Single-cell PBMC Example

Last updated: 2022-03-29

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Introduction

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

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

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

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

Setup

Load Gene Sets

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

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

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

load('data/pbmc-purified/deseq2-pbmc-purified.RData')

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


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

Loading required package: DESeq2

Version	Author	Date
a2bdb56	karltayeb	2022-03-29

Fit logistic SuSiE

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

  # summarise results
  set.summary <- vb.fit$pip %>% 
    as_tibble(rownames='geneSet') %>%
    rename(pip=value) %>%
    mutate(
      top_component = apply(vb.fit$alpha, 2, which.max),
      active_set = top_component %in% vb.fit$sets$cs_index,
      top_component = paste0('L', top_component),
      cs = purrr::map(top_component, ~tryCatch(
        colnames(gs$X)[get(.x, vb.fit$sets$cs)], error = function(e) list())),
      in_cs = geneSet %in% cs,
      beta = colSums(vb.fit$mu * vb.fit$alpha),
      geneListSize = sum(u$y),
      geneSetSize = colSums(u$X),
      overlap = (u$y %*% u$X)[1,],
      nGenes = length(u$y),
      propSetInList = overlap / geneSetSize,
      oddsRatio = (overlap / (geneListSize - overlap)) / (
        (geneSetSize - overlap) / (nGenes - geneSetSize + overlap)),
    pValueHypergeometric = phyper(
      overlap-1, geneListSize, nGenes, geneSetSize, lower.tail= FALSE),
    db = db,
    celltype = celltype,
    thresh = thresh
    ) %>% left_join(gs$geneSet$geneSetDes)
  return(list(fit = vb.fit, set.summary=set.summary))
}

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

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

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

pbmc_res_set_summary <- dplyr::bind_rows(purrr::map(pbmc_res, ~ pluck(.x, 'set.summary')))

Summary functions

Just a few functions to help streamline looking at output

pval_focussed_table = function(thresh=1e-3, filter_db=NULL, filter_celltype=NULL, top.n=50){
  pbmc_res_set_summary %>%
  filter(
    case_when(
      is.null(filter_db) ~ TRUE,
      !is.null(filter_db) ~ db %in% filter_db
    ) &
    thresh == thresh &
    case_when(
      is.null(filter_celltype) ~ TRUE,
      !is.null(filter_celltype) ~ celltype %in% filter_celltype
    )
  )  %>%
  dplyr::arrange(celltype, db, pValueHypergeometric) %>%
  group_by(celltype, db) %>% slice(1:top.n) %>%
  select(celltype, db, geneSet, description, pip, top_component, oddsRatio, propSetInList, pValueHypergeometric) %>%
  mutate_at(vars(celltype, db), factor) %>%
  datatable(filter = 'top')
}

set_focussed_table = function(thresh=1e-3, filter_db=NULL, filter_celltype=NULL){
  pbmc_res_set_summary %>%
  filter(
    case_when(
      is.null(filter_db) ~ TRUE,
      !is.null(filter_db) ~ db %in% filter_db
    ) &
    thresh == 1e-3 &
    in_cs & active_set &
    case_when(
      is.null(filter_celltype) ~ TRUE,
      !is.null(filter_celltype) ~ celltype %in% filter_celltype
    )
  )  %>%
  dplyr::arrange(celltype, db, desc(pip)) %>%
  select(celltype, db, geneSet, description, pip, top_component, oddsRatio, propSetInList, pValueHypergeometric) %>%
  mutate_at(vars(celltype, geneSet, db), factor) %>%
  datatable(filter = 'top')
}

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

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

Results/Explore enrichments

Our goal is to assess 1. The quality of the gene set enrichments we get from each celltype - do reported gene set enrichments seem celltype specific/celltype relevant? - how much “interesting” marginal enrichment do we fail to capture in the multivariate model - how sensitive are we to the choice of pvalue threshold

Results

Lets take a look at what enrichment we’re getting across cell-types.

