Single-cell PBMC Example

Last updated: 2022-03-30

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Introduction

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

If the resulting enrichment results look good/interpretable across multiple/concatenated gene sets
Assess sensitivity to a range of p-value thresholds
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')

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


par(mfrow=c(1,1))
deseq$`CD19+ B` %>% .$padj %>% hist(main='CD19+B p-values')

Loading required package: DESeq2

Version	Author	Date
a2bdb56	karltayeb	2022-03-29

Fitting and reporting helpers

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

  # set up binary y
  y <- data %>%
    as.data.frame %>%
    rownames_to_column('gene') %>%
    dplyr::select(gene, padj) %>%
    filter(!is.na(padj)) %>%
    mutate(y = as.integer(padj < thresh)) %>%
    select(gene, y) %>%
    tibble2namedlist %>%
    convert_labels('ENSEMBL')
  
  u <- process_input(gs$X, y)  # subset to common genes
  vb.fit <- logistic.susie(  # fit model
    u$X, u$y, L=10, init.intercept = 0, verbose=1, maxit=100)

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

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

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

  # set up binary y
  y <- data %>%
    as.data.frame %>%
    rownames_to_column('gene') %>%
    dplyr::select(gene, padj) %>%
    filter(!is.na(padj)) %>%
    mutate(y = as.integer(padj < res$thresh)) %>%
    select(gene, y) %>%
    tibble2namedlist %>%
    convert_labels('ENSEMBL')
  
  u <- process_input(gs$X, y)  # subset to common genes

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

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

  return(credible.set.summary)
}

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

Example usage

db = 'gobp'
celltype = 'CD19+ B'
thresh = 1e-4
res <- logistic_susie_driver(db, celltype, thresh)

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


converged

Joining, by = "geneSet"

credible_set_summary(res) %>% head()

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

# A tibble: 6 × 18
# Groups:   component [1]
  geneSet   component    alpha cumalpha in_cs active_cs geneListSize geneSetSize
  <chr>     <chr>        <dbl>    <dbl> <lgl> <lgl>            <int>       <dbl>
1 GO:00023… L1        1.00e+ 0     0    TRUE  TRUE              6911        2228
2 GO:00069… L1        4.25e- 5     1.00 FALSE TRUE              6911        1526
3 GO:00508… L1        2.34e-12     1.00 FALSE TRUE              6911        6070
4 GO:00022… L1        8.01e-15     1.00 FALSE TRUE              6911         973
5 GO:00026… L1        2.95e-15     1.00 FALSE TRUE              6911        1134
6 GO:00507… L1        7.00e-16     1.00 FALSE TRUE              6911         741
# … with 10 more variables: overlap <dbl>, nGenes <int>, propInList <dbl>,
#   propInSet <dbl>, oddsRatio <dbl>, pValueHypergeometric <dbl>, db <chr>,
#   celltype <chr>, thresh <dbl>, description <chr>

gene_set_summary(res) %>% head()

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

# A tibble: 6 × 14
  geneSet       pip geneListSize geneSetSize overlap nGenes propInList propInSet
  <chr>       <dbl>        <int>       <dbl>   <dbl>  <int>      <dbl>     <dbl>
1 GO:00025… 4.18e-2         6911          95      77  12078     0.0111     0.811
2 GO:00068… 3.91e-4         6911        3750    2317  12078     0.335      0.618
3 GO:00068… 5.74e-4         6911         733     523  12078     0.0757     0.714
4 GO:00081… 7.18e-5         6911       12078    6911  12078     1          0.572
5 GO:00099… 7.70e-5         6911       11191    6442  12078     0.932      0.576
6 GO:00161… 1.36e-3         6911        1610    1055  12078     0.153      0.655
# … with 6 more variables: 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)

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

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

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

Summary functions

Just a few functions to help streamline looking at output

library(kableExtra)
#' takes a tibble
#' organize by database and component
#' report credible set, descriptions, pips, and hypergeometric pvalue
#' in one row, with cs ordered by pip
db_component_kable = function(tbl){
  tbl %>%
  filter(active_set, thresh==1e-4) %>%
  group_by(db, celltype, top_component) %>%
  arrange(db, celltype, top_component, desc(pip)) %>%
  select(geneSet, description, pip, pValueHypergeometric) %>%
  chop(c(geneSet, description, pip, pValueHypergeometric)) %>%
  knitr::kable()
}

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

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

Results

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.

The tables are really long, so for each cell-type I summarize the components into “themes”

library(htmltools)

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

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

CD19+ B

gobp

Adding missing grouping variables: `celltype`, `db`, `component`
`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	component	geneSet	description	alpha	pValueHypergeometric
CD19+ B	gobp	L1	GO:0002376	immune system process	1	2.53e-269
CD19+ B	gobp	L1	GO:0006955	immune response	4.25e-05	1.15e-202
CD19+ B	gobp	L1	GO:0050896	response to stimulus	2.34e-12	0
CD19+ B	gobp	L1	GO:0002252	immune effector process	8.01e-15	9.5e-136
CD19+ B	gobp	L1	GO:0002682	regulation of immune system process	2.95e-15	9.44e-132
CD19+ B	gobp	L1	GO:0050776	regulation of immune response	7e-16	1.44e-98
CD19+ B	gobp	L1	GO:0051716	cellular response to stimulus	6.02e-16	0
CD19+ B	gobp	L1	GO:0006950	response to stress	4.51e-16	7.19e-233
CD19+ B	gobp	L1	GO:0007154	cell communication	1.39e-16	2.2399997657715e-317
CD19+ B	gobp	L1	GO:0034097	response to cytokine	1.28e-16	8.55e-99
CD19+ B	gobp	L2	GO:0045047	protein targeting to ER	0.962	2.53e-36
CD19+ B	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.0208	1.98e-34
CD19+ B	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0138	8.26e-35
CD19+ B	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.00332	9.43e-33
CD19+ B	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	2.52e-07	1.06e-33
CD19+ B	gobp	L2	GO:0006413	translational initiation	2.2e-12	1.35e-36
CD19+ B	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1.77e-14	3.49e-24
CD19+ B	gobp	L2	GO:0006612	protein targeting to membrane	4.35e-15	4.29e-29
CD19+ B	gobp	L2	GO:0043604	amide biosynthetic process	2.51e-18	9.42e-64
CD19+ B	gobp	L2	GO:0006518	peptide metabolic process	2.02e-18	4.63e-66
CD19+ B	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.624	1.61e-25
CD19+ B	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.36	4.06e-25
CD19+ B	gobp	L3	GO:0006119	oxidative phosphorylation	0.0162	2.08e-29
CD19+ B	gobp	L3	GO:0022904	respiratory electron transport chain	7.59e-05	3.6e-22
CD19+ B	gobp	L3	GO:0022900	electron transport chain	4.32e-06	6.53e-28
CD19+ B	gobp	L3	GO:0009123	nucleoside monophosphate metabolic process	6.14e-07	3.08e-41
CD19+ B	gobp	L3	GO:0046034	ATP metabolic process	1.52e-07	1.04e-34
CD19+ B	gobp	L3	GO:0009126	purine nucleoside monophosphate metabolic process	1.06e-07	7.48e-38
CD19+ B	gobp	L3	GO:0009167	purine ribonucleoside monophosphate metabolic process	1.06e-07	7.48e-38
CD19+ B	gobp	L3	GO:0009161	ribonucleoside monophosphate metabolic process	6.22e-08	4.79e-38
CD19+ B	gobp	L5	GO:0001775	cell activation	0.978	4.43e-165
CD19+ B	gobp	L5	GO:0045321	leukocyte activation	0.0217	7.69e-152
CD19+ B	gobp	L5	GO:0002366	leukocyte activation involved in immune response	0.00012	1.41e-97
CD19+ B	gobp	L5	GO:0002263	cell activation involved in immune response	0.000112	8.24e-98
CD19+ B	gobp	L5	GO:0045055	regulated exocytosis	1.89e-05	1.34e-88
CD19+ B	gobp	L5	GO:0006955	immune response	1.46e-05	1.15e-202
CD19+ B	gobp	L5	GO:0002252	immune effector process	8.26e-06	9.5e-136
CD19+ B	gobp	L5	GO:0002274	myeloid leukocyte activation	8.07e-06	1.7e-87
CD19+ B	gobp	L5	GO:0002444	myeloid leukocyte mediated immunity	3.59e-06	3.55e-79
CD19+ B	gobp	L5	GO:0042119	neutrophil activation	2.34e-06	2.04e-73
CD19+ B	gobp	L6	GO:0008380	RNA splicing	0.823	2.99e-36
CD19+ B	gobp	L6	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0492	3.39e-28
CD19+ B	gobp	L6	GO:0000398	mRNA splicing, via spliceosome	0.0492	3.39e-28
CD19+ B	gobp	L6	GO:0000375	RNA splicing, via transesterification reactions	0.0326	6.89e-28
CD19+ B	gobp	L6	GO:0006397	mRNA processing	0.0169	4.15e-35
CD19+ B	gobp	L6	GO:0050684	regulation of mRNA processing	0.00633	6.49e-18
CD19+ B	gobp	L6	GO:0043484	regulation of RNA splicing	0.00555	1.88e-17
CD19+ B	gobp	L6	GO:0000380	alternative mRNA splicing, via spliceosome	0.00085	7.77e-12
CD19+ B	gobp	L6	GO:0016071	mRNA metabolic process	0.000744	1.88e-61
CD19+ B	gobp	L6	GO:0006338	chromatin remodeling	0.00065	8.45e-20

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	4.78e-71
CD19+ B	gobp_nr	L1	GO:0036230	granulocyte activation	0.485	2.94e-71
CD19+ B	gobp_nr	L1	GO:0002576	platelet degranulation	2.06e-13	1.66e-18
CD19+ B	gobp_nr	L1	GO:0001906	cell killing	8.55e-14	2.12e-20
CD19+ B	gobp_nr	L1	GO:0034109	homotypic cell-cell adhesion	2.66e-14	3.44e-13
CD19+ B	gobp_nr	L1	GO:0006338	chromatin remodeling	2.38e-14	3.84e-19
CD19+ B	gobp_nr	L1	GO:0051647	nucleus localization	2.14e-14	8.32e-08
CD19+ B	gobp_nr	L1	GO:0034612	response to tumor necrosis factor	1.88e-14	3.93e-24
CD19+ B	gobp_nr	L1	GO:0070661	leukocyte proliferation	1.81e-14	5.37e-36
CD19+ B	gobp_nr	L1	GO:0002250	adaptive immune response	1.77e-14	4.83e-44
CD19+ B	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	1	7.38e-33
CD19+ B	gobp_nr	L2	GO:0006413	translational initiation	4.2e-05	1.46e-35
CD19+ B	gobp_nr	L2	GO:0090150	establishment of protein localization to membrane	4.14e-11	2.77e-32
CD19+ B	gobp_nr	L2	GO:0006605	protein targeting	5.31e-12	1.7e-36
CD19+ B	gobp_nr	L2	GO:0002181	cytoplasmic translation	2.5e-12	3.18e-14
CD19+ B	gobp_nr	L2	GO:0006401	RNA catabolic process	1.44e-12	4.75e-29
CD19+ B	gobp_nr	L2	GO:0051647	nucleus localization	3.76e-13	8.32e-08
CD19+ B	gobp_nr	L2	GO:0002576	platelet degranulation	2.86e-13	1.66e-18
CD19+ B	gobp_nr	L2	GO:0072348	sulfur compound transport	2.13e-13	0.869
CD19+ B	gobp_nr	L2	GO:0006338	chromatin remodeling	1.69e-13	3.84e-19
CD19+ B	gobp_nr	L4	GO:0009123	nucleoside monophosphate metabolic process	0.984	7.37e-40
CD19+ B	gobp_nr	L4	GO:0009141	nucleoside triphosphate metabolic process	0.0154	2.01e-35
CD19+ B	gobp_nr	L4	GO:0006091	generation of precursor metabolites and energy	8.63e-05	7.23e-39
CD19+ B	gobp_nr	L4	GO:0009259	ribonucleotide metabolic process	1.7e-05	4.05e-37
CD19+ B	gobp_nr	L4	GO:0002576	platelet degranulation	3.54e-06	1.66e-18
CD19+ B	gobp_nr	L4	GO:0010257	NADH dehydrogenase complex assembly	3.51e-06	2.29e-11
CD19+ B	gobp_nr	L4	GO:0033108	mitochondrial respiratory chain complex assembly	2.51e-06	3.9e-13
CD19+ B	gobp_nr	L4	GO:0006338	chromatin remodeling	1.93e-06	3.84e-19
CD19+ B	gobp_nr	L4	GO:0051647	nucleus localization	1.19e-06	8.32e-08
CD19+ B	gobp_nr	L4	GO:0008380	RNA splicing	1.09e-06	9.42e-35
CD19+ B	gobp_nr	L5	GO:0002764	immune response-regulating signaling pathway	0.996	8.09e-55
CD19+ B	gobp_nr	L5	GO:0002250	adaptive immune response	0.00109	4.83e-44
CD19+ B	gobp_nr	L5	GO:0070661	leukocyte proliferation	0.00031	5.37e-36
CD19+ B	gobp_nr	L5	GO:0002694	regulation of leukocyte activation	0.000186	4.27e-53
CD19+ B	gobp_nr	L5	GO:0045088	regulation of innate immune response	0.000112	2.14e-33
CD19+ B	gobp_nr	L5	GO:0042113	B cell activation	0.000102	1.31e-32
CD19+ B	gobp_nr	L5	GO:0050867	positive regulation of cell activation	8.82e-05	6.76e-38
CD19+ B	gobp_nr	L5	GO:0009615	response to virus	8.7e-05	2.4e-28
CD19+ B	gobp_nr	L5	GO:0002576	platelet degranulation	8.44e-05	1.66e-18
CD19+ B	gobp_nr	L5	GO:0034612	response to tumor necrosis factor	7.43e-05	3.93e-24

