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Introduction

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

  1. If the resulting enrichment results look good/interpretable across multiple/concatenated gene sets
  2. Assess sensitivity to a range of p-value thresholds
  3. Evaluate the potential of the summary stat latent model
library(GSEABenchmarkeR)
library(EnrichmentBrowser)
library(tidyverse)
library(susieR)
library(DT)
library(kableExtra)

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

Setup

Load Gene Sets

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

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

genesets <- list(
  gobp=gobp,
  gobp_nr=gobp_nr,
  gomf=gomf,
  kegg=kegg,
  reactome=reactome,
  wikipathway_cancer=wikipathway_cancer,
  wikipathway=wikipathway
)
load('data/pbmc-purified/deseq2-pbmc-purified.RData')
par(mfrow=c(1,1))
deseq$`CD19+ B` %>% .$padj %>% hist(main='CD19+B p-values')
Loading required package: DESeq2

Version Author Date
a2bdb56 karltayeb 2022-03-29

Fitting and reporting helpers

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

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

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

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

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

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

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

  #' report top 50 elements in cs
  credible.set.summary <- t(res$fit$alpha) %>%
    data.frame() %>%
    rownames_to_column(var='geneSet') %>%
    rename_with(~str_replace(., 'X', 'L')) %>%
    rename(L1 = 2) %>%  # rename deals with L=1 case
    pivot_longer(starts_with('L'), names_to='component', values_to = 'alpha') %>%
    arrange(component, desc(alpha)) %>%
    dplyr::group_by(component) %>%
    filter(row_number() < 50) %>%
    mutate(alpha_rank = row_number(), cumalpha = c(0, head(cumsum(alpha), -1))) %>%
    mutate(in_cs = cumalpha < 0.95) %>%
    mutate(active_cs = component %in% names(res$fit$sets$cs)) %>%
    left_join(res$ora) %>%
    left_join(gs$geneSet$geneSetDes)

  return(credible.set.summary)
}

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

Example usage

db = 'gobp_nr'
celltype = 'CD19+ B'
thresh = 1e-4
res <- do_logistic_susie(db, celltype, thresh, susie.args=list(L=1, standardize=TRUE, verbose=TRUE))
'select()' returned 1:many mapping between keys and columns

converged
Joining, by = "geneSet"
get_credible_set_summary(res) %>% filter(active_cs, in_cs)
Joining, by = "geneSet"
Joining, by = c("geneSet", "description")
# A tibble: 2 × 19
# Groups:   component [1]
  geneSet    component alpha alpha_rank cumalpha in_cs active_cs geneListSize
  <chr>      <chr>     <dbl>      <int>    <dbl> <lgl> <lgl>            <int>
1 GO:0002446 L1        0.514          1    0     TRUE  TRUE              6327
2 GO:0036230 L1        0.486          2    0.514 TRUE  TRUE              6327
# … with 11 more variables: geneSetSize <dbl>, overlap <dbl>, nGenes <int>,
#   propInList <dbl>, propInSet <dbl>, oddsRatio <dbl>,
#   pValueHypergeometric <dbl>, db <chr>, celltype <chr>, thresh <dbl>,
#   description <chr>
get_gene_set_summary(res) %>% head()
Joining, by = "geneSet"
Joining, by = c("geneSet", "description")
# A tibble: 6 × 15
  geneSet      pip      beta geneListSize geneSetSize overlap nGenes propInList
  <chr>      <dbl>     <dbl>        <int>       <dbl>   <dbl>  <int>      <dbl>
1 GO:0000002     0 -8.04e-20         6327          28      11  10734    0.00174
2 GO:0000041     0 -7.36e-22         6327          82      47  10734    0.00743
3 GO:0000075     0 -8.87e-22         6327         205     118  10734    0.0187 
4 GO:0000209     0 -2.10e-19         6327         236     119  10734    0.0188 
5 GO:0000726     0 -5.87e-22         6327          80      46  10734    0.00727
6 GO:0000910     0  2.06e-20         6327         134      86  10734    0.0136 
# … with 7 more variables: propInSet <dbl>, oddsRatio <dbl>,
#   pValueHypergeometric <dbl>, db <chr>, celltype <chr>, thresh <dbl>,
#   description <chr>

Fit PBMC data

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

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

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

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

susie.args = list(L=10, standardize=F, verbose=T)
res.l10 = run_logistic_susie(susie.args)
# L =1
susie.args = list(L=1, standardize=F, verbose=T)
res.l1 = run_logistic_susie(susie.args)


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


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

Summary functions

Just a few functions to help streamline looking at output

library(kableExtra)

#' takes a tibble
#' organize by database and component
#' report credible set, descriptions, pips, and hypergeometric pvalue
#' in one row, with cs ordered by pip
make_susie_component_kable = function(tbl, min_alpha=0, max_sets=10){
  tbl_filtered <-
    tbl %>%
    group_by(celltype, db, component) %>%
    arrange(celltype, db, component, desc(alpha)) %>%
    filter(alpha > min_alpha, row_number() <= max_sets)
  tbl_filtered %>%
    select(geneSet, description, alpha, pValueHypergeometric) %>%
    dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
    kbl() %>%
    column_spec(c(4, 5, 6), color=ifelse(tbl_filtered$in_cs, 'green', 'red')) %>%
    collapse_rows(columns = c(1, 2), valign = 'top') %>%
    kableExtra::kable_styling()
}

make_pval_sorted_kable = function(tbl, max_sets=1000){
  tbl_filtered <-
    tbl %>%
    group_by(celltype, db) %>%
    arrange(celltype, db, pValueHypergeometric) %>%
    filter(row_number() <= max_sets)
  
  tbl_filtered %>%
    select(geneSet, description, pip, pValueHypergeometric) %>%
    dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
    kbl() %>%
    column_spec(c(4, 5, 6), color=ifelse(tbl_filtered$in_cs, 'green', 'red')) %>%
    collapse_rows(columns = c(1, 2), valign = 'top') %>%
    kableExtra::kable_styling()
}

Results

A pip centerd view

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

  • Which gene sets would you pick out?
  • How far down would you scroll (e.g what cutoff would you pick)?
  • Would you percieve gene sets high and low in the list as related to one another?
in_cs <- res.l10$cs.summary %>%
  filter(in_cs, active_cs, celltype == 'CD19+ B', db == 'gobp') %>%
  ungroup() %>%
  select(geneSet, celltype, db, in_cs) %>%
  distinct()

res.l10$geneset.summary %>%
  filter(celltype == 'CD19+ B', db == 'gobp') %>%
  left_join(in_cs) %>%
  mutate(in_cs = ifelse(is.na(in_cs), F, T)) %>%
  make_pval_sorted_kable(max_sets = 500)
Joining, by = c("geneSet", "db", "celltype")
Adding missing grouping variables: `celltype`, `db`
`mutate_if()` ignored the following grouping variables:
Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas: 

