA biosynthesis	8.93e-10	1
CD19+ B	kegg	L3	hsa04512	ECM-receptor interaction	7.97e-10	0.999
CD19+ B	kegg	L3	hsa03022	Basal transcription factors	5.82e-10	1
CD19+ B	kegg	L3	hsa00330	Arginine and proline metabolism	5.8e-10	0.00132
CD19+ B	kegg	L3	hsa00900	Terpenoid backbone biosynthesis	4.46e-10	0.999
CD19+ B	kegg	L3	hsa00062	Fatty acid elongation	4.23e-10	0.00361
CD19+ B	kegg	L3	hsa05202	Transcriptional misregulation in cancer	4.09e-10	0.000138
CD19+ B	kegg	L3	hsa03050	Proteasome	3.88e-10	0.00228
CD19+ B	kegg	L3	hsa01200	Carbon metabolism	3.69e-10	0.000567

reactome

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	reactome	L1	R-HSA-168256	Immune System	1	1.25e-22
CD19+ B	reactome	L1	R-HSA-168249	Innate Immune System	1.03e-21	3.33e-20
CD19+ B	reactome	L1	R-HSA-1280218	Adaptive Immune System	2.34e-22	3.22e-06
CD19+ B	reactome	L1	R-HSA-6798695	Neutrophil degranulation	1.98e-29	4.42e-16
CD19+ B	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	9.28e-32	1.74e-11
CD19+ B	reactome	L1	R-HSA-449147	Signaling by Interleukins	7.37e-37	4.16e-09
CD19+ B	reactome	L1	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	6.33e-37	6.61e-11
CD19+ B	reactome	L1	R-HSA-983169	Class I MHC mediated antigen processing & presentation	1.44e-37	0.813
CD19+ B	reactome	L1	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	6.06e-39	0.972
CD19+ B	reactome	L1	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	8.53e-40	3.28e-07
CD19+ B	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	0.761	2.7e-15
CD19+ B	reactome	L2	R-HSA-156902	Peptide chain elongation	0.124	1.16e-14
CD19+ B	reactome	L2	R-HSA-192823	Viral mRNA Translation	0.0667	1.16e-14
CD19+ B	reactome	L2	R-HSA-2408557	Selenocysteine synthesis	0.0255	2.04e-14
CD19+ B	reactome	L2	R-HSA-72764	Eukaryotic Translation Termination	0.0168	2.04e-14
CD19+ B	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	0.00281	4.64e-14
CD19+ B	reactome	L2	R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	0.00229	2.62e-15
CD19+ B	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	0.000532	2.09e-14
CD19+ B	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	0.000371	3.27e-14
CD19+ B	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	7.27e-05	6.24e-13
CD19+ B	reactome	L3	R-HSA-74160	Gene expression (Transcription)	0.885	1
CD19+ B	reactome	L3	R-HSA-212436	Generic Transcription Pathway	0.0727	1
CD19+ B	reactome	L3	R-HSA-73857	RNA Polymerase II Transcription	0.0418	1
CD19+ B	reactome	L3	R-HSA-211000	Gene Silencing by RNA	7.76e-06	1
CD19+ B	reactome	L3	R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript	2.78e-07	0.996
CD19+ B	reactome	L3	R-HSA-159234	Transport of Mature mRNAs Derived from Intronless Transcripts	1.87e-07	0.993
CD19+ B	reactome	L3	R-HSA-5578749	Transcriptional regulation by small RNAs	1.51e-07	0.989
CD19+ B	reactome	L3	R-HSA-72766	Translation	1.51e-07	3.11e-12
CD19+ B	reactome	L3	R-HSA-6807505	RNA polymerase II transcribes snRNA genes	1.05e-07	0.999
CD19+ B	reactome	L3	R-HSA-159227	Transport of the SLBP independent Mature mRNA	9.39e-08	0.993
CD19+ B	reactome	L4	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	0.845	7.04e-09
CD19+ B	reactome	L4	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	0.149	2.65e-08
CD19+ B	reactome	L4	R-HSA-611105	Respiratory electron transport	0.00565	3.72e-07
CD19+ B	reactome	L4	R-HSA-6799198	Complex I biogenesis	4.25e-08	0.000905
CD19+ B	reactome	L4	R-HSA-8949613	Cristae formation	3.74e-08	0.000151
CD19+ B	reactome	L4	R-HSA-163210	Formation of ATP by chemiosmotic coupling	1.26e-08	0.00108
CD19+ B	reactome	L4	R-HSA-1430728	Metabolism	6.7e-09	2.67e-07
CD19+ B	reactome	L4	R-HSA-3700989	Transcriptional Regulation by TP53	6.44e-09	0.266
CD19+ B	reactome	L4	R-HSA-199220	Vitamin B5 (pantothenate) metabolism	4.8e-09	1
CD19+ B	reactome	L4	R-HSA-983189	Kinesins	4.28e-09	0.99
CD19+ B	reactome	L5	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	0.997	0.972
CD19+ B	reactome	L5	R-HSA-983169	Class I MHC mediated antigen processing & presentation	0.00296	0.813
CD19+ B	reactome	L5	R-HSA-8951664	Neddylation	3.8e-11	0.723
CD19+ B	reactome	L5	R-HSA-1280218	Adaptive Immune System	1.55e-13	3.22e-06
CD19+ B	reactome	L5	R-HSA-5619115	Disorders of transmembrane transporters	9.8e-14	0.547
CD19+ B	reactome	L5	R-HSA-4608870	Asymmetric localization of PCP proteins	2.7e-14	0.0208
CD19+ B	reactome	L5	R-HSA-5358346	Hedgehog ligand biogenesis	2.15e-14	0.0165
CD19+ B	reactome	L5	R-HSA-597592	Post-translational protein modification	1.83e-14	0.989
CD19+ B	reactome	L5	R-HSA-4641258	Degradation of DVL	1.34e-14	0.00325
CD19+ B	reactome	L5	R-HSA-4641257	Degradation of AXIN	1.27e-14	0.00433
CD19+ B	reactome	L6	R-HSA-180585	Vif-mediated degradation of APOBEC3G	0.748	1.8e-05
CD19+ B	reactome	L6	R-HSA-1234176	Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha	0.0316	6.47e-05
CD19+ B	reactome	L6	R-HSA-211733	Regulation of activated PAK-2p34 by proteasome mediated degradation	0.0253	8.32e-05
CD19+ B	reactome	L6	R-HSA-69601	Ubiquitin Mediated Degradation of Phosphorylated Cdc25A	0.024	0.000106
CD19+ B	reactome	L6	R-HSA-69610	p53-Independent DNA Damage Response	0.024	0.000106
CD19+ B	reactome	L6	R-HSA-69613	p53-Independent G1/S DNA damage checkpoint	0.024	0.000106
CD19+ B	reactome	L6	R-HSA-69541	Stabilization of p53	0.0222	9.09e-05
CD19+ B	reactome	L6	R-HSA-69229	Ubiquitin-dependent degradation of Cyclin D1	0.0116	0.000152
CD19+ B	reactome	L6	R-HSA-75815	Ubiquitin-dependent degradation of Cyclin D	0.0116	0.000152
CD19+ B	reactome	L6	R-HSA-180534	Vpu mediated degradation of CD4	0.0116	0.000152
CD19+ B	reactome	L8	R-HSA-72163	mRNA Splicing - Major Pathway	0.546	7.62e-05
CD19+ B	reactome	L8	R-HSA-72172	mRNA Splicing	0.444	9.11e-05
CD19+ B	reactome	L8	R-HSA-109688	Cleavage of Growing Transcript in the Termination Region	0.00106	0.0249
CD19+ B	reactome	L8	R-HSA-73856	RNA Polymerase II Transcription Termination	0.00106	0.0249
CD19+ B	reactome	L8	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	0.00037	0.0138
CD19+ B	reactome	L8	R-HSA-72187	mRNA 3’-end processing	0.000246	0.0502
CD19+ B	reactome	L8	R-HSA-983189	Kinesins	0.000155	0.99
CD19+ B	reactome	L8	R-HSA-72766	Translation	0.000117	3.11e-12
CD19+ B	reactome	L8	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.000109	6.61e-11
CD19+ B	reactome	L8	R-HSA-199220	Vitamin B5 (pantothenate) metabolism	0.000107	1
CD19+ B	reactome	L9	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	0.704	6.2e-07
CD19+ B	reactome	L9	R-HSA-114608	Platelet degranulation	0.231	2.36e-06
CD19+ B	reactome	L9	R-HSA-76002	Platelet activation, signaling and aggregation	0.0253	4.91e-07
CD19+ B	reactome	L9	R-HSA-199220	Vitamin B5 (pantothenate) metabolism	0.000735	1
CD19+ B	reactome	L9	R-HSA-8862803	Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models	0.000727	0.000259
CD19+ B	reactome	L9	R-HSA-8863678	Neurodegenerative Diseases	0.000727	0.000259
CD19+ B	reactome	L9	R-HSA-983189	Kinesins	0.000685	0.99
CD19+ B	reactome	L9	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.000492	6.61e-11
CD19+ B	reactome	L9	R-HSA-72766	Translation	0.000489	3.11e-12
CD19+ B	reactome	L9	R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript	0.000465	0.996

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	wikipathway_cancer	L1	WP619	Type II interferon signaling (IFNG)	1	2.79e-05
CD19+ B	wikipathway_cancer	L1	WP4585	Cancer immunotherapy by PD-1 blockade	1.91e-05	0.00342
CD19+ B	wikipathway_cancer	L1	WP254	Apoptosis	1.47e-05	0.000278
CD19+ B	wikipathway_cancer	L1	WP3617	Photodynamic therapy-induced NF-kB survival signaling	7.87e-06	0.00795
CD19+ B	wikipathway_cancer	L1	WP4284	Ultraconserved region 339 modulation of tumor suppressor microRNAs in cancer	7.83e-06	1
CD19+ B	wikipathway_cancer	L1	WP4204	Tumor suppressor activity of SMARCB1	6.8e-06	0.0109
CD19+ B	wikipathway_cancer	L1	WP585	Interferon type I signaling pathways	5.37e-06	0.0227
CD19+ B	wikipathway_cancer	L1	WP704	Methylation Pathways	5.3e-06	0.0707
CD19+ B	wikipathway_cancer	L1	WP2868	TCA Cycle Nutrient Utilization and Invasiveness of Ovarian Cancer	5.17e-06	0.171
CD19+ B	wikipathway_cancer	L1	WP364	IL-6 signaling pathway	4.27e-06	0.0523

wikipathway

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	wikipathway	L1	WP477	Cytoplasmic Ribosomal Proteins	1	5.32e-12
CD19+ B	wikipathway	L1	WP619	Type II interferon signaling (IFNG)	4.5e-15	2.61e-05
CD19+ B	wikipathway	L1	WP4150	Wnt Signaling in Kidney Disease	4.5e-15	1
CD19+ B	wikipathway	L1	WP3945	TYROBP Causal Network	3.47e-15	7.37e-05
CD19+ B	wikipathway	L1	WP3995	Prion disease pathway	3.43e-15	0.000105
CD19+ B	wikipathway	L1	WP183	Proteasome Degradation	2.68e-15	7.37e-05
CD19+ B	wikipathway	L1	WP3613	Photodynamic therapy-induced unfolded protein response	1.92e-15	0.00105
CD19+ B	wikipathway	L1	WP254	Apoptosis	1.54e-15	0.000271
CD19+ B	wikipathway	L1	WP411	mRNA Processing	1.46e-15	0.000384
CD19+ B	wikipathway	L1	WP311	Synthesis and Degradation of Ketone Bodies	1.39e-15	1
CD19+ B	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	1	1.43e-09
CD19+ B	wikipathway	L2	WP623	Oxidative phosphorylation	8.14e-05	7.45e-07
CD19+ B	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	1.42e-08	0.000721
CD19+ B	wikipathway	L2	WP619	Type II interferon signaling (IFNG)	1.75e-09	2.61e-05
CD19+ B	wikipathway	L2	WP4150	Wnt Signaling in Kidney Disease	1.71e-09	1
CD19+ B	wikipathway	L2	WP3995	Prion disease pathway	1.35e-09	0.000105
CD19+ B	wikipathway	L2	WP183	Proteasome Degradation	1.12e-09	7.37e-05
CD19+ B	wikipathway	L2	WP3945	TYROBP Causal Network	1.09e-09	7.37e-05
CD19+ B	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	9.73e-10	0.0135
CD19+ B	wikipathway	L2	WP3613	Photodynamic therapy-induced unfolded protein response	7.53e-10	0.00105