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	3.71e-127
CD19+ B	gomf	L1	GO:0005515	protein binding	0.000249	0
CD19+ B	gomf	L1	GO:0044877	protein-containing complex binding	9.71e-07	9.7e-70
CD19+ B	gomf	L1	GO:0042802	identical protein binding	8.91e-07	4.01e-91
CD19+ B	gomf	L1	GO:0046983	protein dimerization activity	3.56e-07	1.07e-65
CD19+ B	gomf	L1	GO:0019899	enzyme binding	2.08e-07	2.79e-122
CD19+ B	gomf	L1	GO:0042803	protein homodimerization activity	1.51e-07	1.04e-48
CD19+ B	gomf	L1	GO:0003682	chromatin binding	1.09e-07	3.34e-34
CD19+ B	gomf	L1	GO:0019904	protein domain specific binding	4.16e-08	9.31e-44
CD19+ B	gomf	L1	GO:0009055	electron transfer activity	3.72e-08	5.05e-16
CD19+ B	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.995	1.94e-16
CD19+ B	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.005	2.74e-20
CD19+ B	gomf	L2	GO:0140110	transcription regulator activity	5.42e-08	5.42e-34
CD19+ B	gomf	L2	GO:0003677	DNA binding	2.18e-10	9.7e-50
CD19+ B	gomf	L2	GO:0003676	nucleic acid binding	5.53e-15	1.45e-148
CD19+ B	gomf	L2	GO:1901363	heterocyclic compound binding	5.96e-17	3.22e-226
CD19+ B	gomf	L2	GO:0097159	organic cyclic compound binding	2.02e-17	4e-231
CD19+ B	gomf	L2	GO:0046872	metal ion binding	1.27e-19	1.55e-94
CD19+ B	gomf	L2	GO:0000976	transcription regulatory region sequence-specific DNA binding	1.24e-19	5.23e-34
CD19+ B	gomf	L2	GO:0044212	transcription regulatory region DNA binding	9.57e-20	5.77e-36
CD19+ B	gomf	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.487	2.82e-34
CD19+ B	gomf	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	0.431	2.66e-34
CD19+ B	gomf	L3	GO:0000987	proximal promoter sequence-specific DNA binding	0.0364	8.33e-30
CD19+ B	gomf	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	0.0242	2.66e-29
CD19+ B	gomf	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	0.0131	5.23e-34
CD19+ B	gomf	L3	GO:0003690	double-stranded DNA binding	0.00581	8.31e-44
CD19+ B	gomf	L3	GO:1990837	sequence-specific double-stranded DNA binding	0.00128	1.07e-35
CD19+ B	gomf	L3	GO:0001067	regulatory region nucleic acid binding	0.000374	1.99e-36
CD19+ B	gomf	L3	GO:0044212	transcription regulatory region DNA binding	0.000265	5.77e-36
CD19+ B	gomf	L3	GO:0043565	sequence-specific DNA binding	2.39e-05	2.54e-38
CD19+ B	gomf	L6	GO:0003735	structural constituent of ribosome	0.995	2.99e-32
CD19+ B	gomf	L6	GO:0003823	antigen binding	0.000162	1.69e-12
CD19+ B	gomf	L6	GO:0016860	intramolecular oxidoreductase activity	0.000138	1.22e-11
CD19+ B	gomf	L6	GO:0005070	SH3/SH2 adaptor activity	9.78e-05	2.28e-12
CD19+ B	gomf	L6	GO:0042287	MHC protein binding	4.95e-05	9.76e-09
CD19+ B	gomf	L6	GO:0009055	electron transfer activity	4.49e-05	5.05e-16
CD19+ B	gomf	L6	GO:0005515	protein binding	4.4e-05	0
CD19+ B	gomf	L6	GO:0030276	clathrin binding	3.62e-05	1.18e-09
CD19+ B	gomf	L6	GO:0004842	ubiquitin-protein transferase activity	3.19e-05	1.3e-05
CD19+ B	gomf	L6	GO:0061659	ubiquitin-like protein ligase activity	3e-05	0.0152
CD19+ B	gomf	L7	GO:0003954	NADH dehydrogenase activity	0.326	1.39e-13
CD19+ B	gomf	L7	GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.218	3.41e-13
CD19+ B	gomf	L7	GO:0050136	NADH dehydrogenase (quinone) activity	0.218	3.41e-13
CD19+ B	gomf	L7	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	0.177	1.32e-14
CD19+ B	gomf	L7	GO:0016651	oxidoreductase activity, acting on NAD(P)H	0.0382	2.2e-17
CD19+ B	gomf	L7	GO:0009055	electron transfer activity	0.00115	5.05e-16
CD19+ B	gomf	L7	GO:0003823	antigen binding	0.000759	1.69e-12
CD19+ B	gomf	L7	GO:0016491	oxidoreductase activity	0.000748	1.41e-45
CD19+ B	gomf	L7	GO:0016860	intramolecular oxidoreductase activity	0.000667	1.22e-11
CD19+ B	gomf	L7	GO:0005070	SH3/SH2 adaptor activity	0.000431	2.28e-12

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	5.03e-29
CD19+ B	kegg	L1	hsa05012	Parkinson disease	0.002	3.7e-27
CD19+ B	kegg	L1	hsa05010	Alzheimer disease	1.62e-05	9.68e-28
CD19+ B	kegg	L1	hsa05016	Huntington disease	3.95e-07	1.19e-24
CD19+ B	kegg	L1	hsa04714	Thermogenesis	4.8e-08	9e-25
CD19+ B	kegg	L1	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	6.5e-09	5.27e-19
CD19+ B	kegg	L1	hsa04260	Cardiac muscle contraction	1.33e-09	7.49e-10
CD19+ B	kegg	L1	hsa00770	Pantothenate and CoA biosynthesis	1.13e-09	0.941
CD19+ B	kegg	L1	hsa04512	ECM-receptor interaction	9.86e-10	0.295
CD19+ B	kegg	L1	hsa01200	Carbon metabolism	8.65e-10	3.34e-16
CD19+ B	kegg	L2	hsa04640	Hematopoietic cell lineage	1	8.55e-21
CD19+ B	kegg	L2	hsa05332	Graft-versus-host disease	5.56e-05	4.22e-13
CD19+ B	kegg	L2	hsa04659	Th17 cell differentiation	1.8e-05	1.16e-18
CD19+ B	kegg	L2	hsa05330	Allograft rejection	1.73e-05	1.73e-11
CD19+ B	kegg	L2	hsa04940	Type I diabetes mellitus	1.69e-05	1.14e-11
CD19+ B	kegg	L2	hsa04658	Th1 and Th2 cell differentiation	1.06e-05	1.86e-16
CD19+ B	kegg	L2	hsa04612	Antigen processing and presentation	1.05e-05	2.11e-14
CD19+ B	kegg	L2	hsa05169	Epstein-Barr virus infection	7.29e-06	1.83e-25
CD19+ B	kegg	L2	hsa05340	Primary immunodeficiency	6e-06	1.13e-09
CD19+ B	kegg	L2	hsa05320	Autoimmune thyroid disease	5.57e-06	4.12e-10
CD19+ B	kegg	L3	hsa03010	Ribosome	1	3.25e-30
CD19+ B	kegg	L3	hsa00770	Pantothenate and CoA biosynthesis	8.95e-10	0.941
CD19+ B	kegg	L3	hsa04512	ECM-receptor interaction	7.99e-10	0.295
CD19+ B	kegg	L3	hsa03022	Basal transcription factors	5.84e-10	0.722
CD19+ B	kegg	L3	hsa00330	Arginine and proline metabolism	5.81e-10	2.21e-09
CD19+ B	kegg	L3	hsa00900	Terpenoid backbone biosynthesis	4.47e-10	0.845
CD19+ B	kegg	L3	hsa00062	Fatty acid elongation	4.24e-10	1.89e-07
CD19+ B	kegg	L3	hsa05202	Transcriptional misregulation in cancer	4.09e-10	2.41e-21
CD19+ B	kegg	L3	hsa03050	Proteasome	3.89e-10	1.38e-09
CD19+ B	kegg	L3	hsa01200	Carbon metabolism	3.7e-10	3.34e-16

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	7.93e-180
CD19+ B	reactome	L1	R-HSA-168249	Innate Immune System	9.79e-22	4.95e-110
CD19+ B	reactome	L1	R-HSA-1280218	Adaptive Immune System	2.36e-22	1.32e-59
CD19+ B	reactome	L1	R-HSA-6798695	Neutrophil degranulation	1.89e-29	1.03e-66
CD19+ B	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	8.78e-32	2.62e-67
CD19+ B	reactome	L1	R-HSA-449147	Signaling by Interleukins	6.96e-37	3.43e-47
CD19+ B	reactome	L1	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	6.1e-37	3.33e-27
CD19+ B	reactome	L1	R-HSA-983169	Class I MHC mediated antigen processing & presentation	1.43e-37	4.42e-14
CD19+ B	reactome	L1	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	6.01e-39	6.66e-09
CD19+ B	reactome	L1	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	8.15e-40	1.82e-19
CD19+ B	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	0.761	7.99e-32
CD19+ B	reactome	L2	R-HSA-156902	Peptide chain elongation	0.124	1.39e-30
CD19+ B	reactome	L2	R-HSA-192823	Viral mRNA Translation	0.0668	1.39e-30
CD19+ B	reactome	L2	R-HSA-2408557	Selenocysteine synthesis	0.0256	9.15e-31
CD19+ B	reactome	L2	R-HSA-72764	Eukaryotic Translation Termination	0.0169	9.15e-31
CD19+ B	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	0.00282	2.88e-31
CD19+ B	reactome	L2	R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	0.0023	2.25e-34
CD19+ B	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	0.000534	4.39e-33
CD19+ B	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	0.000372	1.1e-32
CD19+ B	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	7.31e-05	4.84e-31
CD19+ B	reactome	L3	R-HSA-74160	Gene expression (Transcription)	0.886	8.3e-30
CD19+ B	reactome	L3	R-HSA-212436	Generic Transcription Pathway	0.0726	2.3e-21
CD19+ B	reactome	L3	R-HSA-73857	RNA Polymerase II Transcription	0.0417	4.5e-27
CD19+ B	reactome	L3	R-HSA-211000	Gene Silencing by RNA	7.75e-06	0.277
CD19+ B	reactome	L3	R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript	2.77e-07	0.415
CD19+ B	reactome	L3	R-HSA-159234	Transport of Mature mRNAs Derived from Intronless Transcripts	1.86e-07	0.34
CD19+ B	reactome	L3	R-HSA-5578749	Transcriptional regulation by small RNAs	1.51e-07	0.0743
CD19+ B	reactome	L3	R-HSA-72766	Translation	1.5e-07	1.05e-46
CD19+ B	reactome	L3	R-HSA-6807505	RNA polymerase II transcribes snRNA genes	1.04e-07	0.208
CD19+ B	reactome	L3	R-HSA-159227	Transport of the SLBP independent Mature mRNA	9.38e-08	0.463
CD19+ B	reactome	L4	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	0.845	9.26e-26
CD19+ B	reactome	L4	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	0.149	5.56e-29
CD19+ B	reactome	L4	R-HSA-611105	Respiratory electron transport	0.00565	1.02e-20
CD19+ B	reactome	L4	R-HSA-6799198	Complex I biogenesis	4.24e-08	9.82e-11
CD19+ B	reactome	L4	R-HSA-8949613	Cristae formation	3.73e-08	1.08e-09
CD19+ B	reactome	L4	R-HSA-163210	Formation of ATP by chemiosmotic coupling	1.26e-08	5.78e-07
CD19+ B	reactome	L4	R-HSA-1430728	Metabolism	6.68e-09	1.35e-133
CD19+ B	reactome	L4	R-HSA-3700989	Transcriptional Regulation by TP53	6.43e-09	9.38e-20
CD19+ B	reactome	L4	R-HSA-199220	Vitamin B5 (pantothenate) metabolism	4.79e-09	0.979
CD19+ B	reactome	L4	R-HSA-983189	Kinesins	4.28e-09	0.251
CD19+ B	reactome	L5	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	0.997	6.66e-09
CD19+ B	reactome	L5	R-HSA-983169	Class I MHC mediated antigen processing & presentation	0.00295	4.42e-14
CD19+ B	reactome	L5	R-HSA-8951664	Neddylation	3.74e-11	1.11e-09
CD19+ B	reactome	L5	R-HSA-1280218	Adaptive Immune System	1.52e-13	1.32e-59
CD19+ B	reactome	L5	R-HSA-5619115	Disorders of transmembrane transporters	9.64e-14	4.41e-06
CD19+ B	reactome	L5	R-HSA-4608870	Asymmetric localization of PCP proteins	2.67e-14	2.61e-08
CD19+ B	reactome	L5	R-HSA-5358346	Hedgehog ligand biogenesis	2.13e-14	1.31e-08
CD19+ B	reactome	L5	R-HSA-597592	Post-translational protein modification	1.77e-14	1.43e-43
CD19+ B	reactome	L5	R-HSA-4641258	Degradation of DVL	1.33e-14	1.32e-09
CD19+ B	reactome	L5	R-HSA-4641257	Degradation of AXIN	1.26e-14	2.79e-09
CD19+ B	reactome	L6	R-HSA-180585	Vif-mediated degradation of APOBEC3G	0.749	2.43e-13
CD19+ B	reactome	L6	R-HSA-1234176	Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha	0.0314	1.74e-13
CD19+ B	reactome	L6	R-HSA-211733	Regulation of activated PAK-2p34 by proteasome mediated degradation	0.0252	7.19e-12
CD19+ B	reactome	L6	R-HSA-69601	Ubiquitin Mediated Degradation of Phosphorylated Cdc25A	0.0239	5.42e-12
CD19+ B	reactome	L6	R-HSA-69610	p53-Independent DNA Damage Response	0.0239	5.42e-12
CD19+ B	reactome	L6	R-HSA-69613	p53-Independent G1/S DNA damage checkpoint	0.0239	5.42e-12
CD19+ B	reactome	L6	R-HSA-69541	Stabilization of p53	0.0221	1.74e-12
CD19+ B	reactome	L6	R-HSA-69229	Ubiquitin-dependent degradation of Cyclin D1	0.0116	1.24e-11
CD19+ B	reactome	L6	R-HSA-75815	Ubiquitin-dependent degradation of Cyclin D	0.0116	1.24e-11
CD19+ B	reactome	L6	R-HSA-180534	Vpu mediated degradation of CD4	0.0116	1.24e-11
CD19+ B	reactome	L7	R-HSA-72163	mRNA Splicing - Major Pathway	0.546	1.51e-22
CD19+ B	reactome	L7	R-HSA-72172	mRNA Splicing	0.444	6.08e-23
CD19+ B	reactome	L7	R-HSA-109688	Cleavage of Growing Transcript in the Termination Region	0.00106	1.75e-08
CD19+ B	reactome	L7	R-HSA-73856	RNA Polymerase II Transcription Termination	0.00106	1.75e-08
CD19+ B	reactome	L7	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	0.000369	5.75e-20
CD19+ B	reactome	L7	R-HSA-72187	mRNA 3’-end processing	0.000246	3.86e-07
CD19+ B	reactome	L7	R-HSA-983189	Kinesins	0.000154	0.251
CD19+ B	reactome	L7	R-HSA-72766	Translation	0.000116	1.05e-46
CD19+ B	reactome	L7	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.000108	3.33e-27
CD19+ B	reactome	L7	R-HSA-199220	Vitamin B5 (pantothenate) metabolism	0.000107	0.979
CD19+ B	reactome	L8	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	0.706	1.61e-20
CD19+ B	reactome	L8	R-HSA-114608	Platelet degranulation	0.231	3.96e-19
CD19+ B	reactome	L8	R-HSA-76002	Platelet activation, signaling and aggregation	0.0249	1.77e-29
CD19+ B	reactome	L8	R-HSA-199220	Vitamin B5 (pantothenate) metabolism	0.000717	0.979
CD19+ B	reactome	L8	R-HSA-8862803	Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models	0.000709	3.44e-08
CD19+ B	reactome	L8	R-HSA-8863678	Neurodegenerative Diseases	0.000709	3.44e-08
CD19+ B	reactome	L8	R-HSA-983189	Kinesins	0.000665	0.251
CD19+ B	reactome	L8	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.000475	3.33e-27
CD19+ B	reactome	L8	R-HSA-72766	Translation	0.000472	1.05e-46
CD19+ B	reactome	L8	R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript	0.000452	0.415