CD19+ B

pbmc_res_set_summary %>%
  filter(celltype == 'CD19+ B') %>%
  filter(active_set, thresh==1e-4) %>%
  db_component_kable

Adding missing grouping variables: `db`, `celltype`, `top_component`

db	celltype	top_component	geneSet	description	pip
gobp	CD19+ B	L1	GO:0002376	immune system process	<span style=" color: green !important;" >0.999957465451611</span>
gobp	CD19+ B	L2	GO:0045047	protein targeting to ER	<span style=" color: green !important;" >0.962052077569581</span>
gobp	CD19+ B	L2	GO:0006613	cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.0216561609975944</span>
gobp	CD19+ B	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.0145368812974931</span>
gobp	CD19+ B	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.00410197009826074</span>
gobp	CD19+ B	L3	GO:0042773	ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.624496308507348</span>
gobp	CD19+ B	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.360022211508933</span>
gobp	CD19+ B	L3	GO:0006119	oxidative phosphorylation	<span style=" color: red !important;" >0.0175238678609325</span>
gobp	CD19+ B	L5	GO:0001775	cell activation	<span style=" color: green !important;" >0.978054175097094</span>
gobp	CD19+ B	L5	GO:0045321	leukocyte activation	<span style=" color: red !important;" >0.0218972720769344</span>
gobp	CD19+ B	L5	GO:0002366	leukocyte activation involved in immune response	<span style=" color: red !important;" >0.000595713062097269</span>
gobp	CD19+ B	L5	GO:0002263	cell activation involved in immune response	<span style=" color: red !important;" >0.000577006708652683</span>
gobp	CD19+ B	L6	GO:0008380	RNA splicing	<span style=" color: red !important;" >0.822736133183297</span>
gobp	CD19+ B	L6	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	<span style=" color: red !important;" >0.049644134105862</span>
gobp	CD19+ B	L6	GO:0000398	mRNA splicing, via spliceosome	<span style=" color: red !important;" >0.049644134105862</span>
gobp	CD19+ B	L6	GO:0000375	RNA splicing, via transesterification reactions	<span style=" color: red !important;" >0.0330051165719797</span>
gobp	CD19+ B	L6	GO:0006397	mRNA processing	<span style=" color: red !important;" >0.0172340532174977</span>
gobp	CD19+ B	L6	GO:0050684	regulation of mRNA processing	<span style=" color: red !important;" >0.0094172042437507</span>
gobp	CD19+ B	L6	GO:0043484	regulation of RNA splicing	<span style=" color: red !important;" >0.00722067130606185</span>
gobp	CD19+ B	L6	GO:0000380	alternative mRNA splicing, via spliceosome	<span style=" color: red !important;" >0.00293948333200866</span>
gobp	CD19+ B	L6	GO:0048024	regulation of mRNA splicing, via spliceosome	<span style=" color: red !important;" >0.00183491753300979</span>
gobp	CD19+ B	L6	GO:0016071	mRNA metabolic process	<span style=" color: red !important;" >0.00105163745213244</span>
gobp_nr	CD19+ B	L1	GO:0002446	neutrophil mediated immunity	<span style=" color: red !important;" >0.515144038268755</span>
gobp_nr	CD19+ B	L1	GO:0036230	granulocyte activation	<span style=" color: red !important;" >0.485735788920244</span>
gobp_nr	CD19+ B	L2	GO:0070972	protein localization to endoplasmic reticulum	<span style=" color: green !important;" >0.999958026971368</span>
gobp_nr	CD19+ B	L4	GO:0009123	nucleoside monophosphate metabolic process	<span style=" color: green !important;" >0.984497563614406</span>
gobp_nr	CD19+ B	L4	GO:0009141	nucleoside triphosphate metabolic process	<span style=" color: red !important;" >0.0164867485447392</span>
gobp_nr	CD19+ B	L5	GO:0002764	immune response-regulating signaling pathway	<span style=" color: green !important;" >0.996185347850837</span>
gomf	CD19+ B	L1	GO:0003723	RNA binding	<span style=" color: green !important;" >0.999743954825178</span>