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

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

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
celltype db geneSet description pip pValueHypergeometric
CD19+ B gobp GO:0002376 immune system process 1 3e-47
CD19+ B gobp GO:0006955 immune response 0.000507 2.03e-42
CD19+ B gobp GO:0001775 cell activation 0.978 1.1e-39
CD19+ B gobp GO:0045321 leukocyte activation 0.0219 1.65e-37
CD19+ B gobp GO:0002252 immune effector process 0.000371 2.96e-31
CD19+ B gobp GO:0002366 leukocyte activation involved in immune response 0.000596 1.23e-26
CD19+ B gobp GO:0002263 cell activation involved in immune response 0.000577 1.26e-26
CD19+ B gobp GO:0002443 leukocyte mediated immunity 0.000344 2.6e-24
CD19+ B gobp GO:0002682 regulation of immune system process 0.000236 7.75e-24
CD19+ B gobp GO:0002274 myeloid leukocyte activation 0.000439 1.15e-23
CD19+ B gobp GO:0050896 response to stimulus 0.00652 3.42e-22
CD19+ B gobp GO:0002444 myeloid leukocyte mediated immunity 0.000582 5.18e-22
CD19+ B gobp GO:0050776 regulation of immune response 0.000818 6.58e-22
CD19+ B gobp GO:0002684 positive regulation of immune system process 0.000444 8.51e-22
CD19+ B gobp GO:0002275 myeloid cell activation involved in immune response 0.00049 3.45e-21
CD19+ B gobp GO:0042119 neutrophil activation 0.000625 6.72e-21
CD19+ B gobp GO:0043299 leukocyte degranulation 0.000491 8.57e-21
CD19+ B gobp GO:0002446 neutrophil mediated immunity 0.000621 9.61e-21
CD19+ B gobp GO:0036230 granulocyte activation 0.000576 9.9e-21
CD19+ B gobp GO:0045055 regulated exocytosis 0.00139 1.45e-20
CD19+ B gobp GO:0002283 neutrophil activation involved in immune response 0.000592 2.38e-20
CD19+ B gobp GO:0043312 neutrophil degranulation 0.000557 6.27e-20
CD19+ B gobp GO:0046649 lymphocyte activation 0.000337 7.91e-20
CD19+ B gobp GO:0034097 response to cytokine 0.0502 4.54e-18
CD19+ B gobp GO:0045047 protein targeting to ER 0.962 8.24e-18
CD19+ B gobp GO:0050778 positive regulation of immune response 0.000754 1.01e-17
CD19+ B gobp GO:0071345 cellular response to cytokine stimulus 0.0562 1.62e-17
CD19+ B gobp GO:0006613 cotranslational protein targeting to membrane 0.0217 3.93e-17
CD19+ B gobp GO:0006950 response to stress 0.00331 1.01e-16
CD19+ B gobp GO:0072599 establishment of protein localization to endoplasmic reticulum 0.0145 1.96e-16
CD19+ B gobp GO:0006887 exocytosis 0.000574 2.73e-16
CD19+ B gobp GO:0006614 SRP-dependent cotranslational protein targeting to membrane 0.0041 3.03e-16
CD19+ B gobp GO:0048534 hematopoietic or lymphoid organ development 0.000309 3.79e-16
CD19+ B gobp GO:0002520 immune system development 0.00029 7.75e-16
CD19+ B gobp GO:0030097 hemopoiesis 0.000306 2.93e-15
CD19+ B gobp GO:0019221 cytokine-mediated signaling pathway 0.029 2.97e-15
CD19+ B gobp GO:0070887 cellular response to chemical stimulus 0.0146 4.74e-15
CD19+ B gobp GO:0006952 defense response 0.000248 1.12e-14
CD19+ B gobp GO:0010033 response to organic substance 0.00577 2.58e-14
CD19+ B gobp GO:0030098 lymphocyte differentiation 0.000689 2.78e-14
CD19+ B gobp GO:0032940 secretion by cell 0.000291 3.78e-14
CD19+ B gobp GO:0070972 protein localization to endoplasmic reticulum 0.000677 7.22e-14
CD19+ B gobp GO:0045087 innate immune response 0.000448 7.95e-14
CD19+ B gobp GO:0002764 immune response-regulating signaling pathway 0.00109 1.14e-13
CD19+ B gobp GO:0051716 cellular response to stimulus 0.00726 1.39e-13
CD19+ B gobp GO:0016192 vesicle-mediated transport 0.00136 1.72e-13
CD19+ B gobp GO:0002253 activation of immune response 0.000856 2.13e-13
CD19+ B gobp GO:0071310 cellular response to organic substance 0.00696 2.19e-13
CD19+ B gobp GO:0050865 regulation of cell activation 0.000472 3.33e-13
CD19+ B gobp GO:0002757 immune response-activating signal transduction 0.00105 6.88e-13
CD19+ B gobp GO:0002694 regulation of leukocyte activation 0.000487 7.35e-13
CD19+ B gobp GO:0002521 leukocyte differentiation 0.000382 9.1e-13
CD19+ B gobp GO:0007154 cell communication 0.00555 9.47e-13
CD19+ B gobp GO:0001816 cytokine production 0.000916 9.98e-13
CD19+ B gobp GO:0006413 translational initiation 0.00629 1.01e-12
CD19+ B gobp GO:0007165 signal transduction 0.0042 1.03e-12
CD19+ B gobp GO:0048583 regulation of response to stimulus 0.000746 1.77e-12
CD19+ B gobp GO:0051234 establishment of localization 0.00051 1.98e-12
CD19+ B gobp GO:0046903 secretion 0.000238 2.18e-12
CD19+ B gobp GO:0023052 signaling 0.00416 2.88e-12
CD19+ B gobp GO:0042110 T cell activation 0.000502 4.2e-12
CD19+ B gobp GO:0006810 transport 0.000391 4.96e-12
CD19+ B gobp GO:0042221 response to chemical 0.00115 5.23e-12
CD19+ B gobp GO:0006119 oxidative phosphorylation 0.0175 5.6e-12
CD19+ B gobp GO:0042773 ATP synthesis coupled electron transport 0.624 6.5e-12
CD19+ B gobp GO:0048518 positive regulation of biological process 0.00135 8.63e-12
CD19+ B gobp GO:0002250 adaptive immune response 0.000594 8.74e-12
CD19+ B gobp GO:0051179 localization 0.000372 9.85e-12
CD19+ B gobp GO:0042775 mitochondrial ATP synthesis coupled electron transport 0.36 1.04e-11
CD19+ B gobp GO:0008219 cell death 0.0252 1.25e-11
CD19+ B gobp GO:1901564 organonitrogen compound metabolic process 0.00734 1.55e-11
CD19+ B gobp GO:0002768 immune response-regulating cell surface receptor signaling pathway 0.00153 1.6e-11
CD19+ B gobp GO:0048584 positive regulation of response to stimulus 0.000282 2.58e-11
CD19+ B gobp GO:0006915 apoptotic process 0.0223 3.35e-11
CD19+ B gobp GO:0012501 programmed cell death 0.0203 4.03e-11
CD19+ B gobp GO:0001817 regulation of cytokine production 0.000708 4.39e-11
CD19+ B gobp GO:0070661 leukocyte proliferation 0.000611 5.52e-11
CD19+ B gobp GO:0046651 lymphocyte proliferation 0.000641 6.82e-11
CD19+ B gobp GO:0051249 regulation of lymphocyte activation 0.000542 7.72e-11
CD19+ B gobp GO:0032943 mononuclear cell proliferation 0.000616 9.76e-11
CD19+ B gobp GO:0009123 nucleoside monophosphate metabolic process 0.00835 1.21e-10
CD19+ B gobp GO:0050851 antigen receptor-mediated signaling pathway 0.0042 1.54e-10
CD19+ B gobp GO:0002696 positive regulation of leukocyte activation 0.000478 1.67e-10
CD19+ B gobp GO:0002429 immune response-activating cell surface receptor signaling pathway 0.00126 1.68e-10
CD19+ B gobp GO:0050867 positive regulation of cell activation 0.000465 2.23e-10
CD19+ B gobp GO:0042113 B cell activation 0.000678 2.91e-10
CD19+ B gobp GO:0009126 purine nucleoside monophosphate metabolic process 0.00285 4.03e-10