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	2.26e-11
CD19+ B	wikipathway_cancer	L1	WP4585	Cancer immunotherapy by PD-1 blockade	1.94e-05	2.48e-07
CD19+ B	wikipathway_cancer	L1	WP254	Apoptosis	1.49e-05	1.7e-15
CD19+ B	wikipathway_cancer	L1	WP3617	Photodynamic therapy-induced NF-kB survival signaling	7.98e-06	2.04e-07
CD19+ B	wikipathway_cancer	L1	WP4284	Ultraconserved region 339 modulation of tumor suppressor microRNAs in cancer	7.93e-06	1
CD19+ B	wikipathway_cancer	L1	WP4204	Tumor suppressor activity of SMARCB1	6.9e-06	4.57e-07
CD19+ B	wikipathway_cancer	L1	WP585	Interferon type I signaling pathways	5.45e-06	5.84e-09
CD19+ B	wikipathway_cancer	L1	WP704	Methylation Pathways	5.38e-06	0.00357
CD19+ B	wikipathway_cancer	L1	WP2868	TCA Cycle Nutrient Utilization and Invasiveness of Ovarian Cancer	5.24e-06	0.0234
CD19+ B	wikipathway_cancer	L1	WP364	IL-6 signaling pathway	4.33e-06	7.41e-07

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	1.25e-28
CD19+ B	wikipathway	L1	WP619	Type II interferon signaling (IFNG)	4.55e-15	2.43e-11
CD19+ B	wikipathway	L1	WP4150	Wnt Signaling in Kidney Disease	4.55e-15	0.951
CD19+ B	wikipathway	L1	WP3945	TYROBP Causal Network	3.5e-15	2.45e-14
CD19+ B	wikipathway	L1	WP3995	Prion disease pathway	3.46e-15	9.73e-11
CD19+ B	wikipathway	L1	WP183	Proteasome Degradation	2.71e-15	2.45e-14
CD19+ B	wikipathway	L1	WP3613	Photodynamic therapy-induced unfolded protein response	1.94e-15	1.88e-08
CD19+ B	wikipathway	L1	WP254	Apoptosis	1.55e-15	2.83e-15
CD19+ B	wikipathway	L1	WP411	mRNA Processing	1.48e-15	3.38e-19
CD19+ B	wikipathway	L1	WP311	Synthesis and Degradation of Ketone Bodies	1.4e-15	1
CD19+ B	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	1	4.73e-27
CD19+ B	wikipathway	L2	WP623	Oxidative phosphorylation	8.14e-05	1.25e-17
CD19+ B	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	1.42e-08	8.84e-20
CD19+ B	wikipathway	L2	WP619	Type II interferon signaling (IFNG)	1.75e-09	2.43e-11
CD19+ B	wikipathway	L2	WP4150	Wnt Signaling in Kidney Disease	1.71e-09	0.951
CD19+ B	wikipathway	L2	WP3995	Prion disease pathway	1.35e-09	9.73e-11
CD19+ B	wikipathway	L2	WP183	Proteasome Degradation	1.12e-09	2.45e-14
CD19+ B	wikipathway	L2	WP3945	TYROBP Causal Network	1.09e-09	2.45e-14
CD19+ B	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	9.74e-10	1.62e-09
CD19+ B	wikipathway	L2	WP3613	Photodynamic therapy-induced unfolded protein response	7.54e-10	1.88e-08

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	2.95e-276
CD56+ NK	gobp	L1	GO:0006955	immune response	1.58e-06	5.77e-208
CD56+ NK	gobp	L1	GO:0001775	cell activation	2.16e-11	2.96e-167
CD56+ NK	gobp	L1	GO:0045321	leukocyte activation	3.07e-12	1.29e-156
CD56+ NK	gobp	L1	GO:0002252	immune effector process	5.34e-17	3.42e-142
CD56+ NK	gobp	L1	GO:0002682	regulation of immune system process	2.27e-21	2.93e-138
CD56+ NK	gobp	L1	GO:0050896	response to stimulus	9.83e-24	0
CD56+ NK	gobp	L1	GO:0050776	regulation of immune response	1.11e-25	1.72e-101
CD56+ NK	gobp	L1	GO:0002443	leukocyte mediated immunity	1.1e-25	1.43e-100
CD56+ NK	gobp	L1	GO:0002366	leukocyte activation involved in immune response	1.1e-25	2.94e-97
CD56+ NK	gobp	L2	GO:0045047	protein targeting to ER	0.683	9.5e-34
CD56+ NK	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.209	1.28e-33
CD56+ NK	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.0706	1.09e-31
CD56+ NK	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.0375	6.69e-32
CD56+ NK	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	2.93e-06	2.39e-31
CD56+ NK	gobp	L2	GO:0006413	translational initiation	7.85e-09	1.09e-37
CD56+ NK	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	6.52e-10	6.67e-26
CD56+ NK	gobp	L2	GO:0006612	protein targeting to membrane	3.91e-11	4.75e-30
CD56+ NK	gobp	L2	GO:0090150	establishment of protein localization to membrane	4.07e-12	2.77e-40
CD56+ NK	gobp	L2	GO:0006518	peptide metabolic process	2.22e-13	5.37e-76
CD56+ NK	gobp	L4	GO:0006119	oxidative phosphorylation	0.982	2.92e-26
CD56+ NK	gobp	L4	GO:0009123	nucleoside monophosphate metabolic process	0.00536	3.2e-41
CD56+ NK	gobp	L4	GO:0042773	ATP synthesis coupled electron transport	0.00439	3.83e-19
CD56+ NK	gobp	L4	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.00291	8.79e-19
CD56+ NK	gobp	L4	GO:0009161	ribonucleoside monophosphate metabolic process	0.00187	6.51e-39
CD56+ NK	gobp	L4	GO:0009126	purine nucleoside monophosphate metabolic process	0.000901	2.43e-37
CD56+ NK	gobp	L4	GO:0009167	purine ribonucleoside monophosphate metabolic process	0.000901	2.43e-37
CD56+ NK	gobp	L4	GO:0022904	respiratory electron transport chain	0.000875	1.99e-19
CD56+ NK	gobp	L4	GO:0022900	electron transport chain	0.000494	8.54e-26
CD56+ NK	gobp	L4	GO:0046034	ATP metabolic process	0.000357	5.93e-33
CD56+ NK	gobp	L5	GO:0008380	RNA splicing	0.591	1.14e-39
CD56+ NK	gobp	L5	GO:0006397	mRNA processing	0.222	2.28e-42
CD56+ NK	gobp	L5	GO:0000375	RNA splicing, via transesterification reactions	0.0579	9.01e-32
CD56+ NK	gobp	L5	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.054	1.55e-31
CD56+ NK	gobp	L5	GO:0000398	mRNA splicing, via spliceosome	0.054	1.55e-31
CD56+ NK	gobp	L5	GO:0016071	mRNA metabolic process	0.0141	3.47e-72
CD56+ NK	gobp	L5	GO:0097237	cellular response to toxic substance	0.000244	1.02e-31
CD56+ NK	gobp	L5	GO:0006333	chromatin assembly or disassembly	0.00021	2.36e-18
CD56+ NK	gobp	L5	GO:0006338	chromatin remodeling	0.000209	1.72e-19
CD56+ NK	gobp	L5	GO:0006518	peptide metabolic process	0.000182	5.37e-76

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	8.81e-72
CD56+ NK	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.335	8.54e-71
CD56+ NK	gobp_nr	L1	GO:0002764	immune response-regulating signaling pathway	2.1e-12	1.99e-58
CD56+ NK	gobp_nr	L1	GO:0002576	platelet degranulation	1.76e-12	1.71e-19
CD56+ NK	gobp_nr	L1	GO:0009615	response to virus	5.06e-13	1.72e-37
CD56+ NK	gobp_nr	L1	GO:0006909	phagocytosis	3.63e-13	1.64e-28
CD56+ NK	gobp_nr	L1	GO:0019882	antigen processing and presentation	3.59e-13	1.21e-21
CD56+ NK	gobp_nr	L1	GO:0052547	regulation of peptidase activity	3.36e-13	8.65e-35
CD56+ NK	gobp_nr	L1	GO:0046677	response to antibiotic	2.61e-13	4.55e-32
CD56+ NK	gobp_nr	L1	GO:0050953	sensory perception of light stimulus	2.6e-13	0.417
CD56+ NK	gobp_nr	L2	GO:0006413	translational initiation	0.995	9.23e-37
CD56+ NK	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	0.00452	1.25e-30
CD56+ NK	gobp_nr	L2	GO:0090150	establishment of protein localization to membrane	1.69e-06	4.51e-39
CD56+ NK	gobp_nr	L2	GO:0006401	RNA catabolic process	1.66e-08	1.81e-35
CD56+ NK	gobp_nr	L2	GO:0006605	protein targeting	9.57e-09	1.52e-39
CD56+ NK	gobp_nr	L2	GO:0002181	cytoplasmic translation	7.05e-09	2.41e-14
CD56+ NK	gobp_nr	L2	GO:0009615	response to virus	2.02e-09	1.72e-37
CD56+ NK	gobp_nr	L2	GO:0002576	platelet degranulation	1.88e-09	1.71e-19
CD56+ NK	gobp_nr	L2	GO:0050953	sensory perception of light stimulus	1.41e-09	0.417
CD56+ NK	gobp_nr	L2	GO:0001578	microtubule bundle formation	1.29e-09	0.621
CD56+ NK	gobp_nr	L3	GO:0042110	T cell activation	0.986	3.06e-58
CD56+ NK	gobp_nr	L3	GO:0007159	leukocyte cell-cell adhesion	0.00655	4.2e-42
CD56+ NK	gobp_nr	L3	GO:0002764	immune response-regulating signaling pathway	0.00509	1.99e-58
CD56+ NK	gobp_nr	L3	GO:0002250	adaptive immune response	0.000849	5.42e-47
CD56+ NK	gobp_nr	L3	GO:0002521	leukocyte differentiation	0.000279	1.39e-54
CD56+ NK	gobp_nr	L3	GO:0009615	response to virus	0.000212	1.72e-37
CD56+ NK	gobp_nr	L3	GO:0022407	regulation of cell-cell adhesion	8.42e-05	2.73e-38
CD56+ NK	gobp_nr	L3	GO:0002576	platelet degranulation	6.71e-05	1.71e-19
CD56+ NK	gobp_nr	L3	GO:1903706	regulation of hemopoiesis	5e-05	1.65e-39
CD56+ NK	gobp_nr	L3	GO:0052547	regulation of peptidase activity	4.82e-05	8.65e-35
CD56+ NK	gobp_nr	L4	GO:0009123	nucleoside monophosphate metabolic process	0.982	5.28e-40
CD56+ NK	gobp_nr	L4	GO:0009141	nucleoside triphosphate metabolic process	0.0147	6.18e-35
CD56+ NK	gobp_nr	L4	GO:0033108	mitochondrial respiratory chain complex assembly	0.00158	9.5e-18
CD56+ NK	gobp_nr	L4	GO:0009259	ribonucleotide metabolic process	0.000451	6.21e-41
CD56+ NK	gobp_nr	L4	GO:0006091	generation of precursor metabolites and energy	0.000313	5.06e-40
CD56+ NK	gobp_nr	L4	GO:0010257	NADH dehydrogenase complex assembly	0.000241	2.31e-13
CD56+ NK	gobp_nr	L4	GO:0002576	platelet degranulation	7.6e-05	1.71e-19
CD56+ NK	gobp_nr	L4	GO:0050953	sensory perception of light stimulus	4.31e-05	0.417
CD56+ NK	gobp_nr	L4	GO:0009615	response to virus	3.8e-05	1.72e-37
CD56+ NK	gobp_nr	L4	GO:0001578	microtubule bundle formation	3.56e-05	0.621
CD56+ NK	gobp_nr	L5	GO:0042113	B cell activation	0.997	9.38e-38
CD56+ NK	gobp_nr	L5	GO:0002764	immune response-regulating signaling pathway	0.00108	1.99e-58
CD56+ NK	gobp_nr	L5	GO:0002250	adaptive immune response	0.000133	5.42e-47
CD56+ NK	gobp_nr	L5	GO:0002576	platelet degranulation	9.28e-05	1.71e-19
CD56+ NK	gobp_nr	L5	GO:0009615	response to virus	9.01e-05	1.72e-37
CD56+ NK	gobp_nr	L5	GO:0050953	sensory perception of light stimulus	6.15e-05	0.417
CD56+ NK	gobp_nr	L5	GO:0001578	microtubule bundle formation	5.35e-05	0.621
CD56+ NK	gobp_nr	L5	GO:0046677	response to antibiotic	4.37e-05	4.55e-32
CD56+ NK	gobp_nr	L5	GO:0052547	regulation of peptidase activity	3.7e-05	8.65e-35
CD56+ NK	gobp_nr	L5	GO:0006338	chromatin remodeling	3.63e-05	6.5e-19

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	1.18e-44
CD56+ NK	gomf	L1	GO:0003723	RNA binding	7.05e-16	5.07e-130
CD56+ NK	gomf	L1	GO:0005198	structural molecule activity	1.56e-16	4.76e-54
CD56+ NK	gomf	L1	GO:0008821	crossover junction endodeoxyribonuclease activity	4.67e-19	1
CD56+ NK	gomf	L1	GO:0016209	antioxidant activity	3.18e-19	7.04e-16
CD56+ NK	gomf	L1	GO:0005515	protein binding	3.11e-19	0
CD56+ NK	gomf	L1	GO:1901682	sulfur compound transmembrane transporter activity	3.05e-19	0.975
CD56+ NK	gomf	L1	GO:0045296	cadherin binding	2.89e-19	5e-32
CD56+ NK	gomf	L1	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	2.69e-19	4.52e-15
CD56+ NK	gomf	L1	GO:0042287	MHC protein binding	2.64e-19	8.95e-10
CD56+ NK	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.997	3.24e-18
CD56+ NK	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.00323	3.41e-22
CD56+ NK	gomf	L2	GO:0140110	transcription regulator activity	9.43e-11	4.86e-39
CD56+ NK	gomf	L2	GO:0003677	DNA binding	3.37e-13	2.85e-56
CD56+ NK	gomf	L2	GO:0046872	metal ion binding	6.11e-23	1.22e-106
CD56+ NK	gomf	L2	GO:0044212	transcription regulatory region DNA binding	1.41e-23	4.44e-38
CD56+ NK	gomf	L2	GO:0001067	regulatory region nucleic acid binding	8.31e-24	1.53e-38
CD56+ NK	gomf	L2	GO:0043169	cation binding	4.61e-24	9.32e-113
CD56+ NK	gomf	L2	GO:0001012	RNA polymerase II regulatory region DNA binding	2.84e-24	2.22e-36
CD56+ NK	gomf	L2	GO:0003676	nucleic acid binding	2.2e-24	4.06e-159
CD56+ NK	gomf	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.525	6.62e-37
CD56+ NK	gomf	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	0.282	8.88e-39
CD56+ NK	gomf	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	0.176	2.22e-36
CD56+ NK	gomf	L3	GO:1990837	sequence-specific double-stranded DNA binding	0.0109	3.66e-40
CD56+ NK	gomf	L3	GO:0003690	double-stranded DNA binding	0.00648	6.12e-47
CD56+ NK	gomf	L3	GO:0043565	sequence-specific DNA binding	0.000385	6.95e-44
CD56+ NK	gomf	L3	GO:0000987	proximal promoter sequence-specific DNA binding	8.45e-05	1.16e-28
CD56+ NK	gomf	L3	GO:0001067	regulatory region nucleic acid binding	7.25e-05	1.53e-38
CD56+ NK	gomf	L3	GO:0044212	transcription regulatory region DNA binding	4.82e-05	4.44e-38
CD56+ NK	gomf	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	2.66e-05	1.07e-27