gomf	CD19+ B	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	<span style=" color: green !important;" >0.995003782967434</span>
gomf	CD19+ B	L2	GO:0003700	DNA-binding transcription factor activity	<span style=" color: red !important;" >0.00505824116754672</span>
gomf	CD19+ B	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	<span style=" color: red !important;" >0.487251391312216</span>
gomf	CD19+ B	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	<span style=" color: red !important;" >0.431399316819835</span>
gomf	CD19+ B	L3	GO:0000987	proximal promoter sequence-specific DNA binding	<span style=" color: red !important;" >0.0365953412200314</span>
gomf	CD19+ B	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	<span style=" color: red !important;" >0.0243679373454444</span>
gomf	CD19+ B	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	<span style=" color: red !important;" >0.0132413813040726</span>
gomf	CD19+ B	L3	GO:0003690	double-stranded DNA binding	<span style=" color: red !important;" >0.00592789564076235</span>
gomf	CD19+ B	L3	GO:1990837	sequence-specific double-stranded DNA binding	<span style=" color: red !important;" >0.00136790369019235</span>
gomf	CD19+ B	L3	GO:0001067	regulatory region nucleic acid binding	<span style=" color: red !important;" >0.00046527212966796</span>
gomf	CD19+ B	L3	GO:0044212	transcription regulatory region DNA binding	<span style=" color: red !important;" >0.000355705894771408</span>
gomf	CD19+ B	L6	GO:0003735	structural constituent of ribosome	<span style=" color: green !important;" >0.995344082600683</span>
gomf	CD19+ B	L7	GO:0003954	NADH dehydrogenase activity	<span style=" color: red !important;" >0.325953617177259</span>
gomf	CD19+ B	L7	GO:0008137	NADH dehydrogenase (ubiquinone) activity	<span style=" color: red !important;" >0.218583180359325</span>
gomf	CD19+ B	L7	GO:0050136	NADH dehydrogenase (quinone) activity	<span style=" color: red !important;" >0.218583180359325</span>
gomf	CD19+ B	L7	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	<span style=" color: red !important;" >0.177265521649769</span>
gomf	CD19+ B	L7	GO:0016651	oxidoreductase activity, acting on NAD(P)H	<span style=" color: red !important;" >0.0387976083993536</span>
kegg	CD19+ B	L1	hsa00190	Oxidative phosphorylation	<span style=" color: green !important;" >0.997990176564082</span>
kegg	CD19+ B	L1	hsa05012	Parkinson disease	<span style=" color: red !important;" >0.0125303037367086</span>
kegg	CD19+ B	L2	hsa04640	Hematopoietic cell lineage	<span style=" color: green !important;" >0.999795101338638</span>
kegg	CD19+ B	L3	hsa03010	Ribosome	<span style=" color: green !important;" >0.999999982887443</span>
reactome	CD19+ B	L1	R-HSA-168256	Immune System	<span style=" color: green !important;" >1</span>
reactome	CD19+ B	L2	R-HSA-156842	Eukaryotic Translation Elongation	<span style=" color: red !important;" >0.760651463839203</span>
reactome	CD19+ B	L2	R-HSA-156902	Peptide chain elongation	<span style=" color: red !important;" >0.12438973980464</span>
reactome	CD19+ B	L2	R-HSA-192823	Viral mRNA Translation	<span style=" color: red !important;" >0.0671329230529306</span>
reactome	CD19+ B	L2	R-HSA-2408557	Selenocysteine synthesis	<span style=" color: red !important;" >0.0260066810882063</span>
reactome	CD19+ B	L2	R-HSA-72764	Eukaryotic Translation Termination	<span style=" color: red !important;" >0.0172676775018812</span>
reactome	CD19+ B	L2	R-HSA-72689	Formation of a pool of free 40S subunits	<span style=" color: red !important;" >0.00330537630812389</span>
reactome	CD19+ B	L2	R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.00313197971436374</span>
reactome	CD19+ B	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	<span style=" color: red !important;" >0.00122676226108998</span>