CD19+ B gobp GO:0009167 purine ribonucleoside monophosphate metabolic process 0.00285 4.03e-10
CD19+ B gobp GO:0046034 ATP metabolic process 0.0018 6.84e-10
CD19+ B gobp GO:0051251 positive regulation of lymphocyte activation 0.000515 7.02e-10
CD19+ B gobp GO:0043207 response to external biotic stimulus 0.000427 9.09e-10
CD19+ B gobp GO:0051707 response to other organism 0.000427 9.09e-10
CD19+ B gobp GO:0009161 ribonucleoside monophosphate metabolic process 0.00293 9.13e-10
CD19+ B gobp GO:0010941 regulation of cell death 0.00614 9.65e-10
CD19+ B gobp GO:1903039 positive regulation of leukocyte cell-cell adhesion 0.000731 1.24e-09
CD19+ B gobp GO:0043067 regulation of programmed cell death 0.007 1.35e-09
CD19+ B gobp GO:0048522 positive regulation of cellular process 0.000978 1.47e-09
CD19+ B gobp GO:0009607 response to biotic stimulus 0.000386 2.55e-09
CD19+ B gobp GO:0050870 positive regulation of T cell activation 0.000722 2.86e-09
CD19+ B gobp GO:0042981 regulation of apoptotic process 0.00528 3.01e-09
CD19+ B gobp GO:0006518 peptide metabolic process 0.0241 3.13e-09
CD19+ B gobp GO:1901701 cellular response to oxygen-containing compound 0.0143 3.23e-09
CD19+ B gobp GO:0044419 interspecies interaction between organisms 0.00762 3.33e-09
CD19+ B gobp GO:0007166 cell surface receptor signaling pathway 0.000288 3.79e-09
CD19+ B gobp GO:0009144 purine nucleoside triphosphate metabolic process 0.00184 3.79e-09
CD19+ B gobp GO:0007159 leukocyte cell-cell adhesion 0.000463 4.3e-09
CD19+ B gobp GO:0009205 purine ribonucleoside triphosphate metabolic process 0.00161 5.16e-09
CD19+ B gobp GO:0045785 positive regulation of cell adhesion 0.000689 5.21e-09
CD19+ B gobp GO:0097190 apoptotic signaling pathway 0.0562 7.22e-09
CD19+ B gobp GO:0009141 nucleoside triphosphate metabolic process 0.00205 7.32e-09
CD19+ B gobp GO:0006612 protein targeting to membrane 0.000585 8.51e-09
CD19+ B gobp GO:0017144 drug metabolic process 0.00858 8.56e-09
CD19+ B gobp GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 0.00069 9.05e-09
CD19+ B gobp GO:0022900 electron transport chain 0.00129 1.01e-08
CD19+ B gobp GO:0022904 respiratory electron transport chain 0.00081 1.04e-08
CD19+ B gobp GO:0051704 multi-organism process 0.000393 1.08e-08
CD19+ B gobp GO:0009199 ribonucleoside triphosphate metabolic process 0.00143 1.11e-08
CD19+ B gobp GO:1903706 regulation of hemopoiesis 0.000421 1.17e-08
CD19+ B gobp GO:0070665 positive regulation of leukocyte proliferation 0.00156 1.23e-08
CD19+ B gobp GO:0016032 viral process 0.0119 1.3e-08
CD19+ B gobp GO:0050863 regulation of T cell activation 0.000558 1.31e-08
CD19+ B gobp GO:0032946 positive regulation of mononuclear cell proliferation 0.0015 1.8e-08
CD19+ B gobp GO:0043604 amide biosynthetic process 0.0364 1.84e-08
CD19+ B gobp GO:1901700 response to oxygen-containing compound 0.00203 2.47e-08
CD19+ B gobp GO:0050671 positive regulation of lymphocyte proliferation 0.00143 2.62e-08
CD19+ B gobp GO:0043603 cellular amide metabolic process 0.0198 2.79e-08
CD19+ B gobp GO:0032944 regulation of mononuclear cell proliferation 0.000586 3.04e-08
CD19+ B gobp GO:0048870 cell motility 0.00127 3.05e-08
CD19+ B gobp GO:0051674 localization of cell 0.00127 3.05e-08
CD19+ B gobp GO:0070663 regulation of leukocyte proliferation 0.000574 3.09e-08
CD19+ B gobp GO:0022409 positive regulation of cell-cell adhesion 0.000578 3.22e-08
CD19+ B gobp GO:0046631 alpha-beta T cell activation 0.00105 3.73e-08
CD19+ B gobp GO:0016477 cell migration 0.000871 3.8e-08
CD19+ B gobp GO:0044403 symbiont process 0.00469 3.84e-08
CD19+ B gobp GO:0050670 regulation of lymphocyte proliferation 0.000581 4.13e-08
CD19+ B gobp GO:0001819 positive regulation of cytokine production 0.000474 4.2e-08
CD19+ B gobp GO:0080134 regulation of response to stress 0.000264 4.75e-08
CD19+ B gobp GO:0002683 negative regulation of immune system process 0.000418 5.04e-08
CD19+ B gobp GO:0048519 negative regulation of biological process 0.00031 5.36e-08
CD19+ B gobp GO:1903037 regulation of leukocyte cell-cell adhesion 0.000533 5.47e-08
CD19+ B gobp GO:0002697 regulation of immune effector process 0.000456 5.84e-08
CD19+ B gobp GO:0043043 peptide biosynthetic process 0.0116 6.59e-08
CD19+ B gobp GO:1902105 regulation of leukocyte differentiation 0.000518 6.84e-08
CD19+ B gobp GO:0035556 intracellular signal transduction 0.00113 7.58e-08
CD19+ B gobp GO:0045619 regulation of lymphocyte differentiation 0.00075 7.85e-08
CD19+ B gobp GO:0030155 regulation of cell adhesion 0.00035 9.37e-08
CD19+ B gobp GO:0030217 T cell differentiation 0.000528 9.82e-08
CD19+ B gobp GO:0051246 regulation of protein metabolic process 0.000903 9.89e-08
CD19+ B gobp GO:0022610 biological adhesion 0.000309 9.93e-08
CD19+ B gobp GO:0002285 lymphocyte activation involved in immune response 0.000671 1.18e-07
CD19+ B gobp GO:0001906 cell killing 0.00183 1.32e-07
CD19+ B gobp GO:0016071 mRNA metabolic process 0.00105 1.33e-07
CD19+ B gobp GO:0007155 cell adhesion 0.000298 1.54e-07
CD19+ B gobp GO:0006412 translation 0.00761 1.56e-07
CD19+ B gobp GO:0050853 B cell receptor signaling pathway 0.00518 1.65e-07
CD19+ B gobp GO:0002449 lymphocyte mediated immunity 0.00056 1.76e-07
CD19+ B gobp GO:0046632 alpha-beta T cell differentiation 0.00141 1.86e-07
CD19+ B gobp GO:1902107 positive regulation of leukocyte differentiation 0.00111 2.25e-07
CD19+ B gobp GO:0008283 cell proliferation 0.000391 2.25e-07
CD19+ B gobp GO:0031347 regulation of defense response 0.000395 2.51e-07
CD19+ B gobp GO:0045088 regulation of innate immune response 0.000458 3.01e-07
CD19+ B gobp GO:1903708 positive regulation of hemopoiesis 0.000865 3.28e-07
CD19+ B gobp GO:0022407 regulation of cell-cell adhesion 0.000483 3.35e-07
CD19+ B gobp GO:0006796 phosphate-containing compound metabolic process 0.000674 3.82e-07
CD19+ B gobp GO:0048872 homeostasis of number of cells 0.000687 3.92e-07
CD19+ B gobp GO:0031349 positive regulation of defense response 0.000422 4.25e-07
CD19+ B gobp GO:0045333 cellular respiration 0.000683 4.5e-07
CD19+ B gobp GO:0006793 phosphorus metabolic process 0.000666 4.96e-07
CD19+ B gobp GO:0030183 B cell differentiation 0.00109 5.02e-07
CD19+ B gobp GO:0010942 positive regulation of cell death 0.00373 5.78e-07
CD19+ B gobp GO:0002699 positive regulation of immune effector process 0.000568 5.84e-07
CD19+ B gobp GO:0090150 establishment of protein localization to membrane 0.000482 6.29e-07