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	9.22e-36
CD56+ NK	kegg	L1	hsa04512	ECM-receptor interaction	1.69e-14	0.345
CD56+ NK	kegg	L1	hsa00730	Thiamine metabolism	1.43e-14	0.938
CD56+ NK	kegg	L1	hsa03460	Fanconi anemia pathway	9.91e-15	0.477
CD56+ NK	kegg	L1	hsa00630	Glyoxylate and dicarboxylate metabolism	9.53e-15	5.85e-08
CD56+ NK	kegg	L1	hsa04650	Natural killer cell mediated cytotoxicity	9.11e-15	5.53e-21
CD56+ NK	kegg	L1	hsa00052	Galactose metabolism	8.8e-15	5.85e-08
CD56+ NK	kegg	L1	hsa05033	Nicotine addiction	7.06e-15	1
CD56+ NK	kegg	L1	hsa00533	Glycosaminoglycan biosynthesis	5.27e-15	3.61e-05
CD56+ NK	kegg	L1	hsa00062	Fatty acid elongation	4.9e-15	3.16e-07
CD56+ NK	kegg	L2	hsa05012	Parkinson disease	1	2.59e-32
CD56+ NK	kegg	L2	hsa00190	Oxidative phosphorylation	1.95e-06	4.18e-24
CD56+ NK	kegg	L2	hsa04714	Thermogenesis	1.9e-07	3.67e-32
CD56+ NK	kegg	L2	hsa05016	Huntington disease	1.8e-08	9.65e-26
CD56+ NK	kegg	L2	hsa05010	Alzheimer disease	1.19e-08	5.81e-25
CD56+ NK	kegg	L2	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	5.28e-10	4.57e-21
CD56+ NK	kegg	L2	hsa04512	ECM-receptor interaction	3.41e-11	0.345
CD56+ NK	kegg	L2	hsa00730	Thiamine metabolism	2.69e-11	0.938
CD56+ NK	kegg	L2	hsa04650	Natural killer cell mediated cytotoxicity	2.2e-11	5.53e-21
CD56+ NK	kegg	L2	hsa04723	Retrograde endocannabinoid signaling	2.1e-11	9.08e-14
CD56+ NK	kegg	L3	hsa04640	Hematopoietic cell lineage	0.998	4.77e-19
CD56+ NK	kegg	L3	hsa04612	Antigen processing and presentation	0.000392	7.9e-16
CD56+ NK	kegg	L3	hsa05332	Graft-versus-host disease	0.000199	2.42e-11
CD56+ NK	kegg	L3	hsa04658	Th1 and Th2 cell differentiation	0.000129	7.71e-16
CD56+ NK	kegg	L3	hsa04650	Natural killer cell mediated cytotoxicity	6.07e-05	5.53e-21
CD56+ NK	kegg	L3	hsa00730	Thiamine metabolism	5.71e-05	0.938
CD56+ NK	kegg	L3	hsa03460	Fanconi anemia pathway	4.82e-05	0.477
CD56+ NK	kegg	L3	hsa00630	Glyoxylate and dicarboxylate metabolism	4.31e-05	5.85e-08
CD56+ NK	kegg	L3	hsa00052	Galactose metabolism	3.99e-05	5.85e-08
CD56+ NK	kegg	L3	hsa05340	Primary immunodeficiency	3.79e-05	2.52e-08

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	9.31e-193
CD56+ NK	reactome	L1	R-HSA-168249	Innate Immune System	3.44e-14	2.67e-117
CD56+ NK	reactome	L1	R-HSA-1280218	Adaptive Immune System	8.59e-20	1.08e-66
CD56+ NK	reactome	L1	R-HSA-6798695	Neutrophil degranulation	3.94e-23	2.5e-68
CD56+ NK	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	5.94e-27	1.89e-65
CD56+ NK	reactome	L1	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	4.21e-31	4.56e-26
CD56+ NK	reactome	L1	R-HSA-449147	Signaling by Interleukins	2.02e-31	7.16e-43
CD56+ NK	reactome	L1	R-HSA-983169	Class I MHC mediated antigen processing & presentation	6.87e-32	1.16e-19
CD56+ NK	reactome	L1	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	4.92e-33	4.6e-14
CD56+ NK	reactome	L1	R-HSA-109581	Apoptosis	1.4e-33	2.08e-24
CD56+ NK	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	0.865	6.21e-34
CD56+ NK	reactome	L2	R-HSA-156902	Peptide chain elongation	0.106	1.06e-32
CD56+ NK	reactome	L2	R-HSA-192823	Viral mRNA Translation	0.0265	1.06e-32
CD56+ NK	reactome	L2	R-HSA-72764	Eukaryotic Translation Termination	0.00176	1.16e-32
CD56+ NK	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	0.000534	2.53e-34
CD56+ NK	reactome	L2	R-HSA-2408557	Selenocysteine synthesis	0.000143	4.17e-31
CD56+ NK	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	1.21e-05	8.93e-36
CD56+ NK	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	9.35e-06	2.23e-35
CD56+ NK	reactome	L2	R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	8.92e-06	1.9e-30
CD56+ NK	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	8.48e-08	3.48e-32
CD56+ NK	reactome	L3	R-HSA-212436	Generic Transcription Pathway	0.681	1.32e-30
CD56+ NK	reactome	L3	R-HSA-74160	Gene expression (Transcription)	0.297	3.1e-41
CD56+ NK	reactome	L3	R-HSA-73857	RNA Polymerase II Transcription	0.0221	2.09e-37
CD56+ NK	reactome	L3	R-HSA-211000	Gene Silencing by RNA	1.79e-08	0.00117
CD56+ NK	reactome	L3	R-HSA-448424	Interleukin-17 signaling	7.77e-09	0.0144
CD56+ NK	reactome	L3	R-HSA-450294	MAP kinase activation	4.16e-09	0.0174
CD56+ NK	reactome	L3	R-HSA-3232142	SUMOylation of ubiquitinylation proteins	4e-09	0.326
CD56+ NK	reactome	L3	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	3.9e-09	2.43e-21
CD56+ NK	reactome	L3	R-HSA-5368286	Mitochondrial translation initiation	3.85e-09	1.27e-14
CD56+ NK	reactome	L3	R-HSA-168138	Toll Like Receptor 9 (TLR9) Cascade	2.94e-09	8.9e-05
CD56+ NK	reactome	L4	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	0.993	1.78e-25
CD56+ NK	reactome	L4	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	0.00561	1.15e-26
CD56+ NK	reactome	L4	R-HSA-611105	Respiratory electron transport	0.00106	7.19e-19
CD56+ NK	reactome	L4	R-HSA-6799198	Complex I biogenesis	1.15e-06	6.16e-12
CD56+ NK	reactome	L4	R-HSA-163210	Formation of ATP by chemiosmotic coupling	4.05e-07	3.2e-08
CD56+ NK	reactome	L4	R-HSA-3700989	Transcriptional Regulation by TP53	3.29e-07	8.12e-24
CD56+ NK	reactome	L4	R-HSA-8949613	Cristae formation	1.73e-07	2.44e-09
CD56+ NK	reactome	L4	R-HSA-1430728	Metabolism	6.44e-08	5.19e-148
CD56+ NK	reactome	L4	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	5.51e-08	2.43e-21
CD56+ NK	reactome	L4	R-HSA-72163	mRNA Splicing - Major Pathway	3.54e-08	3.64e-23
CD56+ NK	reactome	L5	R-HSA-8878171	Transcriptional regulation by RUNX1	0.971	4.65e-25
CD56+ NK	reactome	L5	R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs	0.0185	2.98e-17
CD56+ NK	reactome	L5	R-HSA-157118	Signaling by NOTCH	0.00959	1.64e-27
CD56+ NK	reactome	L5	R-HSA-8878159	Transcriptional regulation by RUNX3	0.000102	1.97e-15
CD56+ NK	reactome	L5	R-HSA-4641257	Degradation of AXIN	7.08e-05	3.59e-12
CD56+ NK	reactome	L5	R-HSA-8948751	Regulation of PTEN stability and activity	6.68e-05	6.86e-14
CD56+ NK	reactome	L5	R-HSA-180585	Vif-mediated degradation of APOBEC3G	5.75e-05	8.01e-12
CD56+ NK	reactome	L5	R-HSA-69481	G2/M Checkpoints	5.42e-05	6.46e-18
CD56+ NK	reactome	L5	R-HSA-8941858	Regulation of RUNX3 expression and activity	2.83e-05	1.35e-11
CD56+ NK	reactome	L5	R-HSA-9013694	Signaling by NOTCH4	2.25e-05	5.79e-14
CD56+ NK	reactome	L6	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	0.881	4.6e-14
CD56+ NK	reactome	L6	R-HSA-983169	Class I MHC mediated antigen processing & presentation	0.119	1.16e-19
CD56+ NK	reactome	L6	R-HSA-8951664	Neddylation	0.000295	1.84e-09
CD56+ NK	reactome	L6	R-HSA-448424	Interleukin-17 signaling	4.14e-06	0.0144
CD56+ NK	reactome	L6	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	3.56e-06	2.43e-21
CD56+ NK	reactome	L6	R-HSA-450321	JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1	2.76e-06	0.525
CD56+ NK	reactome	L6	R-HSA-72163	mRNA Splicing - Major Pathway	2.74e-06	3.64e-23
CD56+ NK	reactome	L6	R-HSA-72172	mRNA Splicing	2.26e-06	1.75e-23
CD56+ NK	reactome	L6	R-HSA-450294	MAP kinase activation	2.12e-06	0.0174
CD56+ NK	reactome	L6	R-HSA-114608	Platelet degranulation	2.12e-06	5.81e-20

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	3.73e-31
CD56+ NK	wikipathway	L1	WP2805	exRNA mechanism of action and biogenesis	5.69e-20	1
CD56+ NK	wikipathway	L1	WP3945	TYROBP Causal Network	3.47e-20	4.57e-16
CD56+ NK	wikipathway	L1	WP183	Proteasome Degradation	1.52e-20	5.7e-14
CD56+ NK	wikipathway	L1	WP410	Exercise-induced Circadian Regulation	1.1e-20	9.72e-11
CD56+ NK	wikipathway	L1	WP254	Apoptosis	7.79e-21	7.82e-15
CD56+ NK	wikipathway	L1	WP43	Oxidation by Cytochrome P450	7.63e-21	0.59
CD56+ NK	wikipathway	L1	WP4150	Wnt Signaling in Kidney Disease	7.27e-21	0.662
CD56+ NK	wikipathway	L1	WP619	Type II interferon signaling (IFNG)	7.14e-21	1.34e-08
CD56+ NK	wikipathway	L1	WP3302	eIF5A regulation in response to inhibition of the nuclear export system	7.12e-21	1
CD56+ NK	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	0.991	3.36e-24
CD56+ NK	wikipathway	L2	WP623	Oxidative phosphorylation	0.00911	3.19e-17
CD56+ NK	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	1.86e-05	2.56e-21
CD56+ NK	wikipathway	L2	WP3945	TYROBP Causal Network	2.61e-06	4.57e-16
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	5.7e-14
CD56+ NK	wikipathway	L2	WP410	Exercise-induced Circadian Regulation	1.38e-06	9.72e-11
CD56+ NK	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	1.28e-06	5.33e-10
CD56+ NK	wikipathway	L2	WP254	Apoptosis	8.6e-07	7.82e-15
CD56+ NK	wikipathway	L2	WP43	Oxidation by Cytochrome P450	7.38e-07	0.59

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	0.998	1.1e-248
T cell	gobp	L1	GO:0045321	leukocyte activation	0.00176	2.33e-226
T cell	gobp	L1	GO:0002263	cell activation involved in immune response	4.39e-09	2.89e-145
T cell	gobp	L1	GO:0002366	leukocyte activation involved in immune response	2.91e-09	3.2e-144
T cell	gobp	L1	GO:0002274	myeloid leukocyte activation	9.46e-10	2.5e-134
T cell	gobp	L1	GO:0002443	leukocyte mediated immunity	2.66e-10	5.41e-152
T cell	gobp	L1	GO:0045055	regulated exocytosis	1.14e-10	1.58e-142
T cell	gobp	L1	GO:0006887	exocytosis	3.13e-11	4.75e-152
T cell	gobp	L1	GO:0043299	leukocyte degranulation	1.81e-11	2.47e-116
T cell	gobp	L1	GO:0042119	neutrophil activation	1.47e-11	1.09e-111
T cell	gobp	L2	GO:0006119	oxidative phosphorylation	0.999	1.89e-33
T cell	gobp	L2	GO:0042773	ATP synthesis coupled electron transport	0.000673	9.26e-25
T cell	gobp	L2	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.000457	2.1e-24
T cell	gobp	L2	GO:0046034	ATP metabolic process	2.91e-06	1.9e-45
T cell	gobp	L2	GO:0022904	respiratory electron transport chain	1.84e-06	1.89e-23
T cell	gobp	L2	GO:0009126	purine nucleoside monophosphate metabolic process	6.9e-08	4.6e-47
T cell	gobp	L2	GO:0009167	purine ribonucleoside monophosphate metabolic process	6.9e-08	4.6e-47
T cell	gobp	L2	GO:0009205	purine ribonucleoside triphosphate metabolic process	3.34e-08	3.43e-45
T cell	gobp	L2	GO:0009123	nucleoside monophosphate metabolic process	2.53e-08	1.58e-49
T cell	gobp	L2	GO:0009144	purine nucleoside triphosphate metabolic process	1.87e-08	1.43e-45
T cell	gobp	L3	GO:0010941	regulation of cell death	0.403	2.14e-192
T cell	gobp	L3	GO:0008219	cell death	0.366	7.03e-238
T cell	gobp	L3	GO:0043067	regulation of programmed cell death	0.0588	3.66e-176
T cell	gobp	L3	GO:0042981	regulation of apoptotic process	0.0585	1.38e-174
T cell	gobp	L3	GO:0012501	programmed cell death	0.0419	1.13e-219
T cell	gobp	L3	GO:0006915	apoptotic process	0.0376	4.51e-213
T cell	gobp	L3	GO:0097190	apoptotic signaling pathway	0.017	1.88e-89
T cell	gobp	L3	GO:0010942	positive regulation of cell death	0.00417	7.69e-95
T cell	gobp	L3	GO:0048518	positive regulation of biological process	0.00213	0
T cell	gobp	L3	GO:0048522	positive regulation of cellular process	0.00108	0
T cell	gobp	L4	GO:0045047	protein targeting to ER	0.422	6.74e-29
T cell	gobp	L4	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.369	2.7e-27
T cell	gobp	L4	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.137	1.07e-28
T cell	gobp	L4	GO:0070972	protein localization to endoplasmic reticulum	0.0423	2.39e-33
T cell	gobp	L4	GO:0006613	cotranslational protein targeting to membrane	0.0302	4.02e-26
T cell	gobp	L4	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	0.000183	3.52e-27
T cell	gobp	L4	GO:0006413	translational initiation	4.8e-05	3.9e-38
T cell	gobp	L4	GO:0006612	protein targeting to membrane	8.81e-06	5.84e-34
T cell	gobp	L4	GO:0090150	establishment of protein localization to membrane	1.22e-07	1.73e-46
T cell	gobp	L4	GO:0016071	mRNA metabolic process	5.06e-08	5.76e-91
T cell	gobp	L5	GO:0002376	immune system process	0.998	0
T cell	gobp	L5	GO:0006955	immune response	0.00153	2.06e-293
T cell	gobp	L5	GO:0002252	immune effector process	3.11e-09	3.3e-199
T cell	gobp	L5	GO:0050896	response to stimulus	3.08e-09	0
T cell	gobp	L5	GO:0006952	defense response	5.29e-10	4.56e-177
T cell	gobp	L5	GO:0032940	secretion by cell	5.18e-10	1.77e-205
T cell	gobp	L5	GO:0048518	positive regulation of biological process	4.73e-10	0
T cell	gobp	L5	GO:0016192	vesicle-mediated transport	3.93e-10	2.5e-247
T cell	gobp	L5	GO:0051716	cellular response to stimulus	2.23e-10	0
T cell	gobp	L5	GO:0006887	exocytosis	1.73e-10	4.75e-152