CD56+ NK

gobp

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD56+ NK	gobp	L1	GO:0002376	immune system process	1	3.12e-41
CD56+ NK	gobp	L1	GO:0006955	immune response	1.64e-06	4.86e-38
CD56+ NK	gobp	L1	GO:0001775	cell activation	2.1e-11	3.09e-35
CD56+ NK	gobp	L1	GO:0045321	leukocyte activation	3.55e-12	8.77e-35
CD56+ NK	gobp	L1	GO:0002252	immune effector process	4.91e-17	9.44e-30
CD56+ NK	gobp	L1	GO:0002682	regulation of immune system process	2.03e-21	3.53e-22
CD56+ NK	gobp	L1	GO:0050896	response to stimulus	1.73e-24	1.84e-19
CD56+ NK	gobp	L1	GO:0002443	leukocyte mediated immunity	8.8e-26	1.49e-22
CD56+ NK	gobp	L1	GO:0050776	regulation of immune response	7.8e-26	5.68e-20
CD56+ NK	gobp	L1	GO:0002366	leukocyte activation involved in immune response	6.52e-26	2.84e-23
CD56+ NK	gobp	L2	GO:0045047	protein targeting to ER	0.684	4.97e-15
CD56+ NK	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.21	1.12e-14
CD56+ NK	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.069	1.2e-14
CD56+ NK	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.0367	1.99e-14
CD56+ NK	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	2.62e-06	2.07e-11
CD56+ NK	gobp	L2	GO:0006413	translational initiation	8.36e-09	3.29e-12
CD56+ NK	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	6.19e-10	4.92e-09
CD56+ NK	gobp	L2	GO:0006612	protein targeting to membrane	3.38e-11	2.31e-08
CD56+ NK	gobp	L2	GO:0090150	establishment of protein localization to membrane	3.7e-12	1e-08
CD56+ NK	gobp	L2	GO:0006518	peptide metabolic process	1.4e-13	1.21e-10
CD56+ NK	gobp	L3	GO:0006357	regulation of transcription by RNA polymerase II	0.185	1
CD56+ NK	gobp	L3	GO:0006366	transcription by RNA polymerase II	0.155	1
CD56+ NK	gobp	L3	GO:0016070	RNA metabolic process	0.0961	0.963
CD56+ NK	gobp	L3	GO:0090304	nucleic acid metabolic process	0.0844	0.983
CD56+ NK	gobp	L3	GO:0019219	regulation of nucleobase-containing compound metabolic process	0.0542	0.993
CD56+ NK	gobp	L3	GO:0010468	regulation of gene expression	0.0501	0.921
CD56+ NK	gobp	L3	GO:2000112	regulation of cellular macromolecule biosynthetic process	0.0426	0.998
CD56+ NK	gobp	L3	GO:0051252	regulation of RNA metabolic process	0.0337	0.994
CD56+ NK	gobp	L3	GO:0010556	regulation of macromolecule biosynthetic process	0.0332	0.996
CD56+ NK	gobp	L3	GO:0006351	transcription, DNA-templated	0.0273	0.998
CD56+ NK	gobp	L4	GO:0006119	oxidative phosphorylation	0.975	3.45e-09
CD56+ NK	gobp	L4	GO:0009123	nucleoside monophosphate metabolic process	0.00823	2.65e-09
CD56+ NK	gobp	L4	GO:0042773	ATP synthesis coupled electron transport	0.00544	4.46e-07
CD56+ NK	gobp	L4	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.00362	6.41e-07
CD56+ NK	gobp	L4	GO:0009161	ribonucleoside monophosphate metabolic process	0.00279	6.1e-09
CD56+ NK	gobp	L4	GO:0009126	purine nucleoside monophosphate metabolic process	0.00132	1.17e-08
CD56+ NK	gobp	L4	GO:0009167	purine ribonucleoside monophosphate metabolic process	0.00132	1.17e-08
CD56+ NK	gobp	L4	GO:0022904	respiratory electron transport chain	0.00116	1.87e-06
CD56+ NK	gobp	L4	GO:0046034	ATP metabolic process	0.00049	6.31e-08
CD56+ NK	gobp	L4	GO:0022900	electron transport chain	0.000355	9.09e-07
CD56+ NK	gobp	L5	GO:0097237	cellular response to toxic substance	0.938	5.25e-09
CD56+ NK	gobp	L5	GO:0071236	cellular response to antibiotic	0.0265	1.18e-07
CD56+ NK	gobp	L5	GO:1990748	cellular detoxification	0.00595	9.35e-06
CD56+ NK	gobp	L5	GO:0098869	cellular oxidant detoxification	0.00454	1.08e-05
CD56+ NK	gobp	L5	GO:0098754	detoxification	0.00166	4.43e-05
CD56+ NK	gobp	L5	GO:0006338	chromatin remodeling	0.00102	8.49e-05
CD56+ NK	gobp	L5	GO:0006333	chromatin assembly or disassembly	0.000921	0.000172
CD56+ NK	gobp	L5	GO:0002576	platelet degranulation	0.000867	8.02e-07
CD56+ NK	gobp	L5	GO:0046677	response to antibiotic	0.000753	4.84e-07
CD56+ NK	gobp	L5	GO:0001775	cell activation	0.000458	3.09e-35
CD56+ NK	gobp	L6	GO:0008380	RNA splicing	0.603	1.15e-05
CD56+ NK	gobp	L6	GO:0006397	mRNA processing	0.224	3.03e-05
CD56+ NK	gobp	L6	GO:0000375	RNA splicing, via transesterification reactions	0.0536	8.39e-05
CD56+ NK	gobp	L6	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0498	8.6e-05
CD56+ NK	gobp	L6	GO:0000398	mRNA splicing, via spliceosome	0.0498	8.6e-05
CD56+ NK	gobp	L6	GO:0016071	mRNA metabolic process	0.0146	3.07e-09
CD56+ NK	gobp	L6	GO:0006333	chromatin assembly or disassembly	0.000231	0.000172
CD56+ NK	gobp	L6	GO:0006338	chromatin remodeling	0.000199	8.49e-05
CD56+ NK	gobp	L6	GO:0007600	sensory perception	0.000138	1
CD56+ NK	gobp	L6	GO:0006518	peptide metabolic process	0.000134	1.21e-10

gobp_nr

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD56+ NK	gobp_nr	L1	GO:0036230	granulocyte activation	0.665	4.89e-16
CD56+ NK	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.335	1.08e-15
CD56+ NK	gobp_nr	L1	GO:0002764	immune response-regulating signaling pathway	2.1e-12	1.89e-11
CD56+ NK	gobp_nr	L1	GO:0002576	platelet degranulation	1.76e-12	3.45e-06
CD56+ NK	gobp_nr	L1	GO:0009615	response to virus	5.06e-13	7.41e-08
CD56+ NK	gobp_nr	L1	GO:0006909	phagocytosis	3.63e-13	6.48e-06
CD56+ NK	gobp_nr	L1	GO:0019882	antigen processing and presentation	3.59e-13	8.3e-05
CD56+ NK	gobp_nr	L1	GO:0052547	regulation of peptidase activity	3.36e-13	1.32e-05
CD56+ NK	gobp_nr	L1	GO:0046677	response to antibiotic	2.6e-13	5.41e-06
CD56+ NK	gobp_nr	L1	GO:0050953	sensory perception of light stimulus	2.6e-13	1
CD56+ NK	gobp_nr	L2	GO:0006413	translational initiation	0.995	5.49e-11
CD56+ NK	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	0.00452	2.04e-10
CD56+ NK	gobp_nr	L2	GO:0090150	establishment of protein localization to membrane	1.69e-06	1.96e-07
CD56+ NK	gobp_nr	L2	GO:0006401	RNA catabolic process	1.66e-08	4e-05
CD56+ NK	gobp_nr	L2	GO:0006605	protein targeting	9.57e-09	5.78e-05
CD56+ NK	gobp_nr	L2	GO:0002181	cytoplasmic translation	7.05e-09	0.000658
CD56+ NK	gobp_nr	L2	GO:0009615	response to virus	2.02e-09	7.41e-08
CD56+ NK	gobp_nr	L2	GO:0002576	platelet degranulation	1.88e-09	3.45e-06
CD56+ NK	gobp_nr	L2	GO:0050953	sensory perception of light stimulus	1.4e-09	1
CD56+ NK	gobp_nr	L2	GO:0001578	microtubule bundle formation	1.29e-09	1
CD56+ NK	gobp_nr	L3	GO:0042110	T cell activation	0.986	3.24e-12
CD56+ NK	gobp_nr	L3	GO:0007159	leukocyte cell-cell adhesion	0.00655	2.7e-09
CD56+ NK	gobp_nr	L3	GO:0002764	immune response-regulating signaling pathway	0.00509	1.89e-11
CD56+ NK	gobp_nr	L3	GO:0002250	adaptive immune response	0.000849	4.48e-10
CD56+ NK	gobp_nr	L3	GO:0002521	leukocyte differentiation	0.000279	1.15e-09
CD56+ NK	gobp_nr	L3	GO:0009615	response to virus	0.000212	7.41e-08
CD56+ NK	gobp_nr	L3	GO:0022407	regulation of cell-cell adhesion	8.42e-05	2.52e-06
CD56+ NK	gobp_nr	L3	GO:0002576	platelet degranulation	6.71e-05	3.45e-06
CD56+ NK	gobp_nr	L3	GO:1903706	regulation of hemopoiesis	5e-05	3.31e-06
CD56+ NK	gobp_nr	L3	GO:0052547	regulation of peptidase activity	4.82e-05	1.32e-05
CD56+ NK	gobp_nr	L4	GO:0009123	nucleoside monophosphate metabolic process	0.982	5.67e-08
CD56+ NK	gobp_nr	L4	GO:0009141	nucleoside triphosphate metabolic process	0.0147	2.93e-06
CD56+ NK	gobp_nr	L4	GO:0033108	mitochondrial respiratory chain complex assembly	0.00158	2.97e-05
CD56+ NK	gobp_nr	L4	GO:0009259	ribonucleotide metabolic process	0.000452	0.000175
CD56+ NK	gobp_nr	L4	GO:0006091	generation of precursor metabolites and energy	0.000313	9.81e-05
CD56+ NK	gobp_nr	L4	GO:0010257	NADH dehydrogenase complex assembly	0.000242	0.00018
CD56+ NK	gobp_nr	L4	GO:0002576	platelet degranulation	7.6e-05	3.45e-06
CD56+ NK	gobp_nr	L4	GO:0050953	sensory perception of light stimulus	4.31e-05	1
CD56+ NK	gobp_nr	L4	GO:0009615	response to virus	3.8e-05	7.41e-08
CD56+ NK	gobp_nr	L4	GO:0001578	microtubule bundle formation	3.56e-05	1
CD56+ NK	gobp_nr	L5	GO:0042113	B cell activation	0.997	1.13e-10
CD56+ NK	gobp_nr	L5	GO:0002764	immune response-regulating signaling pathway	0.00108	1.89e-11
CD56+ NK	gobp_nr	L5	GO:0002250	adaptive immune response	0.000133	4.48e-10
CD56+ NK	gobp_nr	L5	GO:0002576	platelet degranulation	9.27e-05	3.45e-06
CD56+ NK	gobp_nr	L5	GO:0009615	response to virus	9e-05	7.41e-08
CD56+ NK	gobp_nr	L5	GO:0050953	sensory perception of light stimulus	6.14e-05	1
CD56+ NK	gobp_nr	L5	GO:0001578	microtubule bundle formation	5.34e-05	1
CD56+ NK	gobp_nr	L5	GO:0046677	response to antibiotic	4.36e-05	5.41e-06
CD56+ NK	gobp_nr	L5	GO:0052547	regulation of peptidase activity	3.69e-05	1.32e-05
CD56+ NK	gobp_nr	L5	GO:0006338	chromatin remodeling	3.63e-05	0.000348