CD19+ B gobp GO:0002576 platelet degranulation 0.0418 7.18e-07
CD19+ B gobp GO:0006091 generation of precursor metabolites and energy 0.00178 7.96e-07
CD19+ B gobp GO:0042100 B cell proliferation 0.0017 9.36e-07
CD19+ B gobp GO:0042102 positive regulation of T cell proliferation 0.0014 9.53e-07
CD19+ B gobp GO:1901566 organonitrogen compound biosynthetic process 0.00815 9.73e-07
CD19+ B gobp GO:0010605 negative regulation of macromolecule metabolic process 0.000607 1.37e-06
CD19+ B gobp GO:0009117 nucleotide metabolic process 0.00295 1.45e-06
CD19+ B gobp GO:0032268 regulation of cellular protein metabolic process 0.000617 1.51e-06
CD19+ B gobp GO:0001909 leukocyte mediated cytotoxicity 0.00155 1.51e-06
CD19+ B gobp GO:0072657 protein localization to membrane 0.000487 1.58e-06
CD19+ B gobp GO:0034655 nucleobase-containing compound catabolic process 0.000601 1.58e-06
CD19+ B gobp GO:0055086 nucleobase-containing small molecule metabolic process 0.00385 1.61e-06
CD19+ B gobp GO:0044270 cellular nitrogen compound catabolic process 0.000659 1.84e-06
CD19+ B gobp GO:0002286 T cell activation involved in immune response 0.00116 1.92e-06
CD19+ B gobp GO:0042098 T cell proliferation 0.000583 1.93e-06
CD19+ B gobp GO:0009605 response to external stimulus 0.000239 2.06e-06
CD19+ B gobp GO:0006753 nucleoside phosphate metabolic process 0.00262 2.11e-06
CD19+ B gobp GO:0034612 response to tumor necrosis factor 0.00381 2.12e-06
CD19+ B gobp GO:0006954 inflammatory response 0.000351 2.17e-06
CD19+ B gobp GO:0046700 heterocycle catabolic process 0.000623 2.18e-06
CD19+ B gobp GO:0097237 cellular response to toxic substance 0.0308 2.18e-06
CD19+ B gobp GO:0023051 regulation of signaling 0.000446 2.19e-06
CD19+ B gobp GO:0051239 regulation of multicellular organismal process 0.000172 2.24e-06
CD19+ B gobp GO:0045595 regulation of cell differentiation 0.000402 2.29e-06
CD19+ B gobp GO:1901361 organic cyclic compound catabolic process 0.000687 2.34e-06
CD19+ B gobp GO:0009892 negative regulation of metabolic process 0.000415 2.55e-06
CD19+ B gobp GO:0006605 protein targeting 0.000439 2.69e-06
CD19+ B gobp GO:0045089 positive regulation of innate immune response 0.000483 2.97e-06
CD19+ B gobp GO:0010035 response to inorganic substance 0.00635 3.09e-06
CD19+ B gobp GO:0019439 aromatic compound catabolic process 0.000604 3.1e-06
CD19+ B gobp GO:0045621 positive regulation of lymphocyte differentiation 0.00107 3.15e-06
CD19+ B gobp GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 0.000548 3.15e-06
CD19+ B gobp GO:0010646 regulation of cell communication 0.000391 3.18e-06
CD19+ B gobp GO:0002440 production of molecular mediator of immune response 0.000579 3.19e-06
CD19+ B gobp GO:0019637 organophosphate metabolic process 0.00238 3.2e-06
CD19+ B gobp GO:0050852 T cell receptor signaling pathway 0.000977 3.44e-06
CD19+ B gobp GO:0006909 phagocytosis 0.000905 3.54e-06
CD19+ B gobp GO:0019538 protein metabolic process 0.000532 3.67e-06
CD19+ B gobp GO:0046677 response to antibiotic 0.00546 3.74e-06
CD19+ B gobp GO:0002228 natural killer cell mediated immunity 0.00262 3.76e-06
CD19+ B gobp GO:0009966 regulation of signal transduction 0.000374 3.77e-06
CD19+ B gobp GO:0052548 regulation of endopeptidase activity 0.00892 4.16e-06
CD19+ B gobp GO:0071236 cellular response to antibiotic 0.0174 4.38e-06
CD19+ B gobp GO:0030099 myeloid cell differentiation 0.000423 4.41e-06
CD19+ B gobp GO:0072521 purine-containing compound metabolic process 0.00135 4.44e-06
CD19+ B gobp GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage 0.0192 4.48e-06
CD19+ B gobp GO:0009615 response to virus 0.000749 4.58e-06
CD19+ B gobp GO:0042127 regulation of cell proliferation 0.000315 4.69e-06
CD19+ B gobp GO:0043065 positive regulation of apoptotic process 0.00242 4.84e-06
CD19+ B gobp GO:0033036 macromolecule localization 0.000347 4.98e-06
CD19+ B gobp GO:0052547 regulation of peptidase activity 0.00699 5.36e-06
CD19+ B gobp GO:0071356 cellular response to tumor necrosis factor 0.00301 5.37e-06
CD19+ B gobp GO:0032496 response to lipopolysaccharide 0.000961 5.45e-06
CD19+ B gobp GO:0050864 regulation of B cell activation 0.000735 5.49e-06
CD19+ B gobp GO:0043068 positive regulation of programmed cell death 0.00216 5.93e-06
CD19+ B gobp GO:0045580 regulation of T cell differentiation 0.000666 6.09e-06
CD19+ B gobp GO:0006163 purine nucleotide metabolic process 0.00107 6.27e-06
CD19+ B gobp GO:0002262 myeloid cell homeostasis 0.000919 6.27e-06
CD19+ B gobp GO:0046635 positive regulation of alpha-beta T cell activation 0.00156 6.72e-06
CD19+ B gobp GO:0033993 response to lipid 0.00122 7.32e-06
CD19+ B gobp GO:0098542 defense response to other organism 0.000419 7.4e-06
CD19+ B gobp GO:0048523 negative regulation of cellular process 0.000362 7.49e-06
CD19+ B gobp GO:0051641 cellular localization 0.000529 7.61e-06
CD19+ B gobp GO:0043933 protein-containing complex subunit organization 0.000982 7.77e-06
CD19+ B gobp GO:0051649 establishment of localization in cell 0.00038 7.88e-06
CD19+ B gobp GO:0034622 cellular protein-containing complex assembly 0.00153 8.47e-06
CD19+ B gobp GO:0002703 regulation of leukocyte mediated immunity 0.000572 8.62e-06
CD19+ B gobp GO:0019693 ribose phosphate metabolic process 0.00108 8.63e-06
CD19+ B gobp GO:2001233 regulation of apoptotic signaling pathway 0.00518 9.16e-06
CD19+ B gobp GO:0097193 intrinsic apoptotic signaling pathway 0.00649 9.36e-06
CD19+ B gobp GO:0050900 leukocyte migration 0.00052 9.39e-06
CD19+ B gobp GO:0035710 CD4-positive, alpha-beta T cell activation 0.000946 1.01e-05
CD19+ B gobp GO:0034341 response to interferon-gamma 0.00104 1.03e-05
CD19+ B gobp GO:0045184 establishment of protein localization 0.000246 1.04e-05
CD19+ B gobp GO:0032879 regulation of localization 0.000376 1.04e-05
CD19+ B gobp GO:1902531 regulation of intracellular signal transduction 0.000537 1.05e-05
CD19+ B gobp GO:0098609 cell-cell adhesion 0.00045 1.05e-05
CD19+ B gobp GO:0009150 purine ribonucleotide metabolic process 0.000906 1.09e-05
CD19+ B gobp GO:0006897 endocytosis 0.00114 1.1e-05
CD19+ B gobp GO:1901135 carbohydrate derivative metabolic process 0.00389 1.17e-05
CD19+ B gobp GO:0009259 ribonucleotide metabolic process 0.00095 1.26e-05
CD19+ B gobp GO:0044267 cellular protein metabolic process 0.000482 1.29e-05
CD19+ B gobp GO:0002237 response to molecule of bacterial origin 0.000708 1.3e-05
CD19+ B gobp GO:0060333 interferon-gamma-mediated signaling pathway 0.00354 1.32e-05