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	8.89e-111
T cell	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.268	9.71e-110
T cell	gobp_nr	L1	GO:0032103	positive regulation of response to external stimulus	1.12e-27	1.22e-45
T cell	gobp_nr	L1	GO:0098542	defense response to other organism	6.3e-28	6.8e-59
T cell	gobp_nr	L1	GO:0006959	humoral immune response	5.97e-28	9.7e-30
T cell	gobp_nr	L1	GO:0002764	immune response-regulating signaling pathway	4.46e-28	7.65e-74
T cell	gobp_nr	L1	GO:0001819	positive regulation of cytokine production	3.31e-28	8.81e-67
T cell	gobp_nr	L1	GO:0006490	oligosaccharide-lipid intermediate biosynthetic process	3.23e-28	0.818
T cell	gobp_nr	L1	GO:0000959	mitochondrial RNA metabolic process	2.56e-28	0.368
T cell	gobp_nr	L1	GO:0009123	nucleoside monophosphate metabolic process	2.08e-28	1.1e-48
T cell	gobp_nr	L2	GO:0042110	T cell activation	1	2.42e-82
T cell	gobp_nr	L2	GO:0002694	regulation of leukocyte activation	3.06e-06	7.09e-78
T cell	gobp_nr	L2	GO:0007159	leukocyte cell-cell adhesion	2.59e-06	9.16e-58
T cell	gobp_nr	L2	GO:0002521	leukocyte differentiation	1.85e-06	6.93e-78
T cell	gobp_nr	L2	GO:0050867	positive regulation of cell activation	1.27e-06	1.16e-58
T cell	gobp_nr	L2	GO:0045785	positive regulation of cell adhesion	4.91e-07	9.52e-63
T cell	gobp_nr	L2	GO:0002250	adaptive immune response	1.07e-07	1.04e-61
T cell	gobp_nr	L2	GO:0022407	regulation of cell-cell adhesion	4.81e-08	1.3e-57
T cell	gobp_nr	L2	GO:0070661	leukocyte proliferation	6.9e-09	4.95e-45
T cell	gobp_nr	L2	GO:0001819	positive regulation of cytokine production	4.06e-09	8.81e-67
T cell	gobp_nr	L3	GO:0070972	protein localization to endoplasmic reticulum	1	7.08e-33
T cell	gobp_nr	L3	GO:0006413	translational initiation	0.000141	1.53e-37
T cell	gobp_nr	L3	GO:0090150	establishment of protein localization to membrane	9.6e-07	1.16e-45
T cell	gobp_nr	L3	GO:0006490	oligosaccharide-lipid intermediate biosynthetic process	3.5e-07	0.818
T cell	gobp_nr	L3	GO:0000959	mitochondrial RNA metabolic process	2.76e-07	0.368
T cell	gobp_nr	L3	GO:0006401	RNA catabolic process	1.36e-07	6.06e-46
T cell	gobp_nr	L3	GO:0072348	sulfur compound transport	1.32e-07	0.453
T cell	gobp_nr	L3	GO:0070193	synaptonemal complex organization	7.79e-08	0.707
T cell	gobp_nr	L3	GO:0006605	protein targeting	7.78e-08	1.69e-52
T cell	gobp_nr	L3	GO:2001233	regulation of apoptotic signaling pathway	4.76e-08	1.82e-57

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:0005515	protein binding	1	0
T cell	gomf	L1	GO:0005488	binding	4.48e-15	0
T cell	gomf	L1	GO:0003674	molecular_function	7.91e-18	0
T cell	gomf	L1	GO:0019899	enzyme binding	1.19e-40	3.3e-234
T cell	gomf	L1	GO:0003824	catalytic activity	9.43e-43	0
T cell	gomf	L1	GO:0097159	organic cyclic compound binding	8.78e-45	0
T cell	gomf	L1	GO:1901363	heterocyclic compound binding	1.69e-45	0
T cell	gomf	L1	GO:0003723	RNA binding	8.1e-46	1.71e-189
T cell	gomf	L1	GO:0042802	identical protein binding	6.54e-49	3.5e-152
T cell	gomf	L1	GO:0046983	protein dimerization activity	4.86e-49	3.06e-119

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	1.47e-43
T cell	kegg	L1	hsa05012	Parkinson disease	7.16e-07	3.58e-35
T cell	kegg	L1	hsa00190	Oxidative phosphorylation	1.46e-08	1.36e-30
T cell	kegg	L1	hsa05016	Huntington disease	1.63e-09	1.01e-36
T cell	kegg	L1	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	3.42e-11	1.44e-28
T cell	kegg	L1	hsa04714	Thermogenesis	2.27e-12	1.54e-35
T cell	kegg	L1	hsa04723	Retrograde endocannabinoid signaling	1.58e-12	8.39e-22
T cell	kegg	L1	hsa05167	Kaposi sarcoma-associated herpesvirus infection	1.12e-13	1.52e-32
T cell	kegg	L1	hsa04062	Chemokine signaling pathway	8.92e-14	1.42e-30
T cell	kegg	L1	hsa05332	Graft-versus-host disease	7e-14	4.01e-13

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	4.55e-106
T cell	reactome	L1	R-HSA-168249	Innate Immune System	6.29e-13	6.01e-153
T cell	reactome	L1	R-HSA-168256	Immune System	2.78e-16	5.39e-262
T cell	reactome	L1	R-HSA-76002	Platelet activation, signaling and aggregation	5.14e-28	5.32e-42
T cell	reactome	L1	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	4.69e-28	1.32e-26
T cell	reactome	L1	R-HSA-109582	Hemostasis	2.94e-28	7.72e-72
T cell	reactome	L1	R-HSA-162582	Signal Transduction	1.68e-28	7.1e-220
T cell	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	1.47e-28	7.01e-82
T cell	reactome	L1	R-HSA-3781860	Diseases associated with N-glycosylation of proteins	1.34e-28	0.914
T cell	reactome	L1	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	1.25e-28	1.08e-21
T cell	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	0.585	4.81e-34
T cell	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	0.399	1.1e-33
T cell	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	0.00721	4.13e-30
T cell	reactome	L2	R-HSA-72613	Eukaryotic Translation Initiation	0.00282	2.52e-32
T cell	reactome	L2	R-HSA-72737	Cap-dependent Translation Initiation	0.00282	2.52e-32
T cell	reactome	L2	R-HSA-192823	Viral mRNA Translation	0.00122	6.8e-29
T cell	reactome	L2	R-HSA-156902	Peptide chain elongation	0.000931	6.8e-29
T cell	reactome	L2	R-HSA-72764	Eukaryotic Translation Termination	0.000178	9.61e-29
T cell	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	0.000129	2.2e-28
T cell	reactome	L2	R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	6.03e-05	5.62e-28

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	1.27e-152
CD14+ Monocyte	gobp	L1	GO:0001775	cell activation	0.086	4.88e-159
CD14+ Monocyte	gobp	L1	GO:0002376	immune system process	4.67e-06	3.66e-228
CD14+ Monocyte	gobp	L1	GO:0006955	immune response	3.98e-07	8.73e-175
CD14+ Monocyte	gobp	L1	GO:0002443	leukocyte mediated immunity	8.29e-10	1.82e-108
CD14+ Monocyte	gobp	L1	GO:0002366	leukocyte activation involved in immune response	6.44e-10	6.66e-105
CD14+ Monocyte	gobp	L1	GO:0002263	cell activation involved in immune response	5.38e-10	3.79e-105
CD14+ Monocyte	gobp	L1	GO:0002274	myeloid leukocyte activation	2.28e-10	2.2e-100
CD14+ Monocyte	gobp	L1	GO:0042119	neutrophil activation	9.48e-12	8.79e-89
CD14+ Monocyte	gobp	L1	GO:0002275	myeloid cell activation involved in immune response	5.79e-12	7.43e-92
CD14+ Monocyte	gobp	L2	GO:0045047	protein targeting to ER	0.862	6.38e-36
CD14+ Monocyte	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.0573	1.17e-33
CD14+ Monocyte	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.0476	6.35e-34
CD14+ Monocyte	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0334	1.64e-34
CD14+ Monocyte	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	0.000211	6.3e-36
CD14+ Monocyte	gobp	L2	GO:0006612	protein targeting to membrane	4.14e-08	1.55e-34
CD14+ Monocyte	gobp	L2	GO:0090150	establishment of protein localization to membrane	3.13e-09	3.11e-45
CD14+ Monocyte	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	2.76e-09	5.73e-29
CD14+ Monocyte	gobp	L2	GO:0006413	translational initiation	6.92e-10	8.46e-43
CD14+ Monocyte	gobp	L2	GO:0006605	protein targeting	6.28e-12	1.38e-44
CD14+ Monocyte	gobp	L3	GO:0006119	oxidative phosphorylation	0.999	1.78e-31
CD14+ Monocyte	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.000398	7.45e-24
CD14+ Monocyte	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.000223	1.88e-23
CD14+ Monocyte	gobp	L3	GO:0009123	nucleoside monophosphate metabolic process	0.000175	2.02e-45
CD14+ Monocyte	gobp	L3	GO:0009126	purine nucleoside monophosphate metabolic process	5.85e-05	1.11e-42
CD14+ Monocyte	gobp	L3	GO:0009167	purine ribonucleoside monophosphate metabolic process	5.85e-05	1.11e-42
CD14+ Monocyte	gobp	L3	GO:0009161	ribonucleoside monophosphate metabolic process	1.15e-05	4.52e-42
CD14+ Monocyte	gobp	L3	GO:0009144	purine nucleoside triphosphate metabolic process	8.94e-06	1.93e-41
CD14+ Monocyte	gobp	L3	GO:0046034	ATP metabolic process	6.87e-06	8.17e-38
CD14+ Monocyte	gobp	L3	GO:0022904	respiratory electron transport chain	6.08e-06	6.09e-23
CD14+ Monocyte	gobp	L4	GO:0016192	vesicle-mediated transport	0.985	2.93e-145
CD14+ Monocyte	gobp	L4	GO:0002376	immune system process	0.00849	3.66e-228
CD14+ Monocyte	gobp	L4	GO:0006955	immune response	0.00197	8.73e-175
CD14+ Monocyte	gobp	L4	GO:0045055	regulated exocytosis	0.000873	1.87e-97
CD14+ Monocyte	gobp	L4	GO:0006810	transport	0.000864	3.32e-280
CD14+ Monocyte	gobp	L4	GO:0051234	establishment of localization	0.000683	1.58e-285
CD14+ Monocyte	gobp	L4	GO:0006887	exocytosis	0.000639	1.3e-98
CD14+ Monocyte	gobp	L4	GO:0042119	neutrophil activation	0.000259	8.79e-89
CD14+ Monocyte	gobp	L4	GO:0036230	granulocyte activation	0.000175	7.97e-89
CD14+ Monocyte	gobp	L4	GO:0043299	leukocyte degranulation	0.000152	1.41e-91
CD14+ Monocyte	gobp	L5	GO:0006915	apoptotic process	0.272	4.45e-113
CD14+ Monocyte	gobp	L5	GO:0012501	programmed cell death	0.195	8.3e-116
CD14+ Monocyte	gobp	L5	GO:0043067	regulation of programmed cell death	0.194	7.9e-95
CD14+ Monocyte	gobp	L5	GO:0042981	regulation of apoptotic process	0.158	1.19e-93
CD14+ Monocyte	gobp	L5	GO:0010941	regulation of cell death	0.101	4e-100
CD14+ Monocyte	gobp	L5	GO:0008219	cell death	0.0513	1.27e-119
CD14+ Monocyte	gobp	L5	GO:0002376	immune system process	0.00709	3.66e-228
CD14+ Monocyte	gobp	L5	GO:0016032	viral process	0.00345	2.8e-65
CD14+ Monocyte	gobp	L5	GO:0097190	apoptotic signaling pathway	0.00227	1.84e-46
CD14+ Monocyte	gobp	L5	GO:0044419	interspecies interaction between organisms	0.00226	1.33e-70
CD14+ Monocyte	gobp	L6	GO:0006518	peptide metabolic process	0.791	4.68e-78
CD14+ Monocyte	gobp	L6	GO:0006412	translation	0.12	1.09e-65
CD14+ Monocyte	gobp	L6	GO:0043043	peptide biosynthetic process	0.0828	4.55e-66
CD14+ Monocyte	gobp	L6	GO:0043603	cellular amide metabolic process	0.00248	2.33e-80
CD14+ Monocyte	gobp	L6	GO:0070125	mitochondrial translational elongation	0.00176	6.79e-17
CD14+ Monocyte	gobp	L6	GO:0043604	amide biosynthetic process	0.00117	8.36e-66
CD14+ Monocyte	gobp	L6	GO:0070126	mitochondrial translational termination	0.00066	4.56e-16
CD14+ Monocyte	gobp	L6	GO:0006413	translational initiation	0.000301	8.46e-43
CD14+ Monocyte	gobp	L6	GO:0006415	translational termination	0.000143	1.75e-15
CD14+ Monocyte	gobp	L6	GO:0006414	translational elongation	5.84e-05	5.01e-17
CD14+ Monocyte	gobp	L7	GO:0008380	RNA splicing	0.422	9.75e-38
CD14+ Monocyte	gobp	L7	GO:0000375	RNA splicing, via transesterification reactions	0.197	7.44e-32
CD14+ Monocyte	gobp	L7	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.179	1.39e-31
CD14+ Monocyte	gobp	L7	GO:0000398	mRNA splicing, via spliceosome	0.179	1.39e-31
CD14+ Monocyte	gobp	L7	GO:0006397	mRNA processing	0.0211	7.47e-38
CD14+ Monocyte	gobp	L7	GO:0016071	mRNA metabolic process	0.0015	2.42e-69
CD14+ Monocyte	gobp	L7	GO:0016032	viral process	6.58e-05	2.8e-65
CD14+ Monocyte	gobp	L7	GO:0044419	interspecies interaction between organisms	3.83e-05	1.33e-70
CD14+ Monocyte	gobp	L7	GO:0044403	symbiont process	2.46e-05	2.16e-67
CD14+ Monocyte	gobp	L7	GO:0009124	nucleoside monophosphate biosynthetic process	2e-05	8.97e-24