gomf

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD56+ NK	gomf	L1	GO:0003735	structural constituent of ribosome	1	1.16e-18
CD56+ NK	gomf	L1	GO:0003723	RNA binding	7.04e-16	1.45e-10
CD56+ NK	gomf	L1	GO:0005198	structural molecule activity	1.55e-16	2e-07
CD56+ NK	gomf	L1	GO:0008821	crossover junction endodeoxyribonuclease activity	4.65e-19	1
CD56+ NK	gomf	L1	GO:0016209	antioxidant activity	3.17e-19	2.46e-06
CD56+ NK	gomf	L1	GO:0005515	protein binding	3.1e-19	6.5e-17
CD56+ NK	gomf	L1	GO:1901682	sulfur compound transmembrane transporter activity	3.05e-19	1
CD56+ NK	gomf	L1	GO:0045296	cadherin binding	2.89e-19	1.92e-05
CD56+ NK	gomf	L1	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	2.69e-19	3.7e-06
CD56+ NK	gomf	L1	GO:0042287	MHC protein binding	2.63e-19	4.63e-05
CD56+ NK	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.997	1
CD56+ NK	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.00323	1
CD56+ NK	gomf	L2	GO:0140110	transcription regulator activity	9.43e-11	1
CD56+ NK	gomf	L2	GO:0003677	DNA binding	3.37e-13	1
CD56+ NK	gomf	L2	GO:0046872	metal ion binding	6.11e-23	1
CD56+ NK	gomf	L2	GO:0044212	transcription regulatory region DNA binding	1.41e-23	0.112
CD56+ NK	gomf	L2	GO:0001067	regulatory region nucleic acid binding	8.31e-24	0.1
CD56+ NK	gomf	L2	GO:0043169	cation binding	4.61e-24	1
CD56+ NK	gomf	L2	GO:0001012	RNA polymerase II regulatory region DNA binding	2.84e-24	0.0128
CD56+ NK	gomf	L2	GO:0003676	nucleic acid binding	2.19e-24	0.951
CD56+ NK	gomf	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.525	0.00833
CD56+ NK	gomf	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	0.282	0.00976
CD56+ NK	gomf	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	0.176	0.0128
CD56+ NK	gomf	L3	GO:1990837	sequence-specific double-stranded DNA binding	0.0109	0.0156
CD56+ NK	gomf	L3	GO:0003690	double-stranded DNA binding	0.00648	0.00671
CD56+ NK	gomf	L3	GO:0043565	sequence-specific DNA binding	0.000385	0.0931
CD56+ NK	gomf	L3	GO:0000987	proximal promoter sequence-specific DNA binding	8.45e-05	0.0116
CD56+ NK	gomf	L3	GO:0001067	regulatory region nucleic acid binding	7.25e-05	0.1
CD56+ NK	gomf	L3	GO:0044212	transcription regulatory region DNA binding	4.82e-05	0.112
CD56+ NK	gomf	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	2.66e-05	0.0144

kegg

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD56+ NK	kegg	L1	hsa03010	Ribosome	1	2.39e-12
CD56+ NK	kegg	L1	hsa04512	ECM-receptor interaction	1.65e-14	1
CD56+ NK	kegg	L1	hsa00730	Thiamine metabolism	1.4e-14	1
CD56+ NK	kegg	L1	hsa03460	Fanconi anemia pathway	9.68e-15	1
CD56+ NK	kegg	L1	hsa00630	Glyoxylate and dicarboxylate metabolism	9.32e-15	0.00228
CD56+ NK	kegg	L1	hsa04650	Natural killer cell mediated cytotoxicity	9.06e-15	5.29e-06
CD56+ NK	kegg	L1	hsa00052	Galactose metabolism	8.61e-15	0.00228
CD56+ NK	kegg	L1	hsa05033	Nicotine addiction	6.9e-15	1
CD56+ NK	kegg	L1	hsa00533	Glycosaminoglycan biosynthesis	5.15e-15	0.00911
CD56+ NK	kegg	L1	hsa00062	Fatty acid elongation	4.79e-15	0.00748
CD56+ NK	kegg	L2	hsa05012	Parkinson disease	1	1.79e-10
CD56+ NK	kegg	L2	hsa00190	Oxidative phosphorylation	1.94e-06	2.57e-06
CD56+ NK	kegg	L2	hsa04714	Thermogenesis	1.89e-07	3.53e-06
CD56+ NK	kegg	L2	hsa05016	Huntington disease	1.79e-08	8.01e-05
CD56+ NK	kegg	L2	hsa05010	Alzheimer disease	1.18e-08	4.27e-05
CD56+ NK	kegg	L2	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	5.26e-10	0.000295
CD56+ NK	kegg	L2	hsa04512	ECM-receptor interaction	3.39e-11	1
CD56+ NK	kegg	L2	hsa00730	Thiamine metabolism	2.67e-11	1
CD56+ NK	kegg	L2	hsa04650	Natural killer cell mediated cytotoxicity	2.22e-11	5.29e-06
CD56+ NK	kegg	L2	hsa04723	Retrograde endocannabinoid signaling	2.09e-11	0.0133
CD56+ NK	kegg	L3	hsa04640	Hematopoietic cell lineage	0.998	5.3e-06
CD56+ NK	kegg	L3	hsa04612	Antigen processing and presentation	0.000392	3.57e-05
CD56+ NK	kegg	L3	hsa05332	Graft-versus-host disease	2e-04	8.59e-05
CD56+ NK	kegg	L3	hsa04658	Th1 and Th2 cell differentiation	0.000129	0.000234
CD56+ NK	kegg	L3	hsa04650	Natural killer cell mediated cytotoxicity	6.15e-05	5.29e-06
CD56+ NK	kegg	L3	hsa00730	Thiamine metabolism	5.69e-05	1
CD56+ NK	kegg	L3	hsa03460	Fanconi anemia pathway	4.79e-05	1
CD56+ NK	kegg	L3	hsa00630	Glyoxylate and dicarboxylate metabolism	4.29e-05	0.00228
CD56+ NK	kegg	L3	hsa00052	Galactose metabolism	3.97e-05	0.00228
CD56+ NK	kegg	L3	hsa05340	Primary immunodeficiency	3.77e-05	0.00437

reactome

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD56+ NK	reactome	L1	R-HSA-168256	Immune System	1	7.08e-21
CD56+ NK	reactome	L1	R-HSA-168249	Innate Immune System	3.44e-14	3.3e-19
CD56+ NK	reactome	L1	R-HSA-1280218	Adaptive Immune System	8.59e-20	2.28e-06
CD56+ NK	reactome	L1	R-HSA-6798695	Neutrophil degranulation	3.94e-23	2.05e-14
CD56+ NK	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	5.94e-27	1.73e-08
CD56+ NK	reactome	L1	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	4.21e-31	2.55e-09
CD56+ NK	reactome	L1	R-HSA-449147	Signaling by Interleukins	2.02e-31	7.08e-06
CD56+ NK	reactome	L1	R-HSA-983169	Class I MHC mediated antigen processing & presentation	6.87e-32	0.503
CD56+ NK	reactome	L1	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	4.92e-33	0.771
CD56+ NK	reactome	L1	R-HSA-109581	Apoptosis	1.4e-33	1.27e-05
CD56+ NK	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	0.865	5.68e-16
CD56+ NK	reactome	L2	R-HSA-156902	Peptide chain elongation	0.106	2.24e-15
CD56+ NK	reactome	L2	R-HSA-192823	Viral mRNA Translation	0.0265	2.24e-15
CD56+ NK	reactome	L2	R-HSA-72764	Eukaryotic Translation Termination	0.00176	6.62e-15
CD56+ NK	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	0.000534	2.73e-15
CD56+ NK	reactome	L2	R-HSA-2408557	Selenocysteine synthesis	0.000143	9.05e-14
CD56+ NK	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	1.21e-05	3.03e-15
CD56+ NK	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	9.35e-06	4.64e-15
CD56+ NK	reactome	L2	R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	8.92e-06	4.19e-13
CD56+ NK	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	8.48e-08	1.07e-12
CD56+ NK	reactome	L3	R-HSA-212436	Generic Transcription Pathway	0.681	1
CD56+ NK	reactome	L3	R-HSA-74160	Gene expression (Transcription)	0.297	1
CD56+ NK	reactome	L3	R-HSA-73857	RNA Polymerase II Transcription	0.0221	1
CD56+ NK	reactome	L3	R-HSA-211000	Gene Silencing by RNA	1.79e-08	0.959
CD56+ NK	reactome	L3	R-HSA-448424	Interleukin-17 signaling	7.77e-09	0.965
CD56+ NK	reactome	L3	R-HSA-450294	MAP kinase activation	4.16e-09	0.956
CD56+ NK	reactome	L3	R-HSA-3232142	SUMOylation of ubiquitinylation proteins	4e-09	0.994
CD56+ NK	reactome	L3	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	3.9e-09	1.11e-06
CD56+ NK	reactome	L3	R-HSA-5368286	Mitochondrial translation initiation	3.85e-09	0.000607
CD56+ NK	reactome	L3	R-HSA-168138	Toll Like Receptor 9 (TLR9) Cascade	2.94e-09	0.83
CD56+ NK	reactome	L4	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	0.993	7.73e-08
CD56+ NK	reactome	L4	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	0.00561	3.57e-06
CD56+ NK	reactome	L4	R-HSA-611105	Respiratory electron transport	0.00106	1.84e-05
CD56+ NK	reactome	L4	R-HSA-6799198	Complex I biogenesis	1.15e-06	0.00047
CD56+ NK	reactome	L4	R-HSA-163210	Formation of ATP by chemiosmotic coupling	4.05e-07	0.000197
CD56+ NK	reactome	L4	R-HSA-3700989	Transcriptional Regulation by TP53	3.29e-07	0.174
CD56+ NK	reactome	L4	R-HSA-8949613	Cristae formation	1.73e-07	0.000492
CD56+ NK	reactome	L4	R-HSA-1430728	Metabolism	6.44e-08	7.48e-07
CD56+ NK	reactome	L4	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	5.51e-08	1.11e-06
CD56+ NK	reactome	L4	R-HSA-72163	mRNA Splicing - Major Pathway	3.54e-08	0.000259
CD56+ NK	reactome	L5	R-HSA-8878171	Transcriptional regulation by RUNX1	0.971	0.000103
CD56+ NK	reactome	L5	R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs	0.0185	4.04e-05
CD56+ NK	reactome	L5	R-HSA-157118	Signaling by NOTCH	0.00959	1.07e-05
CD56+ NK	reactome	L5	R-HSA-8878159	Transcriptional regulation by RUNX3	0.000102	0.000407
CD56+ NK	reactome	L5	R-HSA-4641257	Degradation of AXIN	7.08e-05	0.000268
CD56+ NK	reactome	L5	R-HSA-8948751	Regulation of PTEN stability and activity	6.68e-05	0.000159
CD56+ NK	reactome	L5	R-HSA-180585	Vif-mediated degradation of APOBEC3G	5.75e-05	0.000369
CD56+ NK	reactome	L5	R-HSA-69481	G2/M Checkpoints	5.42e-05	0.00253
CD56+ NK	reactome	L5	R-HSA-8941858	Regulation of RUNX3 expression and activity	2.83e-05	0.000638
CD56+ NK	reactome	L5	R-HSA-9013694	Signaling by NOTCH4	2.25e-05	0.000628
CD56+ NK	reactome	L6	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	0.881	0.771
CD56+ NK	reactome	L6	R-HSA-983169	Class I MHC mediated antigen processing & presentation	0.119	0.503
CD56+ NK	reactome	L6	R-HSA-8951664	Neddylation	0.000295	0.89
CD56+ NK	reactome	L6	R-HSA-448424	Interleukin-17 signaling	4.14e-06	0.965
CD56+ NK	reactome	L6	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	3.56e-06	1.11e-06
CD56+ NK	reactome	L6	R-HSA-450321	JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1	2.76e-06	0.988
CD56+ NK	reactome	L6	R-HSA-72163	mRNA Splicing - Major Pathway	2.74e-06	0.000259
CD56+ NK	reactome	L6	R-HSA-72172	mRNA Splicing	2.26e-06	0.000343
CD56+ NK	reactome	L6	R-HSA-450294	MAP kinase activation	2.12e-06	0.956
CD56+ NK	reactome	L6	R-HSA-114608	Platelet degranulation	2.12e-06	3.8e-06