CD19+ B gobp GO:0008380 RNA splicing 0.823 1.35e-05
CD19+ B gobp GO:0015980 energy derivation by oxidation of organic compounds 0.000536 1.35e-05
CD19+ B gobp GO:0040011 locomotion 0.000283 1.4e-05
CD19+ B gobp GO:0006338 chromatin remodeling 0.119 1.46e-05
CD19+ B gobp GO:0046907 intracellular transport 0.000408 1.48e-05
CD19+ B gobp GO:0009617 response to bacterium 0.000385 1.5e-05
CD19+ B gobp GO:0006959 humoral immune response 0.000819 1.51e-05
CD19+ B gobp GO:0045582 positive regulation of T cell differentiation 0.00104 1.55e-05
CD19+ B gobp GO:0035690 cellular response to drug 0.00526 1.74e-05
CD19+ B gobp GO:0043069 negative regulation of programmed cell death 0.000631 1.76e-05
CD19+ B gobp GO:0071222 cellular response to lipopolysaccharide 0.0013 1.77e-05
CD19+ B gobp GO:0065008 regulation of biological quality 0.000322 1.78e-05
CD19+ B gobp GO:0002821 positive regulation of adaptive immune response 0.00087 1.79e-05
CD19+ B gobp GO:0070527 platelet aggregation 0.00246 1.81e-05
CD19+ B gobp GO:0006928 movement of cell or subcellular component 0.000351 1.84e-05
CD19+ B gobp GO:0042129 regulation of T cell proliferation 0.000628 1.99e-05
CD19+ B gobp GO:0002705 positive regulation of leukocyte mediated immunity 0.000715 2.03e-05
CD19+ B gobp GO:0008104 protein localization 0.000249 2.1e-05
CD19+ B gobp GO:0042267 natural killer cell mediated cytotoxicity 0.00189 2.1e-05
CD19+ B gobp GO:0051241 negative regulation of multicellular organismal process 0.000376 2.13e-05
CD19+ B gobp GO:0050793 regulation of developmental process 0.000213 2.19e-05
CD19+ B gobp GO:0034109 homotypic cell-cell adhesion 0.00269 2.54e-05
CD19+ B gobp GO:0051247 positive regulation of protein metabolic process 0.000294 2.55e-05
CD19+ B gobp GO:0007599 hemostasis 0.000752 2.62e-05
CD19+ B gobp GO:1902275 regulation of chromatin organization 0.0262 2.67e-05
CD19+ B gobp GO:0060548 negative regulation of cell death 0.000521 2.69e-05
CD19+ B gobp GO:0032663 regulation of interleukin-2 production 0.00243 2.73e-05
CD19+ B gobp GO:0051336 regulation of hydrolase activity 0.00753 2.87e-05
CD19+ B gobp GO:0044281 small molecule metabolic process 0.00741 2.99e-05
CD19+ B gobp GO:0009967 positive regulation of signal transduction 0.000267 3.07e-05
CD19+ B gobp GO:1905269 positive regulation of chromatin organization 0.0136 3.16e-05
CD19+ B gobp GO:0002824 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 0.000852 3.29e-05
CD19+ B gobp GO:0006979 response to oxidative stress 0.00145 3.31e-05
CD19+ B gobp GO:0065003 protein-containing complex assembly 0.000428 3.38e-05
CD19+ B gobp GO:0031056 regulation of histone modification 0.0152 3.48e-05
CD19+ B gobp GO:0000956 nuclear-transcribed mRNA catabolic process 0.000558 3.53e-05
CD19+ B gobp GO:0038093 Fc receptor signaling pathway 0.00085 3.58e-05
CD19+ B gobp GO:0050684 regulation of mRNA processing 0.00942 3.58e-05
CD19+ B gobp GO:0043484 regulation of RNA splicing 0.00722 3.65e-05
CD19+ B gobp GO:0015031 protein transport 0.000209 3.79e-05
CD19+ B gobp GO:0023056 positive regulation of signaling 0.000245 3.91e-05
CD19+ B gobp GO:0031058 positive regulation of histone modification 0.0114 3.98e-05
CD19+ B gobp GO:0016310 phosphorylation 0.000186 4.05e-05
CD19+ B gobp GO:0002218 activation of innate immune response 0.000517 4.21e-05
CD19+ B gobp GO:0031399 regulation of protein modification process 0.000369 4.23e-05
CD19+ B gobp GO:0010952 positive regulation of peptidase activity 0.00373 4.28e-05
CD19+ B gobp GO:0015833 peptide transport 0.000204 4.33e-05
CD19+ B gobp GO:0046634 regulation of alpha-beta T cell activation 0.000793 4.38e-05
CD19+ B gobp GO:1901575 organic substance catabolic process 0.000656 4.54e-05
CD19+ B gobp GO:0002377 immunoglobulin production 0.000797 4.67e-05
CD19+ B gobp GO:0032623 interleukin-2 production 0.00179 4.7e-05
CD19+ B gobp GO:0050866 negative regulation of cell activation 0.000632 4.77e-05
CD19+ B gobp GO:2000145 regulation of cell motility 0.000563 4.87e-05
CD19+ B gobp GO:0034101 erythrocyte homeostasis 0.00094 4.91e-05
CD19+ B gobp GO:0014070 response to organic cyclic compound 0.00127 4.93e-05
CD19+ B gobp GO:0009124 nucleoside monophosphate biosynthetic process 0.0226 5.1e-05
CD19+ B gobp GO:0043066 negative regulation of apoptotic process 0.000507 5.16e-05
CD19+ B gobp GO:0006886 intracellular protein transport 0.000322 5.38e-05
CD19+ B gobp GO:0010647 positive regulation of cell communication 0.000238 5.58e-05
CD19+ B gobp GO:0002695 negative regulation of leukocyte activation 0.000654 5.59e-05
CD19+ B gobp GO:0071346 cellular response to interferon-gamma 0.000957 5.74e-05
CD19+ B gobp GO:0034613 cellular protein localization 0.000377 5.74e-05
CD19+ B gobp GO:0051172 negative regulation of nitrogen compound metabolic process 0.000997 5.91e-05
CD19+ B gobp GO:0030888 regulation of B cell proliferation 0.00116 5.95e-05
CD19+ B gobp GO:0032270 positive regulation of cellular protein metabolic process 0.000292 6.03e-05
CD19+ B gobp GO:0007596 blood coagulation 0.000656 6.08e-05
CD19+ B gobp GO:0002700 regulation of production of molecular mediator of immune response 0.000645 6.27e-05
CD19+ B gobp GO:0048513 animal organ development 0.00017 6.93e-05
CD19+ B gobp GO:0043367 CD4-positive, alpha-beta T cell differentiation 0.000901 6.95e-05
CD19+ B gobp GO:0070727 cellular macromolecule localization 0.000346 7.04e-05
CD19+ B gobp GO:0051345 positive regulation of hydrolase activity 0.00578 7.11e-05
CD19+ B gobp GO:0006401 RNA catabolic process 0.000431 7.2e-05
CD19+ B gobp GO:0051607 defense response to virus 0.000623 7.31e-05
CD19+ B gobp GO:0071219 cellular response to molecule of bacterial origin 0.000856 7.32e-05
CD19+ B gobp GO:1901698 response to nitrogen compound 0.000621 7.36e-05
CD19+ B gobp GO:0030334 regulation of cell migration 0.000495 7.66e-05
CD19+ B gobp GO:0098657 import into cell 0.000704 8.04e-05
CD19+ B gobp GO:0009127 purine nucleoside monophosphate biosynthetic process 0.0105 8.09e-05
CD19+ B gobp GO:0009168 purine ribonucleoside monophosphate biosynthetic process 0.0105 8.09e-05
CD19+ B gobp GO:0006402 mRNA catabolic process 0.000459 8.25e-05
CD19+ B gobp GO:0044093 positive regulation of molecular function 0.000515 8.34e-05
CD19+ B gobp GO:0002292 T cell differentiation involved in immune response 0.000972 8.46e-05
CD19+ B gobp GO:0072594 establishment of protein localization to organelle 0.000367 8.5e-05