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	2.4e-86
CD14+ Monocyte	gobp_nr	L1	GO:0002446	neutrophil mediated immunity	0.0241	1.75e-83
CD14+ Monocyte	gobp_nr	L1	GO:0002532	production of molecular mediator involved in inflammatory response	2.75e-26	4.73e-16
CD14+ Monocyte	gobp_nr	L1	GO:0002764	immune response-regulating signaling pathway	1.12e-26	1.24e-44
CD14+ Monocyte	gobp_nr	L1	GO:0006979	response to oxidative stress	8.64e-28	3.65e-35
CD14+ Monocyte	gobp_nr	L1	GO:0002576	platelet degranulation	7.4e-28	2e-14
CD14+ Monocyte	gobp_nr	L1	GO:2001057	reactive nitrogen species metabolic process	6.91e-28	2.12e-12
CD14+ Monocyte	gobp_nr	L1	GO:0006959	humoral immune response	6.84e-28	6.3e-18
CD14+ Monocyte	gobp_nr	L1	GO:0002250	adaptive immune response	5.86e-28	1.05e-37
CD14+ Monocyte	gobp_nr	L1	GO:0006968	cellular defense response	5.6e-28	3.02e-10
CD14+ Monocyte	gobp_nr	L2	GO:0006413	translational initiation	1	1.13e-41
CD14+ Monocyte	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	5.97e-06	4.74e-35
CD14+ Monocyte	gobp_nr	L2	GO:0002181	cytoplasmic translation	7.07e-09	2.09e-16
CD14+ Monocyte	gobp_nr	L2	GO:0006401	RNA catabolic process	1.85e-09	1.51e-35
CD14+ Monocyte	gobp_nr	L2	GO:0002532	production of molecular mediator involved in inflammatory response	1.46e-09	4.73e-16
CD14+ Monocyte	gobp_nr	L2	GO:0006414	translational elongation	6.35e-10	1.98e-16
CD14+ Monocyte	gobp_nr	L2	GO:0006338	chromatin remodeling	5.41e-10	5.77e-19
CD14+ Monocyte	gobp_nr	L2	GO:0006605	protein targeting	3.47e-10	6.38e-43
CD14+ Monocyte	gobp_nr	L2	GO:0002764	immune response-regulating signaling pathway	3.16e-10	1.24e-44
CD14+ Monocyte	gobp_nr	L2	GO:0042769	DNA damage response, detection of DNA damage	2.54e-10	5.51e-09
CD14+ Monocyte	gobp_nr	L3	GO:0009123	nucleoside monophosphate metabolic process	0.988	5.79e-44
CD14+ Monocyte	gobp_nr	L3	GO:0009141	nucleoside triphosphate metabolic process	0.0117	5.15e-40
CD14+ Monocyte	gobp_nr	L3	GO:0006091	generation of precursor metabolites and energy	3.6e-06	2.13e-41
CD14+ Monocyte	gobp_nr	L3	GO:0033108	mitochondrial respiratory chain complex assembly	5.23e-07	2.43e-18
CD14+ Monocyte	gobp_nr	L3	GO:0009259	ribonucleotide metabolic process	4.64e-07	4.81e-39
CD14+ Monocyte	gobp_nr	L3	GO:0010257	NADH dehydrogenase complex assembly	8.77e-09	1.27e-12
CD14+ Monocyte	gobp_nr	L3	GO:0072522	purine-containing compound biosynthetic process	3.05e-09	9.37e-23
CD14+ Monocyte	gobp_nr	L3	GO:0002532	production of molecular mediator involved in inflammatory response	1.19e-09	4.73e-16
CD14+ Monocyte	gobp_nr	L3	GO:1901293	nucleoside phosphate biosynthetic process	1.13e-09	4.64e-25
CD14+ Monocyte	gobp_nr	L3	GO:1902600	proton transmembrane transport	1.08e-09	5.62e-15
CD14+ Monocyte	gobp_nr	L4	GO:0002521	leukocyte differentiation	0.619	9.45e-48
CD14+ Monocyte	gobp_nr	L4	GO:0042110	T cell activation	0.356	2.31e-47
CD14+ Monocyte	gobp_nr	L4	GO:0002250	adaptive immune response	0.00864	1.05e-37
CD14+ Monocyte	gobp_nr	L4	GO:0042113	B cell activation	0.00749	2.43e-29
CD14+ Monocyte	gobp_nr	L4	GO:0002694	regulation of leukocyte activation	0.00398	1.22e-45
CD14+ Monocyte	gobp_nr	L4	GO:1903706	regulation of hemopoiesis	0.00156	1.24e-35
CD14+ Monocyte	gobp_nr	L4	GO:0050867	positive regulation of cell activation	0.00108	2.63e-33
CD14+ Monocyte	gobp_nr	L4	GO:0002764	immune response-regulating signaling pathway	0.000618	1.24e-44
CD14+ Monocyte	gobp_nr	L4	GO:0007159	leukocyte cell-cell adhesion	0.000441	1.1e-32
CD14+ Monocyte	gobp_nr	L4	GO:0070661	leukocyte proliferation	0.00022	1.04e-28
CD14+ Monocyte	gobp_nr	L5	GO:0008380	RNA splicing	0.877	3.39e-36
CD14+ Monocyte	gobp_nr	L5	GO:0006397	mRNA processing	0.089	3.35e-36
CD14+ Monocyte	gobp_nr	L5	GO:0002532	production of molecular mediator involved in inflammatory response	0.00137	4.73e-16
CD14+ Monocyte	gobp_nr	L5	GO:0006338	chromatin remodeling	0.00135	5.77e-19
CD14+ Monocyte	gobp_nr	L5	GO:0033044	regulation of chromosome organization	0.00129	2.63e-28
CD14+ Monocyte	gobp_nr	L5	GO:1903311	regulation of mRNA metabolic process	0.00128	9.73e-24
CD14+ Monocyte	gobp_nr	L5	GO:0006414	translational elongation	0.00124	1.98e-16
CD14+ Monocyte	gobp_nr	L5	GO:0002764	immune response-regulating signaling pathway	0.000716	1.24e-44
CD14+ Monocyte	gobp_nr	L5	GO:0008213	protein alkylation	0.00058	2.78e-16
CD14+ Monocyte	gobp_nr	L5	GO:0042113	B cell activation	0.000485	2.43e-29
CD14+ Monocyte	gobp_nr	L6	GO:0090150	establishment of protein localization to membrane	0.756	9.08e-44
CD14+ Monocyte	gobp_nr	L6	GO:0070972	protein localization to endoplasmic reticulum	0.238	4.74e-35
CD14+ Monocyte	gobp_nr	L6	GO:0006605	protein targeting	0.00287	6.38e-43
CD14+ Monocyte	gobp_nr	L6	GO:0002532	production of molecular mediator involved in inflammatory response	0.000341	4.73e-16
CD14+ Monocyte	gobp_nr	L6	GO:0006414	translational elongation	0.000159	1.98e-16
CD14+ Monocyte	gobp_nr	L6	GO:0006338	chromatin remodeling	0.000112	5.77e-19
CD14+ Monocyte	gobp_nr	L6	GO:0002764	immune response-regulating signaling pathway	0.000108	1.24e-44
CD14+ Monocyte	gobp_nr	L6	GO:1904950	negative regulation of establishment of protein localization	8.32e-05	1.55e-17
CD14+ Monocyte	gobp_nr	L6	GO:0033044	regulation of chromosome organization	6.05e-05	2.63e-28
CD14+ Monocyte	gobp_nr	L6	GO:0033108	mitochondrial respiratory chain complex assembly	5.56e-05	2.43e-18

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	1.17e-141
CD14+ Monocyte	gomf	L1	GO:0005515	protein binding	1.75e-07	0
CD14+ Monocyte	gomf	L1	GO:0042802	identical protein binding	3.12e-10	1.44e-82
CD14+ Monocyte	gomf	L1	GO:0019899	enzyme binding	2.55e-10	1.68e-117
CD14+ Monocyte	gomf	L1	GO:0044877	protein-containing complex binding	2.34e-10	9.87e-64
CD14+ Monocyte	gomf	L1	GO:0003743	translation initiation factor activity	7.73e-11	1.26e-12
CD14+ Monocyte	gomf	L1	GO:0051082	unfolded protein binding	5.5e-11	9.32e-16
CD14+ Monocyte	gomf	L1	GO:0003682	chromatin binding	3.76e-11	2.63e-33
CD14+ Monocyte	gomf	L1	GO:0044389	ubiquitin-like protein ligase binding	1.63e-11	1.37e-24
CD14+ Monocyte	gomf	L1	GO:0031625	ubiquitin protein ligase binding	1.37e-11	1.65e-23
CD14+ Monocyte	gomf	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	1	1.4e-15
CD14+ Monocyte	gomf	L2	GO:0003700	DNA-binding transcription factor activity	0.000172	1.31e-20
CD14+ Monocyte	gomf	L2	GO:0003677	DNA binding	3.13e-08	5.11e-45
CD14+ Monocyte	gomf	L2	GO:0140110	transcription regulator activity	4.48e-10	1.25e-35
CD14+ Monocyte	gomf	L2	GO:0003676	nucleic acid binding	2.63e-12	2.63e-149
CD14+ Monocyte	gomf	L2	GO:0097159	organic cyclic compound binding	3.17e-15	1.19e-221
CD14+ Monocyte	gomf	L2	GO:1901363	heterocyclic compound binding	2.8e-15	6.92e-220
CD14+ Monocyte	gomf	L2	GO:0000976	transcription regulatory region sequence-specific DNA binding	9.49e-18	2.15e-36
CD14+ Monocyte	gomf	L2	GO:0001067	regulatory region nucleic acid binding	6.02e-18	3.23e-38
CD14+ Monocyte	gomf	L2	GO:0044212	transcription regulatory region DNA binding	5.61e-18	3.42e-38
CD14+ Monocyte	gomf	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	0.66	1.25e-37
CD14+ Monocyte	gomf	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.292	4.37e-37
CD14+ Monocyte	gomf	L3	GO:0000987	proximal promoter sequence-specific DNA binding	0.0358	2.76e-33
CD14+ Monocyte	gomf	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	0.00754	3.45e-32
CD14+ Monocyte	gomf	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	0.003	2.15e-36
CD14+ Monocyte	gomf	L3	GO:1990837	sequence-specific double-stranded DNA binding	0.000625	1.01e-38
CD14+ Monocyte	gomf	L3	GO:0043565	sequence-specific DNA binding	0.000263	5.05e-44
CD14+ Monocyte	gomf	L3	GO:0044212	transcription regulatory region DNA binding	2.75e-05	3.42e-38
CD14+ Monocyte	gomf	L3	GO:0001067	regulatory region nucleic acid binding	2.02e-05	3.23e-38
CD14+ Monocyte	gomf	L3	GO:0003690	double-stranded DNA binding	1.06e-05	5.83e-43
CD14+ Monocyte	gomf	L4	GO:0003735	structural constituent of ribosome	1	4.92e-44
CD14+ Monocyte	gomf	L4	GO:0015370	solute:sodium symporter activity	9.36e-14	0.991
CD14+ Monocyte	gomf	L4	GO:0003823	antigen binding	7.42e-14	3.66e-10
CD14+ Monocyte	gomf	L4	GO:0019199	transmembrane receptor protein kinase activity	6.22e-14	0.894
CD14+ Monocyte	gomf	L4	GO:0005310	dicarboxylic acid transmembrane transporter activity	4.74e-14	0.984
CD14+ Monocyte	gomf	L4	GO:0008157	protein phosphatase 1 binding	4.04e-14	6.26e-08
CD14+ Monocyte	gomf	L4	GO:0004298	threonine-type endopeptidase activity	3.67e-14	2.66e-07
CD14+ Monocyte	gomf	L4	GO:0070003	threonine-type peptidase activity	3.67e-14	2.66e-07
CD14+ Monocyte	gomf	L4	GO:0042287	MHC protein binding	3.2e-14	8.24e-08
CD14+ Monocyte	gomf	L4	GO:0140098	catalytic activity, acting on RNA	3.2e-14	7.85e-08
CD14+ Monocyte	gomf	L5	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	0.827	2.85e-17
CD14+ Monocyte	gomf	L5	GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.0776	9.08e-15
CD14+ Monocyte	gomf	L5	GO:0050136	NADH dehydrogenase (quinone) activity	0.0776	9.08e-15
CD14+ Monocyte	gomf	L5	GO:0003954	NADH dehydrogenase activity	0.0176	5.48e-14
CD14+ Monocyte	gomf	L5	GO:0016651	oxidoreductase activity, acting on NAD(P)H	0.000139	1.13e-15
CD14+ Monocyte	gomf	L5	GO:0009055	electron transfer activity	3.59e-06	3.84e-14
CD14+ Monocyte	gomf	L5	GO:0015370	solute:sodium symporter activity	2.01e-06	0.991
CD14+ Monocyte	gomf	L5	GO:0016491	oxidoreductase activity	1.58e-06	2.38e-39
CD14+ Monocyte	gomf	L5	GO:0003823	antigen binding	1.54e-06	3.66e-10
CD14+ Monocyte	gomf	L5	GO:0019199	transmembrane receptor protein kinase activity	1.28e-06	0.894
CD14+ Monocyte	gomf	L6	GO:0045296	cadherin binding	0.789	4.05e-37
CD14+ Monocyte	gomf	L6	GO:0050839	cell adhesion molecule binding	0.188	1.11e-41
CD14+ Monocyte	gomf	L6	GO:0005515	protein binding	0.0011	0
CD14+ Monocyte	gomf	L6	GO:0042802	identical protein binding	0.000964	1.44e-82
CD14+ Monocyte	gomf	L6	GO:0044877	protein-containing complex binding	0.000567	9.87e-64
CD14+ Monocyte	gomf	L6	GO:0019899	enzyme binding	0.000473	1.68e-117
CD14+ Monocyte	gomf	L6	GO:0051082	unfolded protein binding	0.000388	9.32e-16
CD14+ Monocyte	gomf	L6	GO:0003823	antigen binding	0.000326	3.66e-10
CD14+ Monocyte	gomf	L6	GO:0019199	transmembrane receptor protein kinase activity	0.000265	0.894
CD14+ Monocyte	gomf	L6	GO:0015370	solute:sodium symporter activity	0.000254	0.991