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD56+ NK	wikipathway	L1	WP477	Cytoplasmic Ribosomal Proteins	1	2.87e-13
CD56+ NK	wikipathway	L1	WP2805	exRNA mechanism of action and biogenesis	5.6e-20	1
CD56+ NK	wikipathway	L1	WP3945	TYROBP Causal Network	3.41e-20	1.48e-05
CD56+ NK	wikipathway	L1	WP183	Proteasome Degradation	1.49e-20	0.000229
CD56+ NK	wikipathway	L1	WP410	Exercise-induced Circadian Regulation	1.08e-20	0.000979
CD56+ NK	wikipathway	L1	WP254	Apoptosis	7.66e-21	0.000908
CD56+ NK	wikipathway	L1	WP43	Oxidation by Cytochrome P450	7.51e-21	0.999
CD56+ NK	wikipathway	L1	WP4150	Wnt Signaling in Kidney Disease	7.16e-21	0.999
CD56+ NK	wikipathway	L1	WP619	Type II interferon signaling (IFNG)	7.02e-21	0.00249
CD56+ NK	wikipathway	L1	WP3302	eIF5A regulation in response to inhibition of the nuclear export system	7.01e-21	1
CD56+ NK	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	0.991	2.34e-07
CD56+ NK	wikipathway	L2	WP623	Oxidative phosphorylation	0.00911	2.94e-06
CD56+ NK	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	1.86e-05	0.00046
CD56+ NK	wikipathway	L2	WP3945	TYROBP Causal Network	2.61e-06	1.48e-05
CD56+ NK	wikipathway	L2	WP2805	exRNA mechanism of action and biogenesis	2.25e-06	1
CD56+ NK	wikipathway	L2	WP183	Proteasome Degradation	1.59e-06	0.000229
CD56+ NK	wikipathway	L2	WP410	Exercise-induced Circadian Regulation	1.38e-06	0.000979
CD56+ NK	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	1.28e-06	0.0129
CD56+ NK	wikipathway	L2	WP254	Apoptosis	8.6e-07	0.000908
CD56+ NK	wikipathway	L2	WP43	Oxidation by Cytochrome P450	7.38e-07	0.999

T cell

gobp

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
T cell	gobp	L1	GO:0001775	cell activation	0.999	1.1e-42
T cell	gobp	L1	GO:0045321	leukocyte activation	0.00114	9.22e-40
T cell	gobp	L1	GO:0002263	cell activation involved in immune response	7.17e-10	3.25e-29
T cell	gobp	L1	GO:0002366	leukocyte activation involved in immune response	4.69e-10	6.53e-29
T cell	gobp	L1	GO:0002274	myeloid leukocyte activation	1.42e-10	4.97e-28
T cell	gobp	L1	GO:0002443	leukocyte mediated immunity	3.96e-11	9.03e-29
T cell	gobp	L1	GO:0045055	regulated exocytosis	1.43e-11	1.77e-25
T cell	gobp	L1	GO:0006887	exocytosis	3.5e-12	2.94e-24
T cell	gobp	L1	GO:0043299	leukocyte degranulation	2.05e-12	4.7e-25
T cell	gobp	L1	GO:0002275	myeloid cell activation involved in immune response	1.47e-12	9.28e-25
T cell	gobp	L2	GO:0006119	oxidative phosphorylation	0.999	3.33e-09
T cell	gobp	L2	GO:0042773	ATP synthesis coupled electron transport	0.000644	1.94e-07
T cell	gobp	L2	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.000438	2.55e-07
T cell	gobp	L2	GO:0046034	ATP metabolic process	3.45e-06	5.8e-08
T cell	gobp	L2	GO:0022904	respiratory electron transport chain	1.83e-06	1.46e-05
T cell	gobp	L2	GO:0009126	purine nucleoside monophosphate metabolic process	7.44e-08	8.81e-07
T cell	gobp	L2	GO:0009167	purine ribonucleoside monophosphate metabolic process	7.44e-08	8.81e-07
T cell	gobp	L2	GO:0009205	purine ribonucleoside triphosphate metabolic process	4.15e-08	2.37e-06
T cell	gobp	L2	GO:0009123	nucleoside monophosphate metabolic process	2.62e-08	2.78e-06
T cell	gobp	L2	GO:0009144	purine nucleoside triphosphate metabolic process	2.28e-08	3.59e-06
T cell	gobp	L3	GO:0045047	protein targeting to ER	0.426	9.34e-08
T cell	gobp	L3	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.344	6.63e-08
T cell	gobp	L3	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.139	2.14e-07
T cell	gobp	L3	GO:0070972	protein localization to endoplasmic reticulum	0.0608	5.48e-08
T cell	gobp	L3	GO:0006613	cotranslational protein targeting to membrane	0.0307	6.88e-07
T cell	gobp	L3	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	0.000199	5.9e-06
T cell	gobp	L3	GO:0006413	translational initiation	6.57e-05	5.84e-07
T cell	gobp	L3	GO:0006612	protein targeting to membrane	1.28e-05	1.42e-05
T cell	gobp	L3	GO:0090150	establishment of protein localization to membrane	2.76e-07	4.34e-05
T cell	gobp	L3	GO:0072657	protein localization to membrane	9.68e-08	2.32e-06
T cell	gobp	L4	GO:0002376	immune system process	0.999	6.42e-41
T cell	gobp	L4	GO:0006955	immune response	0.000505	2e-37
T cell	gobp	L4	GO:0050896	response to stimulus	3.37e-09	3.31e-20
T cell	gobp	L4	GO:0048518	positive regulation of biological process	1.05e-09	1.58e-16
T cell	gobp	L4	GO:0002252	immune effector process	3.83e-10	2.31e-30
T cell	gobp	L4	GO:0051716	cellular response to stimulus	3.09e-10	7.43e-15
T cell	gobp	L4	GO:0006952	defense response	1.87e-10	9.39e-17
T cell	gobp	L4	GO:0007154	cell communication	1.81e-10	1.16e-14
T cell	gobp	L4	GO:0023052	signaling	1.11e-10	2.59e-14
T cell	gobp	L4	GO:0032940	secretion by cell	5.21e-11	3.26e-24

gobp_nr

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
T cell	gobp_nr	L1	GO:0036230	granulocyte activation	0.732	2.63e-22
T cell	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.268	5.15e-22
T cell	gobp_nr	L1	GO:0032103	positive regulation of response to external stimulus	1.1e-27	3.22e-08
T cell	gobp_nr	L1	GO:0098542	defense response to other organism	6.23e-28	3.38e-07
T cell	gobp_nr	L1	GO:0006959	humoral immune response	5.91e-28	3.41e-06
T cell	gobp_nr	L1	GO:0002764	immune response-regulating signaling pathway	4.41e-28	1.39e-08
T cell	gobp_nr	L1	GO:0001819	positive regulation of cytokine production	3.27e-28	1.51e-09
T cell	gobp_nr	L1	GO:0006490	oligosaccharide-lipid intermediate biosynthetic process	3.2e-28	1
T cell	gobp_nr	L1	GO:0000959	mitochondrial RNA metabolic process	2.53e-28	1
T cell	gobp_nr	L1	GO:0009123	nucleoside monophosphate metabolic process	2.05e-28	2.25e-05
T cell	gobp_nr	L2	GO:0042110	T cell activation	1	4.09e-13
T cell	gobp_nr	L2	GO:0002694	regulation of leukocyte activation	3.06e-06	3.6e-10
T cell	gobp_nr	L2	GO:0007159	leukocyte cell-cell adhesion	2.59e-06	2.58e-09
T cell	gobp_nr	L2	GO:0002521	leukocyte differentiation	1.85e-06	7.17e-10
T cell	gobp_nr	L2	GO:0050867	positive regulation of cell activation	1.27e-06	2.51e-10
T cell	gobp_nr	L2	GO:0045785	positive regulation of cell adhesion	4.91e-07	1.28e-09
T cell	gobp_nr	L2	GO:0002250	adaptive immune response	1.07e-07	7.28e-09
T cell	gobp_nr	L2	GO:0022407	regulation of cell-cell adhesion	4.81e-08	3.37e-07
T cell	gobp_nr	L2	GO:0070661	leukocyte proliferation	6.91e-09	5.88e-07
T cell	gobp_nr	L2	GO:0001819	positive regulation of cytokine production	4.06e-09	1.51e-09
T cell	gobp_nr	L3	GO:0070972	protein localization to endoplasmic reticulum	1	2.67e-07
T cell	gobp_nr	L3	GO:0006413	translational initiation	0.000139	3.36e-06
T cell	gobp_nr	L3	GO:0090150	establishment of protein localization to membrane	9.47e-07	0.000275
T cell	gobp_nr	L3	GO:0006490	oligosaccharide-lipid intermediate biosynthetic process	3.44e-07	1
T cell	gobp_nr	L3	GO:0000959	mitochondrial RNA metabolic process	2.71e-07	1
T cell	gobp_nr	L3	GO:0006401	RNA catabolic process	1.34e-07	0.00213
T cell	gobp_nr	L3	GO:0072348	sulfur compound transport	1.3e-07	1
T cell	gobp_nr	L3	GO:0006605	protein targeting	7.67e-08	0.00283
T cell	gobp_nr	L3	GO:0070193	synaptonemal complex organization	7.66e-08	1
T cell	gobp_nr	L3	GO:2001233	regulation of apoptotic signaling pathway	4.67e-08	2.16e-06

gomf

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
T cell	gomf	L1	GO:0003723	RNA binding	0.982	1.94e-07
T cell	gomf	L1	GO:0005515	protein binding	0.0167	3.35e-17
T cell	gomf	L1	GO:0003735	structural constituent of ribosome	0.000267	3.09e-07
T cell	gomf	L1	GO:0019899	enzyme binding	8.05e-05	4.94e-07
T cell	gomf	L1	GO:0044877	protein-containing complex binding	4.07e-05	8.27e-06
T cell	gomf	L1	GO:0019904	protein domain specific binding	1.43e-05	1.42e-05
T cell	gomf	L1	GO:0046983	protein dimerization activity	1.4e-05	1.33e-05
T cell	gomf	L1	GO:0003690	double-stranded DNA binding	7.95e-06	8.99e-05
T cell	gomf	L1	GO:0050839	cell adhesion molecule binding	7.36e-06	0.000102
T cell	gomf	L1	GO:0008289	lipid binding	6.61e-06	3.54e-05

kegg

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
T cell	kegg	L1	hsa05010	Alzheimer disease	1	3.83e-10
T cell	kegg	L1	hsa05012	Parkinson disease	7.01e-07	3.64e-08
T cell	kegg	L1	hsa00190	Oxidative phosphorylation	1.43e-08	2.57e-06
T cell	kegg	L1	hsa05016	Huntington disease	1.59e-09	1.01e-05
T cell	kegg	L1	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	3.32e-11	0.000175
T cell	kegg	L1	hsa04714	Thermogenesis	2.2e-12	0.00116
T cell	kegg	L1	hsa04723	Retrograde endocannabinoid signaling	1.53e-12	0.000992
T cell	kegg	L1	hsa05167	Kaposi sarcoma-associated herpesvirus infection	1.08e-13	8.3e-05
T cell	kegg	L1	hsa04062	Chemokine signaling pathway	8.59e-14	3.97e-05
T cell	kegg	L1	hsa05332	Graft-versus-host disease	6.74e-14	1e-04

reactome

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
T cell	reactome	L1	R-HSA-6798695	Neutrophil degranulation	1	4.66e-21
T cell	reactome	L1	R-HSA-168249	Innate Immune System	6.29e-13	1.41e-15
T cell	reactome	L1	R-HSA-168256	Immune System	2.77e-16	6.99e-16
T cell	reactome	L1	R-HSA-76002	Platelet activation, signaling and aggregation	5.12e-28	1.14e-06
T cell	reactome	L1	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	4.67e-28	2.87e-06
T cell	reactome	L1	R-HSA-109582	Hemostasis	2.94e-28	1.33e-05
T cell	reactome	L1	R-HSA-162582	Signal Transduction	1.67e-28	0.000124
T cell	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	1.46e-28	4.68e-05
T cell	reactome	L1	R-HSA-3781860	Diseases associated with N-glycosylation of proteins	1.33e-28	1
T cell	reactome	L1	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	1.24e-28	3.85e-05
T cell	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	0.585	6.25e-10
T cell	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	0.399	8.15e-10
T cell	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	0.00719	1.13e-08
T cell	reactome	L2	R-HSA-72613	Eukaryotic Translation Initiation	0.00281	3.01e-08
T cell	reactome	L2	R-HSA-72737	Cap-dependent Translation Initiation	0.00281	3.01e-08
T cell	reactome	L2	R-HSA-192823	Viral mRNA Translation	0.00121	3.24e-09
T cell	reactome	L2	R-HSA-156902	Peptide chain elongation	0.000927	3.24e-09
T cell	reactome	L2	R-HSA-72764	Eukaryotic Translation Termination	0.000177	1.13e-08
T cell	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	0.000129	1.48e-08
T cell	reactome	L2	R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	5.99e-05	5.36e-08