CD19+ B gobp GO:0031324 negative regulation of cellular metabolic process 0.000803 8.57e-05
CD19+ B gobp GO:0051270 regulation of cellular component movement 0.000485 8.62e-05
CD19+ B gobp GO:0050817 coagulation 0.000611 8.65e-05
CD19+ B gobp GO:0002181 cytoplasmic translation 0.00152 8.73e-05
CD19+ B gobp GO:0051248 negative regulation of protein metabolic process 0.000949 9e-05
CD19+ B gobp GO:0071214 cellular response to abiotic stimulus 0.00702 9.03e-05
CD19+ B gobp GO:0104004 cellular response to environmental stimulus 0.00702 9.03e-05
CD19+ B gobp GO:0050727 regulation of inflammatory response 0.000461 9.16e-05
CD19+ B gobp GO:0032502 developmental process 0.000148 9.21e-05
CD19+ B gobp GO:0032501 multicellular organismal process 0.000117 9.49e-05
CD19+ B gobp GO:0009636 response to toxic substance 0.00191 9.61e-05
CD19+ B gobp GO:0042886 amide transport 0.000194 9.78e-05
CD19+ B gobp GO:0001818 negative regulation of cytokine production 0.00061 0.000101
CD19+ B gobp GO:0002886 regulation of myeloid leukocyte mediated immunity 0.00126 0.00011
CD19+ B gobp GO:0043122 regulation of I-kappaB kinase/NF-kappaB signaling 0.00166 0.00012
CD19+ B gobp GO:0065009 regulation of molecular function 0.00028 0.000131
CD19+ B gobp GO:0071396 cellular response to lipid 0.00105 0.000132
CD19+ B gobp GO:2001242 regulation of intrinsic apoptotic signaling pathway 0.00298 0.000136
CD19+ B gobp GO:1903707 negative regulation of hemopoiesis 0.000782 0.000149
CD19+ B gobp GO:0042592 homeostatic process 0.000268 0.000151
CD19+ B gobp GO:0033365 protein localization to organelle 0.00031 0.000151
CD19+ B gobp GO:0009156 ribonucleoside monophosphate biosynthetic process 0.0101 0.000153
CD19+ B gobp GO:0070555 response to interleukin-1 0.00151 0.000155
CD19+ B gobp GO:0050854 regulation of antigen receptor-mediated signaling pathway 0.00124 0.000158
CD19+ B gobp GO:0001776 leukocyte homeostasis 0.00081 0.00016
CD19+ B gobp GO:1902533 positive regulation of intracellular signal transduction 0.000282 0.00016
CD19+ B gobp GO:0010950 positive regulation of endopeptidase activity 0.00261 0.000166
CD19+ B gobp GO:0007249 I-kappaB kinase/NF-kappaB signaling 0.000992 0.000167
CD19+ B gobp GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 0.0496 0.000168
CD19+ B gobp GO:0000398 mRNA splicing, via spliceosome 0.0496 0.000168
CD19+ B gobp GO:0044248 cellular catabolic process 0.000404 0.00017
CD19+ B gobp GO:0033554 cellular response to stress 0.000957 0.000171
CD19+ B gobp GO:0045637 regulation of myeloid cell differentiation 0.000531 0.000176
CD19+ B gobp GO:0030335 positive regulation of cell migration 0.000587 0.000178
CD19+ B gobp GO:0051250 negative regulation of lymphocyte activation 0.000687 0.000181
CD19+ B gobp GO:0051130 positive regulation of cellular component organization 0.00108 0.000189
CD19+ B gobp GO:0050821 protein stabilization 0.00894 0.000193
CD19+ B gobp GO:0048869 cellular developmental process 0.000148 0.000196
CD19+ B gobp GO:0050777 negative regulation of immune response 0.000689 0.000201
CD19+ B gobp GO:0071705 nitrogen compound transport 0.000183 0.000206
CD19+ B gobp GO:0034340 response to type I interferon 0.00189 0.000206
CD19+ B gobp GO:0009060 aerobic respiration 0.00172 0.000211
CD19+ B gobp GO:0055114 oxidation-reduction process 0.00188 0.000214
CD19+ B gobp GO:0051272 positive regulation of cellular component movement 0.00057 0.000216
CD19+ B gobp GO:0030168 platelet activation 0.000667 0.00022
CD19+ B gobp GO:2000147 positive regulation of cell motility 0.00058 0.000224
CD19+ B gobp GO:0046637 regulation of alpha-beta T cell differentiation 0.000954 0.000225
CD19+ B gobp GO:0002287 alpha-beta T cell activation involved in immune response 0.000953 0.000225
CD19+ B gobp GO:0002293 alpha-beta T cell differentiation involved in immune response 0.000953 0.000225
CD19+ B gobp GO:2000116 regulation of cysteine-type endopeptidase activity 0.00167 0.000226
CD19+ B gobp GO:0009056 catabolic process 0.000365 0.000227
CD19+ B gobp GO:0042060 wound healing 0.000448 0.000231
CD19+ B gobp GO:0019884 antigen processing and presentation of exogenous antigen 0.000981 0.000235
CD19+ B gobp GO:0032269 negative regulation of cellular protein metabolic process 0.000863 0.000239
CD19+ B gobp GO:0097191 extrinsic apoptotic signaling pathway 0.00169 0.000243
CD19+ B gobp GO:0071216 cellular response to biotic stimulus 0.000733 0.000244
CD19+ B gobp GO:0045597 positive regulation of cell differentiation 0.000396 0.000246
CD19+ B gobp GO:0000375 RNA splicing, via transesterification reactions 0.033 0.000249
CD19+ B gobp GO:0000380 alternative mRNA splicing, via spliceosome 0.00294 0.000256
CD19+ B gobp GO:0009145 purine nucleoside triphosphate biosynthetic process 0.00609 0.000257
CD19+ B gobp GO:0071702 organic substance transport 0.00018 0.000258
CD19+ B gobp GO:0002532 production of molecular mediator involved in inflammatory response 0.00162 0.000268
CD19+ B gobp GO:0002819 regulation of adaptive immune response 0.000695 0.000269
CD19+ B gobp GO:0050708 regulation of protein secretion 0.000567 0.000271
CD19+ B gobp GO:0040017 positive regulation of locomotion 0.000544 0.000275
CD19+ B gobp GO:0050790 regulation of catalytic activity 0.000377 0.000281
CD19+ B gobp GO:0051049 regulation of transport 0.000288 0.000291
CD19+ B gobp GO:0002431 Fc receptor mediated stimulatory signaling pathway 0.000992 0.000292
CD19+ B gobp GO:0016043 cellular component organization 0.000434 0.000294
CD19+ B gobp GO:0002758 innate immune response-activating signal transduction 0.00054 0.000301
CD19+ B gobp GO:0034728 nucleosome organization 0.0504 0.000305
CD19+ B gobp GO:0030154 cell differentiation 0.000151 0.000317
CD19+ B gobp GO:0002294 CD4-positive, alpha-beta T cell differentiation involved in immune response 0.000931 0.000319
CD19+ B gobp GO:0006333 chromatin assembly or disassembly 0.058 0.000322
CD19+ B gobp GO:0009206 purine ribonucleoside triphosphate biosynthetic process 0.00529 0.000336
CD19+ B gobp GO:0031325 positive regulation of cellular metabolic process 0.000172 0.000345
CD19+ B gobp GO:0033209 tumor necrosis factor-mediated signaling pathway 0.00206 0.000346
CD19+ B gobp GO:0008285 negative regulation of cell proliferation 0.000689 0.000361
CD19+ B gobp GO:0010257 NADH dehydrogenase complex assembly 0.000807 0.000371
CD19+ B gobp GO:0032981 mitochondrial respiratory chain complex I assembly 0.000807 0.000371
CD19+ B gobp GO:0042493 response to drug 0.000577 0.000374