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	7.45e-35
CD14+ Monocyte	kegg	L1	hsa04640	Hematopoietic cell lineage	5.21e-15	8.77e-16
CD14+ Monocyte	kegg	L1	hsa04659	Th17 cell differentiation	3.25e-15	5.12e-17
CD14+ Monocyte	kegg	L1	hsa04350	TGF-beta signaling pathway	2.86e-15	0.415
CD14+ Monocyte	kegg	L1	hsa04142	Lysosome	2.82e-15	1.26e-15
CD14+ Monocyte	kegg	L1	hsa04512	ECM-receptor interaction	2.58e-15	0.447
CD14+ Monocyte	kegg	L1	hsa04390	Hippo signaling pathway	2.39e-15	0.144
CD14+ Monocyte	kegg	L1	hsa00030	Pentose phosphate pathway	2.37e-15	2.27e-06
CD14+ Monocyte	kegg	L1	hsa00900	Terpenoid backbone biosynthesis	2.31e-15	0.82
CD14+ Monocyte	kegg	L1	hsa05033	Nicotine addiction	2.03e-15	1
CD14+ Monocyte	kegg	L2	hsa05012	Parkinson disease	1	2.61e-33
CD14+ Monocyte	kegg	L2	hsa00190	Oxidative phosphorylation	9.66e-05	3.03e-29
CD14+ Monocyte	kegg	L2	hsa05016	Huntington disease	1.97e-06	1.99e-31
CD14+ Monocyte	kegg	L2	hsa04714	Thermogenesis	2.64e-08	1.86e-31
CD14+ Monocyte	kegg	L2	hsa05010	Alzheimer disease	1.14e-08	1.2e-26
CD14+ Monocyte	kegg	L2	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	4.24e-12	2.34e-18
CD14+ Monocyte	kegg	L2	hsa04723	Retrograde endocannabinoid signaling	3.46e-13	8.1e-14
CD14+ Monocyte	kegg	L2	hsa04640	Hematopoietic cell lineage	9.59e-14	8.77e-16
CD14+ Monocyte	kegg	L2	hsa04659	Th17 cell differentiation	5.98e-14	5.12e-17
CD14+ Monocyte	kegg	L2	hsa05152	Tuberculosis	5.56e-14	4.88e-20

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	3.11e-81
CD14+ Monocyte	reactome	L1	R-HSA-168249	Innate Immune System	4.65e-06	8.93e-111
CD14+ Monocyte	reactome	L1	R-HSA-168256	Immune System	9.77e-14	8.76e-160
CD14+ Monocyte	reactome	L1	R-HSA-449147	Signaling by Interleukins	3.46e-26	1.04e-36
CD14+ Monocyte	reactome	L1	R-HSA-109582	Hemostasis	2.09e-26	1.61e-39
CD14+ Monocyte	reactome	L1	R-HSA-76002	Platelet activation, signaling and aggregation	1.47e-26	4.48e-25
CD14+ Monocyte	reactome	L1	R-HSA-1280215	Cytokine Signaling in Immune system	1.17e-26	1.93e-46
CD14+ Monocyte	reactome	L1	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	1e-26	1.99e-16
CD14+ Monocyte	reactome	L1	R-HSA-5663205	Infectious disease	8.41e-27	4.06e-48
CD14+ Monocyte	reactome	L1	R-HSA-8953897	Cellular responses to external stimuli	6.25e-27	2.42e-32
CD14+ Monocyte	reactome	L2	R-HSA-72766	Translation	1	5.17e-59
CD14+ Monocyte	reactome	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	1.51e-13	1.05e-40
CD14+ Monocyte	reactome	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	3.15e-14	1.48e-39
CD14+ Monocyte	reactome	L2	R-HSA-72613	Eukaryotic Translation Initiation	3.21e-15	3.57e-38
CD14+ Monocyte	reactome	L2	R-HSA-72737	Cap-dependent Translation Initiation	3.21e-15	3.57e-38
CD14+ Monocyte	reactome	L2	R-HSA-72689	Formation of a pool of free 40S subunits	6.26e-16	1.98e-36
CD14+ Monocyte	reactome	L2	R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	3.36e-16	1.21e-36
CD14+ Monocyte	reactome	L2	R-HSA-156842	Eukaryotic Translation Elongation	2.2e-17	3.46e-34
CD14+ Monocyte	reactome	L2	R-HSA-2408522	Selenoamino acid metabolism	4.76e-18	3.97e-33
CD14+ Monocyte	reactome	L2	R-HSA-156902	Peptide chain elongation	4.19e-18	6.69e-33
CD14+ Monocyte	reactome	L3	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	1	1.29e-30
CD14+ Monocyte	reactome	L3	R-HSA-611105	Respiratory electron transport	0.000365	2.56e-24
CD14+ Monocyte	reactome	L3	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	2.39e-05	2.02e-28
CD14+ Monocyte	reactome	L3	R-HSA-6799198	Complex I biogenesis	2.81e-10	7.22e-13
CD14+ Monocyte	reactome	L3	R-HSA-8949613	Cristae formation	4.75e-11	3.54e-11
CD14+ Monocyte	reactome	L3	R-HSA-163210	Formation of ATP by chemiosmotic coupling	1.31e-11	1.25e-08
CD14+ Monocyte	reactome	L3	R-HSA-1592230	Mitochondrial biogenesis	3.27e-12	1.76e-14
CD14+ Monocyte	reactome	L3	R-HSA-1430728	Metabolism	1.04e-12	8.22e-117
CD14+ Monocyte	reactome	L3	R-HSA-202433	Generation of second messenger molecules	2.29e-13	1.53e-09
CD14+ Monocyte	reactome	L3	R-HSA-2871809	FCERI mediated Ca+2 mobilization	2e-13	1.32e-09
CD14+ Monocyte	reactome	L5	R-HSA-72172	mRNA Splicing	0.675	2.54e-25
CD14+ Monocyte	reactome	L5	R-HSA-72163	mRNA Splicing - Major Pathway	0.306	3.29e-24
CD14+ Monocyte	reactome	L5	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	0.018	2.1e-25
CD14+ Monocyte	reactome	L5	R-HSA-109688	Cleavage of Growing Transcript in the Termination Region	3.96e-05	3.41e-10
CD14+ Monocyte	reactome	L5	R-HSA-73856	RNA Polymerase II Transcription Termination	3.96e-05	3.41e-10
CD14+ Monocyte	reactome	L5	R-HSA-72187	mRNA 3’-end processing	3.31e-05	1.7e-09
CD14+ Monocyte	reactome	L5	R-HSA-5663205	Infectious disease	2.31e-05	4.06e-48
CD14+ Monocyte	reactome	L5	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	2.27e-05	1.99e-16
CD14+ Monocyte	reactome	L5	R-HSA-202433	Generation of second messenger molecules	1.91e-05	1.53e-09
CD14+ Monocyte	reactome	L5	R-HSA-2871809	FCERI mediated Ca+2 mobilization	1.78e-05	1.32e-09
CD14+ Monocyte	reactome	L6	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	0.997	5.1e-21
CD14+ Monocyte	reactome	L6	R-HSA-168256	Immune System	0.00054	8.76e-160
CD14+ Monocyte	reactome	L6	R-HSA-1280218	Adaptive Immune System	0.000359	1.66e-53
CD14+ Monocyte	reactome	L6	R-HSA-202433	Generation of second messenger molecules	0.000136	1.53e-09
CD14+ Monocyte	reactome	L6	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	5.37e-05	1.99e-16
CD14+ Monocyte	reactome	L6	R-HSA-2871809	FCERI mediated Ca+2 mobilization	3.47e-05	1.32e-09
CD14+ Monocyte	reactome	L6	R-HSA-6782315	tRNA modification in the nucleus and cytosol	2.24e-05	0.891
CD14+ Monocyte	reactome	L6	R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers	2.23e-05	7.73e-09
CD14+ Monocyte	reactome	L6	R-HSA-3299685	Detoxification of Reactive Oxygen Species	2.2e-05	3.81e-09
CD14+ Monocyte	reactome	L6	R-HSA-8856825	Cargo recognition for clathrin-mediated endocytosis	2.13e-05	2.5e-12
CD14+ Monocyte	reactome	L7	R-HSA-379726	Mitochondrial tRNA aminoacylation	0.997	0.693
CD14+ Monocyte	reactome	L7	R-HSA-202433	Generation of second messenger molecules	7.9e-05	1.53e-09
CD14+ Monocyte	reactome	L7	R-HSA-379724	tRNA Aminoacylation	7.71e-05	0.000221
CD14+ Monocyte	reactome	L7	R-HSA-2871809	FCERI mediated Ca+2 mobilization	6.76e-05	1.32e-09
CD14+ Monocyte	reactome	L7	R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	5.07e-05	1.99e-16
CD14+ Monocyte	reactome	L7	R-HSA-3299685	Detoxification of Reactive Oxygen Species	4.37e-05	3.81e-09
CD14+ Monocyte	reactome	L7	R-HSA-877312	Regulation of IFNG signaling	4e-05	7.16e-07
CD14+ Monocyte	reactome	L7	R-HSA-6782315	tRNA modification in the nucleus and cytosol	3.99e-05	0.891
CD14+ Monocyte	reactome	L7	R-HSA-1433557	Signaling by SCF-KIT	2.81e-05	7.59e-10
CD14+ Monocyte	reactome	L7	R-HSA-5578775	Ion homeostasis	2.81e-05	3.29e-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:

celltype	db	component	geneSet	description	alpha	pValueHypergeometric
CD14+ Monocyte	wikipathway	L1	WP477	Cytoplasmic Ribosomal Proteins	1	1.21e-29
CD14+ Monocyte	wikipathway	L1	WP3945	TYROBP Causal Network	7.93e-17	5.9e-14
CD14+ Monocyte	wikipathway	L1	WP2805	exRNA mechanism of action and biogenesis	6.57e-17	1
CD14+ Monocyte	wikipathway	L1	WP619	Type II interferon signaling (IFNG)	5.36e-17	4.08e-09
CD14+ Monocyte	wikipathway	L1	WP4304	Oligodendrocyte Specification and differentiation(including remyelination), leading to Myelin Components for CNS	3.06e-17	0.911
CD14+ Monocyte	wikipathway	L1	WP2328	Allograft Rejection	2.92e-17	2.7e-12
CD14+ Monocyte	wikipathway	L1	WP3888	VEGFA-VEGFR2 Signaling Pathway	2.48e-17	6.32e-35
CD14+ Monocyte	wikipathway	L1	WP411	mRNA Processing	2.3e-17	2.78e-17
CD14+ Monocyte	wikipathway	L1	WP4204	Tumor suppressor activity of SMARCB1	2.17e-17	2.47e-07
CD14+ Monocyte	wikipathway	L1	WP3931	ESC Pluripotency Pathways	2.07e-17	0.273
CD14+ Monocyte	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	1	9.06e-28
CD14+ Monocyte	wikipathway	L2	WP623	Oxidative phosphorylation	0.00017	1.42e-19
CD14+ Monocyte	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	2.87e-09	1.53e-12
CD14+ Monocyte	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	2.81e-10	9.27e-18
CD14+ Monocyte	wikipathway	L2	WP3945	TYROBP Causal Network	4.08e-11	5.9e-14
CD14+ Monocyte	wikipathway	L2	WP619	Type II interferon signaling (IFNG)	3.57e-11	4.08e-09
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	2.7e-12
CD14+ Monocyte	wikipathway	L2	WP4304	Oligodendrocyte Specification and differentiation(including remyelination), leading to Myelin Components for CNS	1.94e-11	0.911
CD14+ Monocyte	wikipathway	L2	WP411	mRNA Processing	1.66e-11	2.78e-17

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	2.63e-189
CD34+	gobp	L1	GO:0045321	leukocyte activation	0.013	3.97e-173
CD34+	gobp	L1	GO:0002376	immune system process	2.22e-08	8.2e-308
CD34+	gobp	L1	GO:0002443	leukocyte mediated immunity	3.37e-11	5.91e-114
CD34+	gobp	L1	GO:0006955	immune response	3.15e-11	7.56e-218
CD34+	gobp	L1	GO:0002366	leukocyte activation involved in immune response	2.18e-11	8.13e-107
CD34+	gobp	L1	GO:0002263	cell activation involved in immune response	1.72e-11	6.65e-107
CD34+	gobp	L1	GO:0046649	lymphocyte activation	6.57e-13	1.91e-98
CD34+	gobp	L1	GO:0002252	immune effector process	1.19e-13	2.02e-145
CD34+	gobp	L1	GO:0043299	leukocyte degranulation	2.36e-14	9.84e-85
CD34+	gobp	L2	GO:0006613	cotranslational protein targeting to membrane	0.813	7.18e-30
CD34+	gobp	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.152	2.12e-28
CD34+	gobp	L2	GO:0045047	protein targeting to ER	0.0274	4.08e-30
CD34+	gobp	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	0.00688	6.23e-30
CD34+	gobp	L2	GO:0070972	protein localization to endoplasmic reticulum	2.82e-06	2.47e-29
CD34+	gobp	L2	GO:0006413	translational initiation	4.51e-07	5.03e-39
CD34+	gobp	L2	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1.09e-07	2.52e-25
CD34+	gobp	L2	GO:0006612	protein targeting to membrane	3.21e-09	2.61e-30
CD34+	gobp	L2	GO:0043043	peptide biosynthetic process	3.02e-10	3.37e-78
CD34+	gobp	L2	GO:0006412	translation	1.89e-10	4e-75
CD34+	gobp	L3	GO:0006119	oxidative phosphorylation	0.999	4.56e-31
CD34+	gobp	L3	GO:0042773	ATP synthesis coupled electron transport	0.000526	6.68e-22
CD34+	gobp	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.000367	1.5e-21
CD34+	gobp	L3	GO:0046034	ATP metabolic process	8.31e-05	4.95e-41
CD34+	gobp	L3	GO:0022904	respiratory electron transport chain	3.74e-05	2.46e-22
CD34+	gobp	L3	GO:0009123	nucleoside monophosphate metabolic process	8.85e-06	4.08e-47
CD34+	gobp	L3	GO:0009126	purine nucleoside monophosphate metabolic process	7.62e-06	2.32e-43
CD34+	gobp	L3	GO:0009167	purine ribonucleoside monophosphate metabolic process	7.62e-06	2.32e-43
CD34+	gobp	L3	GO:0009161	ribonucleoside monophosphate metabolic process	6.53e-06	1.45e-44
CD34+	gobp	L3	GO:0009199	ribonucleoside triphosphate metabolic process	4.25e-06	1.61e-42
CD34+	gobp	L4	GO:0044419	interspecies interaction between organisms	0.42	2.03e-99
CD34+	gobp	L4	GO:0016032	viral process	0.383	3.87e-91
CD34+	gobp	L4	GO:0044403	symbiont process	0.194	3.24e-95
CD34+	gobp	L4	GO:0070887	cellular response to chemical stimulus	0.000206	4.8e-265
CD34+	gobp	L4	GO:0051716	cellular response to stimulus	0.000151	0
CD34+	gobp	L4	GO:0043933	protein-containing complex subunit organization	9.07e-05	5.77e-201
CD34+	gobp	L4	GO:0032984	protein-containing complex disassembly	9.03e-05	2.49e-41
CD34+	gobp	L4	GO:0010033	response to organic substance	8.85e-05	5.22e-265
CD34+	gobp	L4	GO:0019058	viral life cycle	7.06e-05	3.9e-38
CD34+	gobp	L4	GO:0002376	immune system process	6.4e-05	8.2e-308