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

CD14+ Monocyte

gobp

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	gobp	L1	GO:0045321	leukocyte activation	0.914	2.65e-42
CD14+ Monocyte	gobp	L1	GO:0001775	cell activation	0.0861	3e-41
CD14+ Monocyte	gobp	L1	GO:0002376	immune system process	4.67e-06	7.78e-37
CD14+ Monocyte	gobp	L1	GO:0006955	immune response	3.99e-07	6.61e-35
CD14+ Monocyte	gobp	L1	GO:0002443	leukocyte mediated immunity	8.31e-10	5.82e-33
CD14+ Monocyte	gobp	L1	GO:0002366	leukocyte activation involved in immune response	6.45e-10	1.79e-33
CD14+ Monocyte	gobp	L1	GO:0002263	cell activation involved in immune response	5.39e-10	1.78e-33
CD14+ Monocyte	gobp	L1	GO:0002274	myeloid leukocyte activation	2.29e-10	1.48e-33
CD14+ Monocyte	gobp	L1	GO:0042119	neutrophil activation	9.5e-12	5.91e-32
CD14+ Monocyte	gobp	L1	GO:0002275	myeloid cell activation involved in immune response	5.81e-12	5.26e-32
CD14+ Monocyte	gobp	L2	GO:0045047	protein targeting to ER	0.862	2.98e-18
CD14+ Monocyte	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.0573	1.34e-17
CD14+ Monocyte	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.0476	1.92e-17
CD14+ Monocyte	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0334	5.89e-17
CD14+ Monocyte	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	0.000211	3.51e-16
CD14+ Monocyte	gobp	L2	GO:0006612	protein targeting to membrane	4.14e-08	9.54e-13
CD14+ Monocyte	gobp	L2	GO:0090150	establishment of protein localization to membrane	3.13e-09	9.75e-14
CD14+ Monocyte	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	2.76e-09	1.93e-12
CD14+ Monocyte	gobp	L2	GO:0006413	translational initiation	6.92e-10	1.37e-17
CD14+ Monocyte	gobp	L2	GO:0006605	protein targeting	6.28e-12	3.26e-10
CD14+ Monocyte	gobp	L3	GO:0006119	oxidative phosphorylation	0.999	4.53e-14
CD14+ Monocyte	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.000398	2.83e-11
CD14+ Monocyte	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.000223	4.6e-11
CD14+ Monocyte	gobp	L3	GO:0009123	nucleoside monophosphate metabolic process	0.000174	5.26e-14
CD14+ Monocyte	gobp	L3	GO:0009126	purine nucleoside monophosphate metabolic process	5.84e-05	8.7e-14
CD14+ Monocyte	gobp	L3	GO:0009167	purine ribonucleoside monophosphate metabolic process	5.84e-05	8.7e-14
CD14+ Monocyte	gobp	L3	GO:0009161	ribonucleoside monophosphate metabolic process	1.15e-05	6.11e-13
CD14+ Monocyte	gobp	L3	GO:0009144	purine nucleoside triphosphate metabolic process	8.93e-06	4.77e-13
CD14+ Monocyte	gobp	L3	GO:0046034	ATP metabolic process	6.87e-06	1.49e-12
CD14+ Monocyte	gobp	L3	GO:0022904	respiratory electron transport chain	6.09e-06	9.59e-10
CD14+ Monocyte	gobp	L4	GO:0016192	vesicle-mediated transport	0.985	2.75e-20
CD14+ Monocyte	gobp	L4	GO:0002376	immune system process	0.00848	7.78e-37
CD14+ Monocyte	gobp	L4	GO:0006955	immune response	0.00197	6.61e-35
CD14+ Monocyte	gobp	L4	GO:0045055	regulated exocytosis	0.000873	1.19e-27
CD14+ Monocyte	gobp	L4	GO:0006810	transport	0.000864	4.68e-19
CD14+ Monocyte	gobp	L4	GO:0051234	establishment of localization	0.000683	1.11e-18
CD14+ Monocyte	gobp	L4	GO:0006887	exocytosis	0.00064	6.43e-25
CD14+ Monocyte	gobp	L4	GO:0042119	neutrophil activation	0.000259	5.91e-32
CD14+ Monocyte	gobp	L4	GO:0036230	granulocyte activation	0.000175	1.02e-31
CD14+ Monocyte	gobp	L4	GO:0043299	leukocyte degranulation	0.000152	3e-32
CD14+ Monocyte	gobp	L5	GO:0006915	apoptotic process	0.272	1.09e-11
CD14+ Monocyte	gobp	L5	GO:0012501	programmed cell death	0.195	1.29e-11
CD14+ Monocyte	gobp	L5	GO:0043067	regulation of programmed cell death	0.194	1.32e-11
CD14+ Monocyte	gobp	L5	GO:0042981	regulation of apoptotic process	0.158	1.93e-11
CD14+ Monocyte	gobp	L5	GO:0010941	regulation of cell death	0.101	1.13e-11
CD14+ Monocyte	gobp	L5	GO:0008219	cell death	0.0513	3.75e-11
CD14+ Monocyte	gobp	L5	GO:0002376	immune system process	0.0071	7.78e-37
CD14+ Monocyte	gobp	L5	GO:0016032	viral process	0.00345	2.54e-12
CD14+ Monocyte	gobp	L5	GO:0097190	apoptotic signaling pathway	0.00227	5.85e-08
CD14+ Monocyte	gobp	L5	GO:0044419	interspecies interaction between organisms	0.00226	6.26e-13
CD14+ Monocyte	gobp	L6	GO:0006518	peptide metabolic process	0.791	5.43e-16
CD14+ Monocyte	gobp	L6	GO:0006412	translation	0.12	3.38e-14
CD14+ Monocyte	gobp	L6	GO:0043043	peptide biosynthetic process	0.0828	7.64e-14
CD14+ Monocyte	gobp	L6	GO:0043603	cellular amide metabolic process	0.00248	8.39e-12
CD14+ Monocyte	gobp	L6	GO:0070125	mitochondrial translational elongation	0.00176	1.94e-06
CD14+ Monocyte	gobp	L6	GO:0043604	amide biosynthetic process	0.00117	6.89e-11
CD14+ Monocyte	gobp	L6	GO:0070126	mitochondrial translational termination	0.00066	5.98e-06
CD14+ Monocyte	gobp	L6	GO:0006413	translational initiation	0.000301	1.37e-17
CD14+ Monocyte	gobp	L6	GO:0006415	translational termination	0.000143	3.99e-05
CD14+ Monocyte	gobp	L6	GO:0006414	translational elongation	5.84e-05	6.6e-05
CD14+ Monocyte	gobp	L7	GO:0008380	RNA splicing	0.422	4.04e-07
CD14+ Monocyte	gobp	L7	GO:0000375	RNA splicing, via transesterification reactions	0.197	1.22e-06
CD14+ Monocyte	gobp	L7	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.179	1.34e-06
CD14+ Monocyte	gobp	L7	GO:0000398	mRNA splicing, via spliceosome	0.179	1.34e-06
CD14+ Monocyte	gobp	L7	GO:0006397	mRNA processing	0.0211	6.94e-06
CD14+ Monocyte	gobp	L7	GO:0016071	mRNA metabolic process	0.0015	3.3e-12
CD14+ Monocyte	gobp	L7	GO:0016032	viral process	6.57e-05	2.54e-12
CD14+ Monocyte	gobp	L7	GO:0044419	interspecies interaction between organisms	3.83e-05	6.26e-13
CD14+ Monocyte	gobp	L7	GO:0044403	symbiont process	2.46e-05	4.42e-12
CD14+ Monocyte	gobp	L7	GO:0009124	nucleoside monophosphate biosynthetic process	2e-05	5.81e-08

gobp_nr

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	gobp_nr	L1	GO:0036230	granulocyte activation	0.976	2.21e-28
CD14+ Monocyte	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.0241	7.34e-27
CD14+ Monocyte	gobp_nr	L1	GO:0002532	production of molecular mediator involved in inflammatory response	2.75e-26	6.8e-08
CD14+ Monocyte	gobp_nr	L1	GO:0002764	immune response-regulating signaling pathway	1.12e-26	1.7e-08
CD14+ Monocyte	gobp_nr	L1	GO:0006979	response to oxidative stress	8.64e-28	1.11e-05
CD14+ Monocyte	gobp_nr	L1	GO:0002576	platelet degranulation	7.4e-28	0.000203
CD14+ Monocyte	gobp_nr	L1	GO:2001057	reactive nitrogen species metabolic process	6.91e-28	5.23e-05
CD14+ Monocyte	gobp_nr	L1	GO:0006959	humoral immune response	6.84e-28	3.97e-05
CD14+ Monocyte	gobp_nr	L1	GO:0002250	adaptive immune response	5.86e-28	2.54e-08
CD14+ Monocyte	gobp_nr	L1	GO:0006968	cellular defense response	5.6e-28	0.000278
CD14+ Monocyte	gobp_nr	L2	GO:0006413	translational initiation	1	4.86e-16
CD14+ Monocyte	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	5.97e-06	6.22e-15
CD14+ Monocyte	gobp_nr	L2	GO:0002181	cytoplasmic translation	7.06e-09	8.01e-06
CD14+ Monocyte	gobp_nr	L2	GO:0006401	RNA catabolic process	1.85e-09	4.33e-07
CD14+ Monocyte	gobp_nr	L2	GO:0002532	production of molecular mediator involved in inflammatory response	1.46e-09	6.8e-08
CD14+ Monocyte	gobp_nr	L2	GO:0006414	translational elongation	6.34e-10	0.000282
CD14+ Monocyte	gobp_nr	L2	GO:0006338	chromatin remodeling	5.4e-10	2.75e-05
CD14+ Monocyte	gobp_nr	L2	GO:0006605	protein targeting	3.47e-10	1.6e-08
CD14+ Monocyte	gobp_nr	L2	GO:0002764	immune response-regulating signaling pathway	3.15e-10	1.7e-08
CD14+ Monocyte	gobp_nr	L2	GO:0042769	DNA damage response, detection of DNA damage	2.54e-10	0.000784
CD14+ Monocyte	gobp_nr	L3	GO:0009123	nucleoside monophosphate metabolic process	0.988	2.91e-12
CD14+ Monocyte	gobp_nr	L3	GO:0009141	nucleoside triphosphate metabolic process	0.0117	1.07e-10
CD14+ Monocyte	gobp_nr	L3	GO:0006091	generation of precursor metabolites and energy	3.6e-06	1.84e-07
CD14+ Monocyte	gobp_nr	L3	GO:0033108	mitochondrial respiratory chain complex assembly	5.23e-07	1.48e-06
CD14+ Monocyte	gobp_nr	L3	GO:0009259	ribonucleotide metabolic process	4.64e-07	6.2e-06
CD14+ Monocyte	gobp_nr	L3	GO:0010257	NADH dehydrogenase complex assembly	8.77e-09	9.79e-05
CD14+ Monocyte	gobp_nr	L3	GO:0072522	purine-containing compound biosynthetic process	3.05e-09	0.000203
CD14+ Monocyte	gobp_nr	L3	GO:0002532	production of molecular mediator involved in inflammatory response	1.19e-09	6.8e-08
CD14+ Monocyte	gobp_nr	L3	GO:1901293	nucleoside phosphate biosynthetic process	1.13e-09	0.000702
CD14+ Monocyte	gobp_nr	L3	GO:1902600	proton transmembrane transport	1.08e-09	0.000794
CD14+ Monocyte	gobp_nr	L4	GO:0002521	leukocyte differentiation	0.619	1.03e-09
CD14+ Monocyte	gobp_nr	L4	GO:0042110	T cell activation	0.357	2.67e-10
CD14+ Monocyte	gobp_nr	L4	GO:0002250	adaptive immune response	0.00864	2.54e-08
CD14+ Monocyte	gobp_nr	L4	GO:0042113	B cell activation	0.00749	3.76e-08
CD14+ Monocyte	gobp_nr	L4	GO:0002694	regulation of leukocyte activation	0.00398	5.28e-09
CD14+ Monocyte	gobp_nr	L4	GO:1903706	regulation of hemopoiesis	0.00156	8.9e-07
CD14+ Monocyte	gobp_nr	L4	GO:0050867	positive regulation of cell activation	0.00108	8.74e-08
CD14+ Monocyte	gobp_nr	L4	GO:0002764	immune response-regulating signaling pathway	0.000618	1.7e-08
CD14+ Monocyte	gobp_nr	L4	GO:0007159	leukocyte cell-cell adhesion	0.000441	3.65e-07
CD14+ Monocyte	gobp_nr	L4	GO:0070661	leukocyte proliferation	0.00022	6.69e-07
CD14+ Monocyte	gobp_nr	L5	GO:0008380	RNA splicing	0.877	9.49e-06
CD14+ Monocyte	gobp_nr	L5	GO:0006397	mRNA processing	0.089	0.000139
CD14+ Monocyte	gobp_nr	L5	GO:0002532	production of molecular mediator involved in inflammatory response	0.00137	6.8e-08
CD14+ Monocyte	gobp_nr	L5	GO:0006338	chromatin remodeling	0.00135	2.75e-05
CD14+ Monocyte	gobp_nr	L5	GO:0033044	regulation of chromosome organization	0.00129	0.000107
CD14+ Monocyte	gobp_nr	L5	GO:1903311	regulation of mRNA metabolic process	0.00128	0.000202
CD14+ Monocyte	gobp_nr	L5	GO:0006414	translational elongation	0.00124	0.000282
CD14+ Monocyte	gobp_nr	L5	GO:0002764	immune response-regulating signaling pathway	0.000716	1.7e-08
CD14+ Monocyte	gobp_nr	L5	GO:0008213	protein alkylation	0.00058	0.00143
CD14+ Monocyte	gobp_nr	L5	GO:0042113	B cell activation	0.000485	3.76e-08
CD14+ Monocyte	gobp_nr	L6	GO:0090150	establishment of protein localization to membrane	0.756	5.32e-12
CD14+ Monocyte	gobp_nr	L6	GO:0070972	protein localization to endoplasmic reticulum	0.238	6.22e-15
CD14+ Monocyte	gobp_nr	L6	GO:0006605	protein targeting	0.00287	1.6e-08
CD14+ Monocyte	gobp_nr	L6	GO:0002532	production of molecular mediator involved in inflammatory response	0.000342	6.8e-08
CD14+ Monocyte	gobp_nr	L6	GO:0006414	translational elongation	0.000159	0.000282
CD14+ Monocyte	gobp_nr	L6	GO:0006338	chromatin remodeling	0.000112	2.75e-05
CD14+ Monocyte	gobp_nr	L6	GO:0002764	immune response-regulating signaling pathway	0.000108	1.7e-08
CD14+ Monocyte	gobp_nr	L6	GO:1904950	negative regulation of establishment of protein localization	8.32e-05	0.000154
CD14+ Monocyte	gobp_nr	L6	GO:0033044	regulation of chromosome organization	6.05e-05	0.000107
CD14+ Monocyte	gobp_nr	L6	GO:0033108	mitochondrial respiratory chain complex assembly	5.56e-05	1.48e-06