CD19+ B gobp GO:0050789 regulation of biological process 9.68e-05 0.000378
CD19+ B gobp GO:0008625 extrinsic apoptotic signaling pathway via death domain receptors 0.00377 0.000389
CD19+ B gobp GO:0045596 negative regulation of cell differentiation 0.000662 0.000394
CD19+ B gobp GO:0070201 regulation of establishment of protein localization 0.000468 0.000401
CD19+ B gobp GO:0071840 cellular component organization or biogenesis 0.000352 0.00041
CD19+ B gobp GO:0002822 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 0.000721 0.000411
CD19+ B gobp GO:0040012 regulation of locomotion 0.000326 0.00042
CD19+ B gobp GO:0045576 mast cell activation 0.00096 0.000421
CD19+ B gobp GO:0002478 antigen processing and presentation of exogenous peptide antigen 0.000971 0.000423
CD19+ B gobp GO:0006397 mRNA processing 0.0172 0.000426
CD19+ B gobp GO:0009628 response to abiotic stimulus 0.000632 0.00044
CD19+ B gobp GO:2001252 positive regulation of chromosome organization 0.00714 0.000442
CD19+ B gobp GO:0002706 regulation of lymphocyte mediated immunity 0.000686 0.000449
CD19+ B gobp GO:0051128 regulation of cellular component organization 0.000867 0.00047
CD19+ B gobp GO:0006754 ATP biosynthetic process 0.00471 0.000479
CD19+ B gobp GO:0065007 biological regulation 9.72e-05 0.000484
CD19+ B gobp GO:0010243 response to organonitrogen compound 0.000457 0.000499
CD19+ B gobp GO:0002708 positive regulation of lymphocyte mediated immunity 0.00071 0.000512
CD19+ B gobp GO:0031341 regulation of cell killing 0.000862 0.000523
CD19+ B gobp GO:0002433 immune response-regulating cell surface receptor signaling pathway involved in phagocytosis 0.000991 0.000534
CD19+ B gobp GO:0038096 Fc-gamma receptor signaling pathway involved in phagocytosis 0.000991 0.000534
CD19+ B gobp GO:0048010 vascular endothelial growth factor receptor signaling pathway 0.00177 0.000534
CD19+ B gobp GO:0038094 Fc-gamma receptor signaling pathway 0.000937 0.000534
CD19+ B gobp GO:0071407 cellular response to organic cyclic compound 0.00136 0.000542
CD19+ B gobp GO:0071229 cellular response to acid chemical 0.00342 0.000544
CD19+ B gobp GO:0009142 nucleoside triphosphate biosynthetic process 0.00567 0.000547
CD19+ B gobp GO:0031343 positive regulation of cell killing 0.00112 0.000554
CD19+ B gobp GO:1903311 regulation of mRNA metabolic process 0.0012 0.000561
CD19+ B gobp GO:0031497 chromatin assembly 0.0315 0.000568
CD19+ B gobp GO:0034614 cellular response to reactive oxygen species 0.00207 0.000572
CD19+ B gobp GO:0030218 erythrocyte differentiation 0.000774 0.000588
CD19+ B gobp GO:0032635 interleukin-6 production 0.000765 0.000588
CD19+ B gobp GO:0043085 positive regulation of catalytic activity 0.000456 0.00059
CD19+ B gobp GO:0051090 regulation of DNA-binding transcription factor activity 0.000493 0.000595
CD19+ B gobp GO:0002792 negative regulation of peptide secretion 0.0024 0.000627
CD19+ B gobp GO:0033108 mitochondrial respiratory chain complex assembly 0.00077 0.000627
CD19+ B gobp GO:0042093 T-helper cell differentiation 0.000899 0.000636
CD19+ B gobp GO:0051240 positive regulation of multicellular organismal process 0.000391 0.00064
CD19+ B gobp GO:0009201 ribonucleoside triphosphate biosynthetic process 0.00414 0.000652
CD19+ B gobp GO:0010629 negative regulation of gene expression 0.000225 0.000653
CD19+ B gobp GO:0019882 antigen processing and presentation 0.000603 0.000654
CD19+ B gobp GO:0031400 negative regulation of protein modification process 0.0012 0.000655
CD19+ B gobp GO:2001056 positive regulation of cysteine-type endopeptidase activity 0.00184 0.000663
CD19+ B gobp GO:0001836 release of cytochrome c from mitochondria 0.00455 0.000666
CD19+ B gobp GO:0006334 nucleosome assembly 0.0263 0.000677
CD19+ B gobp GO:0016575 histone deacetylation 0.0107 0.000691
CD19+ B gobp GO:0048024 regulation of mRNA splicing, via spliceosome 0.00184 0.000691
CD19+ B gobp GO:0002791 regulation of peptide secretion 0.000465 0.000715
CD19+ B gobp GO:0060337 type I interferon signaling pathway 0.00142 0.000721
CD19+ B gobp GO:0071357 cellular response to type I interferon 0.00142 0.000721
CD19+ B gobp GO:0071384 cellular response to corticosteroid stimulus 0.00454 0.000726
CD19+ B gobp GO:0006325 chromatin organization 0.0179 0.000735
CD19+ B gobp GO:0033044 regulation of chromosome organization 0.00857 0.000744
CD19+ B gobp GO:0032880 regulation of protein localization 0.000416 0.000759
CD19+ B gobp GO:0042542 response to hydrogen peroxide 0.00146 0.000764
CD19+ B gobp GO:0050709 negative regulation of protein secretion 0.00213 0.000844
CD19+ B gobp GO:0002221 pattern recognition receptor signaling pathway 0.000582 0.00086
CD19+ B gobp GO:0098732 macromolecule deacylation 0.0118 0.000873
CD19+ B gobp GO:0042325 regulation of phosphorylation 0.000232 0.000873
CD19+ B gobp GO:0034599 cellular response to oxidative stress 0.00112 0.000884
CD19+ B gobp GO:0019058 viral life cycle 0.000681 0.000884
CD19+ B gobp GO:2000514 regulation of CD4-positive, alpha-beta T cell activation 0.000886 0.000892
CD19+ B gobp GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress 0.00292 0.000892
CD19+ B gobp GO:0014066 regulation of phosphatidylinositol 3-kinase signaling 0.00214 0.000893
CD19+ B gobp GO:0048856 anatomical structure development 0.000126 0.000929
CD19+ B gobp GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process 0.00218 0.000934
CD19+ B gobp GO:0006457 protein folding 0.0166 0.000983
CD19+ B gobp GO:0050792 regulation of viral process 0.00131 0.00101
CD19+ B gobp GO:0031401 positive regulation of protein modification process 0.000271 0.00102
CD19+ B gobp GO:0042326 negative regulation of phosphorylation 0.00112 0.00104
CD19+ B gobp GO:0033043 regulation of organelle organization 0.00224 0.00106
CD19+ B gobp GO:0051224 negative regulation of protein transport 0.00257 0.00107
CD19+ B gobp GO:0018193 peptidyl-amino acid modification 0.000631 0.00108
CD19+ B gobp GO:2001234 negative regulation of apoptotic signaling pathway 0.00147 0.00111
CD19+ B gobp GO:0035601 protein deacylation 0.01 0.00112
CD19+ B gobp GO:0060326 cell chemotaxis 0.000542 0.00112
CD19+ B gobp GO:0002367 cytokine production involved in immune response 0.000712 0.00114
CD19+ B gobp GO:0009306 protein secretion 0.000394 0.00116
CD19+ B gobp GO:0000302 response to reactive oxygen species 0.000964 0.00119
CD19+ B gobp GO:0002702 positive regulation of production of molecular mediator of immune response 0.000724 0.00121