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	1.59e-76
CD34+	gobp_nr	L1	GO:0036230	granulocyte activation	0.393	1.32e-76
CD34+	gobp_nr	L1	GO:0009123	nucleoside monophosphate metabolic process	2.7e-09	2.05e-46
CD34+	gobp_nr	L1	GO:0052547	regulation of peptidase activity	2.15e-09	8.57e-45
CD34+	gobp_nr	L1	GO:0006091	generation of precursor metabolites and energy	1.38e-09	1.05e-55
CD34+	gobp_nr	L1	GO:0006457	protein folding	1.34e-09	2.08e-29
CD34+	gobp_nr	L1	GO:0019058	viral life cycle	1.14e-09	1.53e-37
CD34+	gobp_nr	L1	GO:0006338	chromatin remodeling	1.04e-09	2.63e-24
CD34+	gobp_nr	L1	GO:0032984	protein-containing complex disassembly	8.68e-10	1.16e-40
CD34+	gobp_nr	L1	GO:0009141	nucleoside triphosphate metabolic process	7.22e-10	5.76e-42
CD34+	gobp_nr	L2	GO:0006413	translational initiation	1	1.65e-38
CD34+	gobp_nr	L2	GO:0070972	protein localization to endoplasmic reticulum	0.000335	5.99e-29
CD34+	gobp_nr	L2	GO:0090150	establishment of protein localization to membrane	7.81e-07	2.76e-41
CD34+	gobp_nr	L2	GO:0006401	RNA catabolic process	4.43e-07	3.94e-42
CD34+	gobp_nr	L2	GO:0006338	chromatin remodeling	1.31e-07	2.63e-24
CD34+	gobp_nr	L2	GO:0009123	nucleoside monophosphate metabolic process	1.16e-07	2.05e-46
CD34+	gobp_nr	L2	GO:0032984	protein-containing complex disassembly	1.08e-07	1.16e-40
CD34+	gobp_nr	L2	GO:0006605	protein targeting	9.03e-08	3.22e-47
CD34+	gobp_nr	L2	GO:0010257	NADH dehydrogenase complex assembly	8.33e-08	1.83e-15
CD34+	gobp_nr	L2	GO:0052547	regulation of peptidase activity	7.68e-08	8.57e-45

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	4.13e-42
CD34+	gomf	L1	GO:0003723	RNA binding	4.15e-12	4.44e-179
CD34+	gomf	L1	GO:0005198	structural molecule activity	8.87e-15	5.62e-62
CD34+	gomf	L1	GO:0052744	phosphatidylinositol monophosphate phosphatase activity	6.94e-15	0.977
CD34+	gomf	L1	GO:0004438	phosphatidylinositol-3-phosphatase activity	3.07e-15	0.965
CD34+	gomf	L1	GO:0052629	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity	1.71e-15	0.973
CD34+	gomf	L1	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	1.65e-15	1.11e-16
CD34+	gomf	L1	GO:0008137	NADH dehydrogenase (ubiquinone) activity	1.52e-15	6.24e-15
CD34+	gomf	L1	GO:0050136	NADH dehydrogenase (quinone) activity	1.52e-15	6.24e-15
CD34+	gomf	L1	GO:0043812	phosphatidylinositol-4-phosphate phosphatase activity	7.83e-16	1
CD34+	gomf	L2	GO:0005515	protein binding	1	0
CD34+	gomf	L2	GO:0005488	binding	3.49e-13	0
CD34+	gomf	L2	GO:0003674	molecular_function	3.67e-15	0
CD34+	gomf	L2	GO:0019899	enzyme binding	1.55e-31	1.28e-207
CD34+	gomf	L2	GO:0003824	catalytic activity	9.91e-37	0
CD34+	gomf	L2	GO:0003723	RNA binding	7.77e-38	4.44e-179
CD34+	gomf	L2	GO:0042802	identical protein binding	1.72e-39	2.63e-134
CD34+	gomf	L2	GO:0044877	protein-containing complex binding	7.71e-41	7.68e-100
CD34+	gomf	L2	GO:0097159	organic cyclic compound binding	1.83e-41	0
CD34+	gomf	L2	GO:1901363	heterocyclic compound binding	5.95e-42	0

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	4.89e-32
CD34+	kegg	L1	hsa05012	Parkinson disease	0.00739	6.35e-33
CD34+	kegg	L1	hsa05010	Alzheimer disease	0.000527	8e-37
CD34+	kegg	L1	hsa05016	Huntington disease	2.37e-06	1.2e-32
CD34+	kegg	L1	hsa04714	Thermogenesis	1.19e-06	7.54e-36
CD34+	kegg	L1	hsa04932	Non-alcoholic fatty liver disease (NAFLD)	3.53e-08	2.53e-24
CD34+	kegg	L1	hsa04723	Retrograde endocannabinoid signaling	5.87e-09	4.75e-19
CD34+	kegg	L1	hsa04260	Cardiac muscle contraction	2.18e-09	7.21e-12
CD34+	kegg	L1	hsa05130	Pathogenic Escherichia coli infection	1.36e-09	1.67e-13
CD34+	kegg	L1	hsa04640	Hematopoietic cell lineage	1.23e-09	2.31e-18
CD34+	kegg	L2	hsa03010	Ribosome	1	5.68e-34
CD34+	kegg	L2	hsa05130	Pathogenic Escherichia coli infection	2.32e-10	1.67e-13
CD34+	kegg	L2	hsa04640	Hematopoietic cell lineage	2.11e-10	2.31e-18
CD34+	kegg	L2	hsa04720	Long-term potentiation	2.08e-10	3.3e-14
CD34+	kegg	L2	hsa04512	ECM-receptor interaction	1.56e-10	0.0742
CD34+	kegg	L2	hsa00780	Biotin metabolism	1.25e-10	1
CD34+	kegg	L2	hsa00430	Taurine and hypotaurine metabolism	1.08e-10	0.934
CD34+	kegg	L2	hsa00790	Folate biosynthesis	1.03e-10	0.476
CD34+	kegg	L2	hsa04670	Leukocyte transendothelial migration	9.03e-11	1.11e-17
CD34+	kegg	L2	hsa00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	7.9e-11	0.356

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	2.28e-33
CD34+	reactome	L1	R-HSA-156902	Peptide chain elongation	0.00453	7.76e-32
CD34+	reactome	L1	R-HSA-156842	Eukaryotic Translation Elongation	0.00214	5.5e-33
CD34+	reactome	L1	R-HSA-192823	Viral mRNA Translation	0.000224	4.8e-30
CD34+	reactome	L1	R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	6.05e-05	1.13e-30
CD34+	reactome	L1	R-HSA-72689	Formation of a pool of free 40S subunits	3.12e-06	6.37e-33
CD34+	reactome	L1	R-HSA-2408557	Selenocysteine synthesis	3.49e-07	1.99e-28
CD34+	reactome	L1	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	2.51e-07	1.79e-35
CD34+	reactome	L1	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	2.39e-07	4.23e-35
CD34+	reactome	L1	R-HSA-72613	Eukaryotic Translation Initiation	4.7e-10	8.82e-34
CD34+	reactome	L2	R-HSA-6798695	Neutrophil degranulation	0.986	1.52e-75
CD34+	reactome	L2	R-HSA-168249	Innate Immune System	0.0137	6.47e-123
CD34+	reactome	L2	R-HSA-168256	Immune System	1.27e-05	8.36e-210
CD34+	reactome	L2	R-HSA-109582	Hemostasis	9.23e-10	1.39e-62
CD34+	reactome	L2	R-HSA-5357801	Programmed Cell Death	1.96e-10	1.09e-26
CD34+	reactome	L2	R-HSA-76002	Platelet activation, signaling and aggregation	1.46e-10	1.02e-31
CD34+	reactome	L2	R-HSA-109581	Apoptosis	1.33e-10	8.98e-26
CD34+	reactome	L2	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	1.28e-10	7.78e-20
CD34+	reactome	L2	R-HSA-381676	Glucagon-like Peptide-1 (GLP1) regulates insulin secretion	1.23e-10	1.68e-11
CD34+	reactome	L2	R-HSA-3781865	Diseases of glycosylation	9.01e-11	0.0404
CD34+	reactome	L3	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	0.998	8.43e-32
CD34+	reactome	L3	R-HSA-611105	Respiratory electron transport	0.0022	2.83e-25
CD34+	reactome	L3	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	7.2e-05	3.97e-32
CD34+	reactome	L3	R-HSA-6799198	Complex I biogenesis	2.49e-07	1.44e-14
CD34+	reactome	L3	R-HSA-163210	Formation of ATP by chemiosmotic coupling	2.56e-09	1.2e-07
CD34+	reactome	L3	R-HSA-2453902	The canonical retinoid cycle in rods (twilight vision)	1.04e-09	0.975
CD34+	reactome	L3	R-HSA-3781865	Diseases of glycosylation	5.12e-10	0.0404
CD34+	reactome	L3	R-HSA-381676	Glucagon-like Peptide-1 (GLP1) regulates insulin secretion	4.54e-10	1.68e-11
CD34+	reactome	L3	R-HSA-2214320	Anchoring fibril formation	4.34e-10	0.976
CD34+	reactome	L3	R-HSA-8949613	Cristae formation	3.57e-10	1.66e-08
CD34+	reactome	L4	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	1	1.15e-26
CD34+	reactome	L4	R-HSA-2453902	The canonical retinoid cycle in rods (twilight vision)	1.62e-06	0.975
CD34+	reactome	L4	R-HSA-3781865	Diseases of glycosylation	9.02e-07	0.0404
CD34+	reactome	L4	R-HSA-168256	Immune System	8.13e-07	8.36e-210
CD34+	reactome	L4	R-HSA-381676	Glucagon-like Peptide-1 (GLP1) regulates insulin secretion	7.71e-07	1.68e-11
CD34+	reactome	L4	R-HSA-109582	Hemostasis	7.47e-07	1.39e-62
CD34+	reactome	L4	R-HSA-2214320	Anchoring fibril formation	4.09e-07	0.976
CD34+	reactome	L4	R-HSA-211935	Fatty acids	4.02e-07	0.976
CD34+	reactome	L4	R-HSA-8862803	Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models	3.78e-07	8.38e-09
CD34+	reactome	L4	R-HSA-8863678	Neurodegenerative Diseases	3.78e-07	8.38e-09

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	1.33e-30
CD34+	wikipathway	L1	WP4661	Amino Acid Metabolism Pathway Excerpt (Histidine catabolism extension)	1.4e-20	1
CD34+	wikipathway	L1	WP4545	Oxysterols derived from cholesterol	2.34e-21	0.778
CD34+	wikipathway	L1	WP3945	TYROBP Causal Network	1.95e-21	2.01e-15
CD34+	wikipathway	L1	WP2272	Pathogenic Escherichia coli infection	1.57e-21	2.45e-13
CD34+	wikipathway	L1	WP400	p38 MAPK Signaling Pathway	1.13e-21	0.232
CD34+	wikipathway	L1	WP229	Irinotecan Pathway	9.94e-22	0.87
CD34+	wikipathway	L1	WP2645	Heroin metabolism	7.31e-22	1
CD34+	wikipathway	L1	WP2826	Cocaine metabolism	7.31e-22	1
CD34+	wikipathway	L1	WP43	Oxidation by Cytochrome P450	6.27e-22	0.263
CD34+	wikipathway	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	1	1.52e-31
CD34+	wikipathway	L2	WP623	Oxidative phosphorylation	2.91e-06	2.63e-21
CD34+	wikipathway	L2	WP4396	Nonalcoholic fatty liver disease	3.88e-12	2.78e-24
CD34+	wikipathway	L2	WP4324	Mitochondrial complex I assembly model OXPHOS system	1.21e-12	2.47e-12
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	0.778
CD34+	wikipathway	L2	WP2272	Pathogenic Escherichia coli infection	1.03e-13	2.45e-13
CD34+	wikipathway	L2	WP3945	TYROBP Causal Network	9.66e-14	2.01e-15
CD34+	wikipathway	L2	WP400	p38 MAPK Signaling Pathway	7.36e-14	0.232
CD34+	wikipathway	L2	WP229	Irinotecan Pathway	5.54e-14	0.87

Designing visualizations

There are a lot of facets of the enrichment results we might want to communicate.

Its common to plot against the proportion of the genes in the list, but this obscures the sensitivity of the analysis to gene set size. Recreating a standard enrichment plot.

ct = celltypes[1]
gs = 'gobp'

cs.summary %>%
  filter(celltype == ct, db == gs, active_cs, row_number() <= 10) %>%
  mutate(geneSet=factor(geneSet, levels=geneSet[order((propInList))])) %>%
  arrange(component, desc(propInList)) %>%
  ggplot(aes(x=propInList, y=geneSet, size=geneSetSize, color=-log10(pValueHypergeometric))) +
  geom_point() + facet_wrap(vars(component), scale='free_y', ncol = 1)

Version	Author	Date
e572f0a	karltayeb	2022-03-30

The strongest marginal enticements come from the largest gene sets. But SuSiE is able to prioritizing smaller gene sets. The right ones? Who knows.

cs.summary %>%
  ggplot(aes(x=-log10(pValueHypergeometric), y=geneSetSize)) +
  geom_point() + geom_smooth()

`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'

Warning: Removed 198 rows containing non-finite values (stat_smooth).

Version	Author	Date
e572f0a	karltayeb	2022-03-30

Here, for the gene sets assigned to SuSiE components, we plot the proportion of the gene set observed. The bubble size is given by the gene set size, and the color indicates alpha, the posterior probability that the gene set is selected by the component.

I’m surprised to see gene sets with large alpha, but only modest proportion

cs.summary %>%
  filter(celltype == ct, db == 'gobp', active_cs, row_number() <= 10) %>%
  mutate(geneSet=factor(geneSet, levels=geneSet[order((propInList))])) %>%
  arrange(component, desc(propInList)) %>%
  ggplot(aes(x=propInList, y=geneSet, color=alpha, size=geneSetSize)) +
  geom_point() + facet_wrap(vars(component), scale='free_y', ncol = 1)

Version	Author	Date
e572f0a	karltayeb	2022-03-30

cs.summary %>%
  filter(celltype == ct, db == 'gobp', active_cs, row_number() <= 10) %>%
  mutate(geneSet=factor(geneSet, levels=geneSet[order((propInList))])) %>%
  arrange(component, desc(propInList)) %>%
  ggplot(aes(x=propInList, y=geneSet, color=in_cs, size=geneSetSize)) +
  geom_point() + facet_wrap(vars(component), scale='free_y', ncol = 1)

Version	Author	Date
e572f0a	karltayeb	2022-03-30

Credible set distributions

cs.summary %>%
  group_by(celltype, db, component) %>%
  summarise(entropy = -sum(alpha * log(alpha)), n = n()) %>%
  ggplot(aes(x=entropy)) + geom_histogram() + labs(title='component entropy')

`summarise()` has grouped output by 'celltype', 'db'. You can override using
the `.groups` argument.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

cs.summary %>%
  filter(active_cs, in_cs) %>%
  group_by(celltype, db, component) %>%
  summarise( n = n()) %>%
  ggplot(aes(x=n)) + geom_histogram() + labs(title='95% Credible set size')

`summarise()` has grouped output by 'celltype', 'db'. You can override using
the `.groups` argument.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

knitr::knit_exit()

Single-cell PBMC Example

karltayeb

2022-03-16

Introduction

Setup

Load Gene Sets

Fitting and reporting helpers

Example usage

Fit PBMC data

Summary functions

Results

CD19+ B

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

CD56+ NK

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

T cell

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

CD14+ Monocyte

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

CD34+

gobp

gobp_nr

gomf

kegg

reactome

wikipathway_cancer

wikipathway

Designing visualizations

Credible set distributions