gomf

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	gomf	L1	GO:0003723	RNA binding	1	4.13e-22
CD14+ Monocyte	gomf	L1	GO:0005515	protein binding	1.75e-07	1.19e-16
CD14+ Monocyte	gomf	L1	GO:0042802	identical protein binding	3.12e-10	6.6e-06
CD14+ Monocyte	gomf	L1	GO:0019899	enzyme binding	2.55e-10	5.06e-07
CD14+ Monocyte	gomf	L1	GO:0044877	protein-containing complex binding	2.34e-10	5.83e-07
CD14+ Monocyte	gomf	L1	GO:0003743	translation initiation factor activity	7.73e-11	7.55e-06
CD14+ Monocyte	gomf	L1	GO:0051082	unfolded protein binding	5.5e-11	3.56e-05
CD14+ Monocyte	gomf	L1	GO:0003682	chromatin binding	3.76e-11	6.05e-05
CD14+ Monocyte	gomf	L1	GO:0044389	ubiquitin-like protein ligase binding	1.63e-11	0.000147
CD14+ Monocyte	gomf	L1	GO:0031625	ubiquitin protein ligase binding	1.37e-11	0.000193
CD14+ Monocyte	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	1	1
CD14+ Monocyte	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.000172	1
CD14+ Monocyte	gomf	L2	GO:0003677	DNA binding	3.13e-08	1
CD14+ Monocyte	gomf	L2	GO:0140110	transcription regulator activity	4.48e-10	1
CD14+ Monocyte	gomf	L2	GO:0003676	nucleic acid binding	2.63e-12	0.151
CD14+ Monocyte	gomf	L2	GO:0097159	organic cyclic compound binding	3.17e-15	0.615
CD14+ Monocyte	gomf	L2	GO:1901363	heterocyclic compound binding	2.8e-15	0.583
CD14+ Monocyte	gomf	L2	GO:0000976	transcription regulatory region sequence-specific DNA binding	9.49e-18	0.000717
CD14+ Monocyte	gomf	L2	GO:0001067	regulatory region nucleic acid binding	6.02e-18	0.00412
CD14+ Monocyte	gomf	L2	GO:0044212	transcription regulatory region DNA binding	5.61e-18	0.00397
CD14+ Monocyte	gomf	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	0.66	0.000104
CD14+ Monocyte	gomf	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.292	0.000123
CD14+ Monocyte	gomf	L3	GO:0000987	proximal promoter sequence-specific DNA binding	0.0358	1.01e-05
CD14+ Monocyte	gomf	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	0.00754	1.62e-05
CD14+ Monocyte	gomf	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	0.003	0.000717
CD14+ Monocyte	gomf	L3	GO:1990837	sequence-specific double-stranded DNA binding	0.000625	0.000602
CD14+ Monocyte	gomf	L3	GO:0043565	sequence-specific DNA binding	0.000263	0.00204
CD14+ Monocyte	gomf	L3	GO:0044212	transcription regulatory region DNA binding	2.75e-05	0.00397
CD14+ Monocyte	gomf	L3	GO:0001067	regulatory region nucleic acid binding	2.02e-05	0.00412
CD14+ Monocyte	gomf	L3	GO:0003690	double-stranded DNA binding	1.06e-05	0.00058
CD14+ Monocyte	gomf	L4	GO:0003735	structural constituent of ribosome	1	1.8e-20
CD14+ Monocyte	gomf	L4	GO:0015370	solute:sodium symporter activity	9.36e-14	1
CD14+ Monocyte	gomf	L4	GO:0003823	antigen binding	7.41e-14	0.000176
CD14+ Monocyte	gomf	L4	GO:0019199	transmembrane receptor protein kinase activity	6.22e-14	1
CD14+ Monocyte	gomf	L4	GO:0005310	dicarboxylic acid transmembrane transporter activity	4.74e-14	1
CD14+ Monocyte	gomf	L4	GO:0008157	protein phosphatase 1 binding	4.04e-14	6.99e-05
CD14+ Monocyte	gomf	L4	GO:0004298	threonine-type endopeptidase activity	3.67e-14	0.000332
CD14+ Monocyte	gomf	L4	GO:0070003	threonine-type peptidase activity	3.67e-14	0.000332
CD14+ Monocyte	gomf	L4	GO:0042287	MHC protein binding	3.2e-14	0.000476
CD14+ Monocyte	gomf	L4	GO:0140098	catalytic activity, acting on RNA	3.2e-14	0.981
CD14+ Monocyte	gomf	L5	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	0.827	1.9e-08
CD14+ Monocyte	gomf	L5	GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.0776	1.51e-07
CD14+ Monocyte	gomf	L5	GO:0050136	NADH dehydrogenase (quinone) activity	0.0776	1.51e-07
CD14+ Monocyte	gomf	L5	GO:0003954	NADH dehydrogenase activity	0.0176	6.46e-07
CD14+ Monocyte	gomf	L5	GO:0016651	oxidoreductase activity, acting on NAD(P)H	0.000139	2.11e-05
CD14+ Monocyte	gomf	L5	GO:0009055	electron transfer activity	3.59e-06	0.000166
CD14+ Monocyte	gomf	L5	GO:0015370	solute:sodium symporter activity	2.01e-06	1
CD14+ Monocyte	gomf	L5	GO:0016491	oxidoreductase activity	1.58e-06	0.000283
CD14+ Monocyte	gomf	L5	GO:0003823	antigen binding	1.54e-06	0.000176
CD14+ Monocyte	gomf	L5	GO:0019199	transmembrane receptor protein kinase activity	1.28e-06	1
CD14+ Monocyte	gomf	L6	GO:0045296	cadherin binding	0.789	1.01e-09
CD14+ Monocyte	gomf	L6	GO:0050839	cell adhesion molecule binding	0.188	1.07e-08
CD14+ Monocyte	gomf	L6	GO:0005515	protein binding	0.0011	1.19e-16
CD14+ Monocyte	gomf	L6	GO:0042802	identical protein binding	0.000964	6.6e-06
CD14+ Monocyte	gomf	L6	GO:0044877	protein-containing complex binding	0.000567	5.83e-07
CD14+ Monocyte	gomf	L6	GO:0019899	enzyme binding	0.000473	5.06e-07
CD14+ Monocyte	gomf	L6	GO:0051082	unfolded protein binding	0.000388	3.56e-05
CD14+ Monocyte	gomf	L6	GO:0003823	antigen binding	0.000326	0.000176
CD14+ Monocyte	gomf	L6	GO:0019199	transmembrane receptor protein kinase activity	0.000265	1
CD14+ Monocyte	gomf	L6	GO:0015370	solute:sodium symporter activity	0.000254	1

kegg

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	kegg	L1	hsa03010	Ribosome	1	7.77e-14
CD14+ Monocyte	kegg	L1	hsa04640	Hematopoietic cell lineage	5.2e-15	3.06e-05
CD14+ Monocyte	kegg	L1	hsa04659	Th17 cell differentiation	3.24e-15	3.84e-05
CD14+ Monocyte	kegg	L1	hsa04350	TGF-beta signaling pathway	2.85e-15	1
CD14+ Monocyte	kegg	L1	hsa04142	Lysosome	2.81e-15	0.000967
CD14+ Monocyte	kegg	L1	hsa04512	ECM-receptor interaction	2.58e-15	0.999
CD14+ Monocyte	kegg	L1	hsa04390	Hippo signaling pathway	2.39e-15	1
CD14+ Monocyte	kegg	L1	hsa00030	Pentose phosphate pathway	2.36e-15	0.00882
CD14+ Monocyte	kegg	L1	hsa00900	Terpenoid backbone biosynthesis	2.31e-15	0.998
CD14+ Monocyte	kegg	L1	hsa05033	Nicotine addiction	2.03e-15	1
CD14+ Monocyte	kegg	L2	hsa05012	Parkinson disease	1	4.04e-13
CD14+ Monocyte	kegg	L2	hsa00190	Oxidative phosphorylation	9.66e-05	7.13e-11
CD14+ Monocyte	kegg	L2	hsa05016	Huntington disease	1.97e-06	2.14e-09
CD14+ Monocyte	kegg	L2	hsa04714	Thermogenesis	2.64e-08	7.2e-08
CD14+ Monocyte	kegg	L2	hsa05010	Alzheimer disease	1.14e-08	1.6e-07
CD14+ Monocyte	kegg	L2	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	4.23e-12	0.000243
CD14+ Monocyte	kegg	L2	hsa04723	Retrograde endocannabinoid signaling	3.46e-13	0.00192
CD14+ Monocyte	kegg	L2	hsa04640	Hematopoietic cell lineage	9.57e-14	3.06e-05
CD14+ Monocyte	kegg	L2	hsa04659	Th17 cell differentiation	5.96e-14	3.84e-05
CD14+ Monocyte	kegg	L2	hsa05152	Tuberculosis	5.54e-14	9.54e-05