A set focussed view

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

res.l10$cs.summary %>%
  filter(in_cs, active_cs, celltype == 'CD19+ B', db == 'gobp') %>%
  left_join(in_cs) %>%
  mutate(in_cs = ifelse(is.na(in_cs), F, T)) %>%
  make_susie_component_kable()
Joining, by = c("geneSet", "in_cs", "db", "celltype")
Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:
celltype db component geneSet description alpha pValueHypergeometric
CD19+ B gobp L1 GO:0002376 immune system process 1 3e-47
CD19+ B gobp L2 GO:0045047 protein targeting to ER 0.962 8.24e-18
CD19+ B gobp L3 GO:0042773 ATP synthesis coupled electron transport 0.624 6.5e-12
CD19+ B gobp L3 GO:0042775 mitochondrial ATP synthesis coupled electron transport 0.36 1.04e-11
CD19+ B gobp L5 GO:0001775 cell activation 0.978 1.1e-39
CD19+ B gobp L6 GO:0008380 RNA splicing 0.823 1.35e-05
CD19+ B gobp L6 GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 0.0492 0.000168
CD19+ B gobp L6 GO:0000398 mRNA splicing, via spliceosome 0.0492 0.000168
CD19+ B gobp L6 GO:0000375 RNA splicing, via transesterification reactions 0.0326 0.000249

Credible set sizes

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

Version Author Date
2f395f0 karltayeb 2022-04-03

CS vs pValues

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


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

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

plots <- purrr::map(geneset_sources, ~do.or.plot(
  res.l10, ct=celltype, g=.x, x='nl10p'))
for(i in 1:length(plots)){
  cat('###', geneset_sources[[i]], '\n')
  print(plots[[i]])
  cat('\n')
}

gobp

Version Author Date
114f1f8 karltayeb 2022-04-03

gobp_nr

### gomf ### kegg ### reactome ### wikipathway_cancer ### wikipathway

A long list of results

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

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

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

library(htmltools)

make_susie_html_table = function(ct, g){
  res.l10$cs.summary %>%
        filter(celltype == ct, db == g, active_cs) %>%
        make_susie_component_kable() %>%
        htmltools::HTML()
}
possibly_make_susie_html_table = possibly(make_susie_html_table, otherwise="nothing to report...")

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

CD19+ B

gobp

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

gobp_nr

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

gomf

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

kegg

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

reactome

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

wikipathway_cancer

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

wikipathway

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

CD56+ NK

gobp

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

gobp_nr

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

gomf

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

kegg

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

reactome

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

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:
Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

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

T cell

gobp

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

gobp_nr

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

gomf

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

kegg

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

reactome

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

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:
Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:
Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

CD14+ Monocyte

gobp

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

gobp_nr

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

gomf

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

kegg

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

reactome

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

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:
Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

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

CD34+

gobp

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

gobp_nr

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

gomf

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

kegg

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

reactome

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

wikipathway_cancer

Adding missing grouping variables: `celltype`, `db`, `component`
`mutate_if()` ignored the following grouping variables:
Warning in ensure_len_html(color, nrows, "color"): The number of provided values
in color does not equal to the number of rows.

[1] “nothing to report…”

wikipathway

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