reactome

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	reactome	L1	R-HSA-6798695	Neutrophil degranulation	1	1.05e-25
CD14+ Monocyte	reactome	L1	R-HSA-168249	Innate Immune System	4.65e-06	2.98e-23
CD14+ Monocyte	reactome	L1	R-HSA-168256	Immune System	9.78e-14	2.03e-19
CD14+ Monocyte	reactome	L1	R-HSA-449147	Signaling by Interleukins	3.46e-26	6.39e-06
CD14+ Monocyte	reactome	L1	R-HSA-109582	Hemostasis	2.09e-26	5.43e-05
CD14+ Monocyte	reactome	L1	R-HSA-76002	Platelet activation, signaling and aggregation	1.47e-26	1.13e-05
CD14+ Monocyte	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	1.17e-26	2.67e-05
CD14+ Monocyte	reactome	L1	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	1e-26	8e-06
CD14+ Monocyte	reactome	L1	R-HSA-5663205	Infectious disease	8.41e-27	2.96e-11
CD14+ Monocyte	reactome	L1	R-HSA-8953897	Cellular responses to external stimuli	6.25e-27	0.00164
CD14+ Monocyte	reactome	L2	R-HSA-72766	Translation	1	2.19e-20
CD14+ Monocyte	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	1.51e-13	8.37e-21
CD14+ Monocyte	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	3.15e-14	8e-20
CD14+ Monocyte	reactome	L2	R-HSA-72613	Eukaryotic Translation Initiation	3.21e-15	3.78e-18
CD14+ Monocyte	reactome	L2	R-HSA-72737	Cap-dependent Translation Initiation	3.21e-15	3.78e-18
CD14+ Monocyte	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	6.26e-16	1.63e-18
CD14+ Monocyte	reactome	L2	R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	3.36e-16	1.22e-17
CD14+ Monocyte	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	2.2e-17	1.08e-17
CD14+ Monocyte	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	4.76e-18	5e-15
CD14+ Monocyte	reactome	L2	R-HSA-156902	Peptide chain elongation	4.19e-18	5.29e-17
CD14+ Monocyte	reactome	L3	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	1	1.59e-12
CD14+ Monocyte	reactome	L3	R-HSA-611105	Respiratory electron transport	0.000365	7.33e-10
CD14+ Monocyte	reactome	L3	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	2.39e-05	1.1e-08
CD14+ Monocyte	reactome	L3	R-HSA-6799198	Complex I biogenesis	2.81e-10	2.84e-05
CD14+ Monocyte	reactome	L3	R-HSA-8949613	Cristae formation	4.75e-11	8.73e-06
CD14+ Monocyte	reactome	L3	R-HSA-163210	Formation of ATP by chemiosmotic coupling	1.31e-11	4.38e-05
CD14+ Monocyte	reactome	L3	R-HSA-1592230	Mitochondrial biogenesis	3.27e-12	0.000168
CD14+ Monocyte	reactome	L3	R-HSA-1430728	Metabolism	1.04e-12	6.47e-06
CD14+ Monocyte	reactome	L3	R-HSA-202433	Generation of second messenger molecules	2.29e-13	0.000106
CD14+ Monocyte	reactome	L3	R-HSA-2871809	FCERI mediated Ca+2 mobilization	2e-13	0.000155
CD14+ Monocyte	reactome	L5	R-HSA-72172	mRNA Splicing	0.675	2.11e-06
CD14+ Monocyte	reactome	L5	R-HSA-72163	mRNA Splicing - Major Pathway	0.306	3.8e-06
CD14+ Monocyte	reactome	L5	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	0.018	5.36e-05
CD14+ Monocyte	reactome	L5	R-HSA-109688	Cleavage of Growing Transcript in the Termination Region	3.96e-05	0.00244
CD14+ Monocyte	reactome	L5	R-HSA-73856	RNA Polymerase II Transcription Termination	3.96e-05	0.00244
CD14+ Monocyte	reactome	L5	R-HSA-72187	mRNA 3’-end processing	3.31e-05	0.0025
CD14+ Monocyte	reactome	L5	R-HSA-5663205	Infectious disease	2.31e-05	2.96e-11
CD14+ Monocyte	reactome	L5	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	2.27e-05	8e-06
CD14+ Monocyte	reactome	L5	R-HSA-202433	Generation of second messenger molecules	1.91e-05	0.000106
CD14+ Monocyte	reactome	L5	R-HSA-2871809	FCERI mediated Ca+2 mobilization	1.78e-05	0.000155
CD14+ Monocyte	reactome	L6	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.997	1.36e-07
CD14+ Monocyte	reactome	L6	R-HSA-168256	Immune System	0.00054	2.03e-19
CD14+ Monocyte	reactome	L6	R-HSA-1280218	Adaptive Immune System	0.000359	1.33e-05
CD14+ Monocyte	reactome	L6	R-HSA-202433	Generation of second messenger molecules	0.000136	0.000106
CD14+ Monocyte	reactome	L6	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	5.37e-05	8e-06
CD14+ Monocyte	reactome	L6	R-HSA-2871809	FCERI mediated Ca+2 mobilization	3.47e-05	0.000155
CD14+ Monocyte	reactome	L6	R-HSA-6782315	tRNA modification in the nucleus and cytosol	2.24e-05	1
CD14+ Monocyte	reactome	L6	R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers	2.23e-05	0.00037
CD14+ Monocyte	reactome	L6	R-HSA-3299685	Detoxification of Reactive Oxygen Species	2.2e-05	0.000167
CD14+ Monocyte	reactome	L6	R-HSA-8856825	Cargo recognition for clathrin-mediated endocytosis	2.13e-05	0.000946
CD14+ Monocyte	reactome	L7	R-HSA-379726	Mitochondrial tRNA aminoacylation	0.997	0.993
CD14+ Monocyte	reactome	L7	R-HSA-202433	Generation of second messenger molecules	7.9e-05	0.000106
CD14+ Monocyte	reactome	L7	R-HSA-379724	tRNA Aminoacylation	7.71e-05	0.225
CD14+ Monocyte	reactome	L7	R-HSA-2871809	FCERI mediated Ca+2 mobilization	6.76e-05	0.000155
CD14+ Monocyte	reactome	L7	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	5.07e-05	8e-06
CD14+ Monocyte	reactome	L7	R-HSA-3299685	Detoxification of Reactive Oxygen Species	4.37e-05	0.000167
CD14+ Monocyte	reactome	L7	R-HSA-877312	Regulation of IFNG signaling	4e-05	0.000408
CD14+ Monocyte	reactome	L7	R-HSA-6782315	tRNA modification in the nucleus and cytosol	3.99e-05	1
CD14+ Monocyte	reactome	L7	R-HSA-1433557	Signaling by SCF-KIT	2.81e-05	0.00026
CD14+ Monocyte	reactome	L7	R-HSA-5578775	Ion homeostasis	2.81e-05	0.00203

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	wikipathway	L1	WP477	Cytoplasmic Ribosomal Proteins	1	1.46e-13
CD14+ Monocyte	wikipathway	L1	WP3945	TYROBP Causal Network	7.89e-17	4.32e-05
CD14+ Monocyte	wikipathway	L1	WP2805	exRNA mechanism of action and biogenesis	6.53e-17	1
CD14+ Monocyte	wikipathway	L1	WP619	Type II interferon signaling (IFNG)	5.33e-17	0.000444
CD14+ Monocyte	wikipathway	L1	WP4304	Oligodendrocyte Specification and differentiation(including remyelination), leading to Myelin Components for CNS	3.05e-17	0.999
CD14+ Monocyte	wikipathway	L1	WP2328	Allograft Rejection	2.9e-17	0.000532
CD14+ Monocyte	wikipathway	L1	WP3888	VEGFA-VEGFR2 Signaling Pathway	2.47e-17	0.00168
CD14+ Monocyte	wikipathway	L1	WP411	mRNA Processing	2.29e-17	0.000632
CD14+ Monocyte	wikipathway	L1	WP4204	Tumor suppressor activity of SMARCB1	2.16e-17	0.00427
CD14+ Monocyte	wikipathway	L1	WP3931	ESC Pluripotency Pathways	2.06e-17	1
CD14+ Monocyte	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	1	5.73e-11
CD14+ Monocyte	wikipathway	L2	WP623	Oxidative phosphorylation	0.00017	1.03e-08
CD14+ Monocyte	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	2.87e-09	0.000167
CD14+ Monocyte	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	2.81e-10	0.00106
CD14+ Monocyte	wikipathway	L2	WP3945	TYROBP Causal Network	4.08e-11	4.32e-05
CD14+ Monocyte	wikipathway	L2	WP619	Type II interferon signaling (IFNG)	3.57e-11	0.000444
CD14+ Monocyte	wikipathway	L2	WP2805	exRNA mechanism of action and biogenesis	3.27e-11	1
CD14+ Monocyte	wikipathway	L2	WP2328	Allograft Rejection	2.06e-11	0.000532
CD14+ Monocyte	wikipathway	L2	WP4304	Oligodendrocyte Specification and differentiation(including remyelination), leading to Myelin Components for CNS	1.94e-11	0.999
CD14+ Monocyte	wikipathway	L2	WP411	mRNA Processing	1.66e-11	0.000632

CD34+

gobp

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD34+	gobp	L1	GO:0001775	cell activation	0.987	1.45e-25
CD34+	gobp	L1	GO:0045321	leukocyte activation	0.013	2.95e-24
CD34+	gobp	L1	GO:0002376	immune system process	2.22e-08	6.17e-23
CD34+	gobp	L1	GO:0002443	leukocyte mediated immunity	3.37e-11	4.9e-17
CD34+	gobp	L1	GO:0006955	immune response	3.15e-11	1.06e-19
CD34+	gobp	L1	GO:0002366	leukocyte activation involved in immune response	2.18e-11	1.45e-16
CD34+	gobp	L1	GO:0002263	cell activation involved in immune response	1.72e-11	1.85e-16
CD34+	gobp	L1	GO:0046649	lymphocyte activation	6.57e-13	8.91e-16
CD34+	gobp	L1	GO:0002252	immune effector process	1.19e-13	6.98e-16
CD34+	gobp	L1	GO:0043299	leukocyte degranulation	2.36e-14	6.03e-14
CD34+	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.813	3.7e-10
CD34+	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.152	1.32e-09
CD34+	gobp	L2	GO:0045047	protein targeting to ER	0.0274	1.42e-09
CD34+	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.00688	3.3e-09
CD34+	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	2.82e-06	3.92e-07
CD34+	gobp	L2	GO:0006413	translational initiation	4.5e-07	7.18e-09
CD34+	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1.09e-07	4.64e-06
CD34+	gobp	L2	GO:0006612	protein targeting to membrane	3.21e-09	2.66e-05
CD34+	gobp	L2	GO:0043043	peptide biosynthetic process	3.01e-10	5.58e-07
CD34+	gobp	L2	GO:0006412	translation	1.89e-10	1.32e-06
CD34+	gobp	L3	GO:0006119	oxidative phosphorylation	0.999	4.68e-09
CD34+	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.000526	1.24e-06
CD34+	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.000367	1.65e-06
CD34+	gobp	L3	GO:0046034	ATP metabolic process	8.31e-05	1.07e-07
CD34+	gobp	L3	GO:0022904	respiratory electron transport chain	3.74e-05	7.22e-06
CD34+	gobp	L3	GO:0009123	nucleoside monophosphate metabolic process	8.84e-06	3.64e-07
CD34+	gobp	L3	GO:0009126	purine nucleoside monophosphate metabolic process	7.62e-06	5.07e-07
CD34+	gobp	L3	GO:0009167	purine ribonucleoside monophosphate metabolic process	7.62e-06	5.07e-07
CD34+	gobp	L3	GO:0009161	ribonucleoside monophosphate metabolic process	6.52e-06	5.61e-07
CD34+	gobp	L3	GO:0009199	ribonucleoside triphosphate metabolic process	4.25e-06	1.1e-06
CD34+	gobp	L4	GO:0044419	interspecies interaction between organisms	0.42	4.23e-10
CD34+	gobp	L4	GO:0016032	viral process	0.383	1.53e-09
CD34+	gobp	L4	GO:0044403	symbiont process	0.194	2.19e-09
CD34+	gobp	L4	GO:0070887	cellular response to chemical stimulus	0.000206	1.69e-10
CD34+	gobp	L4	GO:0051716	cellular response to stimulus	0.000151	1.47e-10
CD34+	gobp	L4	GO:0043933	protein-containing complex subunit organization	9.06e-05	7.69e-08
CD34+	gobp	L4	GO:0032984	protein-containing complex disassembly	9.02e-05	7.62e-05
CD34+	gobp	L4	GO:0010033	response to organic substance	8.85e-05	5.93e-10
CD34+	gobp	L4	GO:0019058	viral life cycle	7.06e-05	2.15e-05
CD34+	gobp	L4	GO:0002376	immune system process	6.41e-05	6.17e-23

gobp_nr

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD34+	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.607	7.68e-11
CD34+	gobp_nr	L1	GO:0036230	granulocyte activation	0.393	9.73e-11
CD34+	gobp_nr	L1	GO:0009123	nucleoside monophosphate metabolic process	2.69e-09	2.2e-06
CD34+	gobp_nr	L1	GO:0052547	regulation of peptidase activity	2.15e-09	1.67e-05
CD34+	gobp_nr	L1	GO:0006091	generation of precursor metabolites and energy	1.38e-09	2.11e-05
CD34+	gobp_nr	L1	GO:0006457	protein folding	1.34e-09	0.000381
CD34+	gobp_nr	L1	GO:0019058	viral life cycle	1.14e-09	8.8e-05
CD34+	gobp_nr	L1	GO:0006338	chromatin remodeling	1.04e-09	0.000224
CD34+	gobp_nr	L1	GO:0032984	protein-containing complex disassembly	8.69e-10	0.000321
CD34+	gobp_nr	L1	GO:0009141	nucleoside triphosphate metabolic process	7.19e-10	2.86e-05
CD34+	gobp_nr	L2	GO:0006413	translational initiation	1	3.55e-08
CD34+	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	0.000335	1.3e-06
CD34+	gobp_nr	L2	GO:0090150	establishment of protein localization to membrane	7.81e-07	0.000167
CD34+	gobp_nr	L2	GO:0006401	RNA catabolic process	4.43e-07	0.000777
CD34+	gobp_nr	L2	GO:0006338	chromatin remodeling	1.31e-07	0.000224
CD34+	gobp_nr	L2	GO:0009123	nucleoside monophosphate metabolic process	1.16e-07	2.2e-06
CD34+	gobp_nr	L2	GO:0032984	protein-containing complex disassembly	1.07e-07	0.000321
CD34+	gobp_nr	L2	GO:0006605	protein targeting	9.02e-08	0.00148
CD34+	gobp_nr	L2	GO:0010257	NADH dehydrogenase complex assembly	8.31e-08	0.000315
CD34+	gobp_nr	L2	GO:0052547	regulation of peptidase activity	7.67e-08	1.67e-05

gomf

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD34+	gomf	L1	GO:0003735	structural constituent of ribosome	1	7.46e-13
CD34+	gomf	L1	GO:0003723	RNA binding	4.17e-12	1.82e-10
CD34+	gomf	L1	GO:0005198	structural molecule activity	8.84e-15	0.000143
CD34+	gomf	L1	GO:0052744	phosphatidylinositol monophosphate phosphatase activity	6.82e-15	1
CD34+	gomf	L1	GO:0004438	phosphatidylinositol-3-phosphatase activity	3.02e-15	1
CD34+	gomf	L1	GO:0052629	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity	1.68e-15	1
CD34+	gomf	L1	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	1.63e-15	1.18e-05
CD34+	gomf	L1	GO:0008137	NADH dehydrogenase (ubiquinone) activity	1.5e-15	1.19e-05
CD34+	gomf	L1	GO:0050136	NADH dehydrogenase (quinone) activity	1.5e-15	1.19e-05
CD34+	gomf	L1	GO:0043812	phosphatidylinositol-4-phosphate phosphatase activity	7.75e-16	1
CD34+	gomf	L2	GO:0005515	protein binding	1	1.76e-14
CD34+	gomf	L2	GO:0005488	binding	3.51e-13	0.00225
CD34+	gomf	L2	GO:0003674	molecular_function	3.68e-15	1
CD34+	gomf	L2	GO:0019899	enzyme binding	1.71e-31	1.04e-07
CD34+	gomf	L2	GO:0003824	catalytic activity	1.07e-36	0.396
CD34+	gomf	L2	GO:0003723	RNA binding	8.74e-38	1.82e-10
CD34+	gomf	L2	GO:0042802	identical protein binding	1.92e-39	0.000151
CD34+	gomf	L2	GO:0044877	protein-containing complex binding	8.64e-41	9.8e-06
CD34+	gomf	L2	GO:0097159	organic cyclic compound binding	2e-41	0.691
CD34+	gomf	L2	GO:1901363	heterocyclic compound binding	6.54e-42	0.741

kegg

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD34+	kegg	L1	hsa00190	Oxidative phosphorylation	0.992	2.2e-08
CD34+	kegg	L1	hsa05012	Parkinson disease	0.00737	2.21e-08
CD34+	kegg	L1	hsa05010	Alzheimer disease	0.000525	2.65e-08
CD34+	kegg	L1	hsa05016	Huntington disease	2.36e-06	1.77e-05
CD34+	kegg	L1	hsa04714	Thermogenesis	1.19e-06	3.89e-05
CD34+	kegg	L1	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	3.52e-08	0.000674
CD34+	kegg	L1	hsa04723	Retrograde endocannabinoid signaling	5.84e-09	0.0019
CD34+	kegg	L1	hsa04260	Cardiac muscle contraction	2.17e-09	0.00794
CD34+	kegg	L1	hsa05130	Pathogenic Escherichia coli infection	1.35e-09	0.000325
CD34+	kegg	L1	hsa04640	Hematopoietic cell lineage	1.23e-09	0.000296
CD34+	kegg	L2	hsa03010	Ribosome	1	1.04e-08
CD34+	kegg	L2	hsa05130	Pathogenic Escherichia coli infection	2.31e-10	0.000325
CD34+	kegg	L2	hsa04640	Hematopoietic cell lineage	2.1e-10	0.000296
CD34+	kegg	L2	hsa04720	Long-term potentiation	2.07e-10	0.000191
CD34+	kegg	L2	hsa04512	ECM-receptor interaction	1.55e-10	0.999
CD34+	kegg	L2	hsa00780	Biotin metabolism	1.25e-10	1
CD34+	kegg	L2	hsa00430	Taurine and hypotaurine metabolism	1.07e-10	0.998
CD34+	kegg	L2	hsa00790	Folate biosynthesis	1.03e-10	0.998
CD34+	kegg	L2	hsa04670	Leukocyte transendothelial migration	9e-11	0.00105
CD34+	kegg	L2	hsa00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	7.88e-11	0.997

reactome

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD34+	reactome	L1	R-HSA-72764	Eukaryotic Translation Termination	0.993	5.58e-13
CD34+	reactome	L1	R-HSA-156902	Peptide chain elongation	0.00456	2.22e-12
CD34+	reactome	L1	R-HSA-156842	Eukaryotic Translation Elongation	0.00217	7.88e-13
CD34+	reactome	L1	R-HSA-192823	Viral mRNA Translation	0.000226	4.16e-11
CD34+	reactome	L1	R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	6.14e-05	7.39e-11
CD34+	reactome	L1	R-HSA-72689	Formation of a pool of free 40S subunits	3.19e-06	1.05e-11
CD34+	reactome	L1	R-HSA-2408557	Selenocysteine synthesis	3.56e-07	1.35e-09
CD34+	reactome	L1	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	2.58e-07	3.29e-12
CD34+	reactome	L1	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	2.46e-07	4.54e-12
CD34+	reactome	L1	R-HSA-72613	Eukaryotic Translation Initiation	4.88e-10	1.92e-10
CD34+	reactome	L2	R-HSA-6798695	Neutrophil degranulation	0.986	5.03e-11
CD34+	reactome	L2	R-HSA-168249	Innate Immune System	0.0137	5.38e-11
CD34+	reactome	L2	R-HSA-168256	Immune System	1.27e-05	1.92e-10
CD34+	reactome	L2	R-HSA-109582	Hemostasis	9.22e-10	2.48e-05
CD34+	reactome	L2	R-HSA-5357801	Programmed Cell Death	1.96e-10	0.000312
CD34+	reactome	L2	R-HSA-76002	Platelet activation, signaling and aggregation	1.46e-10	0.000304
CD34+	reactome	L2	R-HSA-109581	Apoptosis	1.33e-10	0.000516
CD34+	reactome	L2	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	1.28e-10	0.000395
CD34+	reactome	L2	R-HSA-381676	Glucagon-like Peptide-1 (GLP1) regulates insulin secretion	1.23e-10	5.15e-05
CD34+	reactome	L2	R-HSA-3781865	Diseases of glycosylation	8.98e-11	1
CD34+	reactome	L3	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	0.998	7.39e-09
CD34+	reactome	L3	R-HSA-611105	Respiratory electron transport	0.0022	6.14e-07
CD34+	reactome	L3	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	7.2e-05	5.16e-06
CD34+	reactome	L3	R-HSA-6799198	Complex I biogenesis	2.49e-07	0.000224
CD34+	reactome	L3	R-HSA-163210	Formation of ATP by chemiosmotic coupling	2.56e-09	0.00176
CD34+	reactome	L3	R-HSA-2453902	The canonical retinoid cycle in rods (twilight vision)	1.04e-09	1
CD34+	reactome	L3	R-HSA-3781865	Diseases of glycosylation	5.1e-10	1
CD34+	reactome	L3	R-HSA-381676	Glucagon-like Peptide-1 (GLP1) regulates insulin secretion	4.53e-10	5.15e-05
CD34+	reactome	L3	R-HSA-2214320	Anchoring fibril formation	4.34e-10	1
CD34+	reactome	L3	R-HSA-8949613	Cristae formation	3.57e-10	0.00784
CD34+	reactome	L4	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	1	2.12e-07
CD34+	reactome	L4	R-HSA-2453902	The canonical retinoid cycle in rods (twilight vision)	1.62e-06	1
CD34+	reactome	L4	R-HSA-3781865	Diseases of glycosylation	8.99e-07	1
CD34+	reactome	L4	R-HSA-168256	Immune System	8.13e-07	1.92e-10
CD34+	reactome	L4	R-HSA-381676	Glucagon-like Peptide-1 (GLP1) regulates insulin secretion	7.69e-07	5.15e-05
CD34+	reactome	L4	R-HSA-109582	Hemostasis	7.47e-07	2.48e-05
CD34+	reactome	L4	R-HSA-2214320	Anchoring fibril formation	4.09e-07	1
CD34+	reactome	L4	R-HSA-211935	Fatty acids	4.01e-07	1
CD34+	reactome	L4	R-HSA-8862803	Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models	3.78e-07	0.00061
CD34+	reactome	L4	R-HSA-8863678	Neurodegenerative Diseases	3.78e-07	0.00061

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD34+	wikipathway	L1	WP477	Cytoplasmic Ribosomal Proteins	1	1.06e-10
CD34+	wikipathway	L1	WP4661	Amino Acid Metabolism Pathway Excerpt (Histidine catabolism extension)	1.38e-20	1
CD34+	wikipathway	L1	WP4545	Oxysterols derived from cholesterol	2.3e-21	0.999
CD34+	wikipathway	L1	WP3945	TYROBP Causal Network	1.93e-21	0.000484
CD34+	wikipathway	L1	WP2272	Pathogenic Escherichia coli infection	1.55e-21	0.000582
CD34+	wikipathway	L1	WP400	p38 MAPK Signaling Pathway	1.12e-21	0.999
CD34+	wikipathway	L1	WP229	Irinotecan Pathway	9.81e-22	0.998
CD34+	wikipathway	L1	WP2645	Heroin metabolism	7.21e-22	1
CD34+	wikipathway	L1	WP2826	Cocaine metabolism	7.21e-22	1
CD34+	wikipathway	L1	WP43	Oxidation by Cytochrome P450	6.19e-22	0.998
CD34+	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	1	1.83e-09
CD34+	wikipathway	L2	WP623	Oxidative phosphorylation	2.91e-06	1.9e-07
CD34+	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	3.88e-12	0.00201
CD34+	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	1.21e-12	0.00896
CD34+	wikipathway	L2	WP4661	Amino Acid Metabolism Pathway Excerpt (Histidine catabolism extension)	5.8e-13	1
CD34+	wikipathway	L2	WP4545	Oxysterols derived from cholesterol	1.38e-13	0.999
CD34+	wikipathway	L2	WP2272	Pathogenic Escherichia coli infection	1.03e-13	0.000582
CD34+	wikipathway	L2	WP3945	TYROBP Causal Network	9.65e-14	0.000484
CD34+	wikipathway	L2	WP400	p38 MAPK Signaling Pathway	7.35e-14	0.999
CD34+	wikipathway	L2	WP229	Irinotecan Pathway	5.53e-14	0.998

knitr::knit_exit()