reactome	CD19+ B	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	<span style=" color: red !important;" >0.00100083013030172</span>
reactome	CD19+ B	L3	R-HSA-74160	Gene expression (Transcription)	<span style=" color: red !important;" >0.885679352792777</span>
reactome	CD19+ B	L3	R-HSA-212436	Generic Transcription Pathway	<span style=" color: red !important;" >0.0726625717379175</span>
reactome	CD19+ B	L3	R-HSA-73857	RNA Polymerase II Transcription	<span style=" color: red !important;" >0.041834760675025</span>
reactome	CD19+ B	L4	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	<span style=" color: red !important;" >0.845323000060671</span>
reactome	CD19+ B	L4	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	<span style=" color: red !important;" >0.14938336590149</span>
reactome	CD19+ B	L4	R-HSA-611105	Respiratory electron transport	<span style=" color: red !important;" >0.00596574446721121</span>
reactome	CD19+ B	L5	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	<span style=" color: green !important;" >0.997049696139591</span>
reactome	CD19+ B	L5	R-HSA-983169	Class I MHC mediated antigen processing & presentation	<span style=" color: red !important;" >0.00311879186973374</span>
reactome	CD19+ B	L6	R-HSA-180585	Vif-mediated degradation of APOBEC3G	<span style=" color: red !important;" >0.749039310761527</span>
reactome	CD19+ B	L6	R-HSA-1234176	Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha	<span style=" color: red !important;" >0.0319137208638701</span>
reactome	CD19+ B	L6	R-HSA-211733	Regulation of activated PAK-2p34 by proteasome mediated degradation	<span style=" color: red !important;" >0.0256472437189241</span>
reactome	CD19+ B	L6	R-HSA-69601	Ubiquitin Mediated Degradation of Phosphorylated Cdc25A	<span style=" color: red !important;" >0.0242873384108474</span>
reactome	CD19+ B	L6	R-HSA-69610	p53-Independent DNA Damage Response	<span style=" color: red !important;" >0.0242873384108474</span>
reactome	CD19+ B	L6	R-HSA-69613	p53-Independent G1/S DNA damage checkpoint	<span style=" color: red !important;" >0.0242873384108474</span>
reactome	CD19+ B	L6	R-HSA-69541	Stabilization of p53	<span style=" color: red !important;" >0.0225422403485689</span>
reactome	CD19+ B	L6	R-HSA-69229	Ubiquitin-dependent degradation of Cyclin D1	<span style=" color: red !important;" >0.0120133659466743</span>
reactome	CD19+ B	L6	R-HSA-75815	Ubiquitin-dependent degradation of Cyclin D	<span style=" color: red !important;" >0.0120133659466743</span>
reactome	CD19+ B	L6	R-HSA-180534	Vpu mediated degradation of CD4	<span style=" color: red !important;" >0.0119846232558787</span>
reactome	CD19+ B	L6	R-HSA-169911	Regulation of Apoptosis	<span style=" color: red !important;" >0.0108046763000044</span>
reactome	CD19+ B	L6	R-HSA-349425	Autodegradation of the E3 ubiquitin ligase COP1	<span style=" color: red !important;" >0.0101911528157629</span>
reactome	CD19+ B	L6	R-HSA-9604323	Negative regulation of NOTCH4 signaling	<span style=" color: red !important;" >0.0071579855747933</span>
reactome	CD19+ B	L6	R-HSA-8854050	FBXL7 down-regulates AURKA during mitotic entry and in early mitosis	<span style=" color: red !important;" >0.00703778872278604</span>
reactome	CD19+ B	L6	R-HSA-1236978	Cross-presentation of soluble exogenous antigens (endosomes)	<span style=" color: red !important;" >0.00406554835881989</span>
reactome	CD19+ B	L6	R-HSA-174154	APC/C:Cdc20 mediated degradation of Securin	<span style=" color: red !important;" >0.00385891217123191</span>
reactome	CD19+ B	L6	R-HSA-1169091	Activation of NF-kappaB in B cells	<span style=" color: red !important;" >0.00376792382128477</span>
reactome	CD19+ B	L6	R-HSA-174084	Autodegradation of Cdh1 by Cdh1:APC/C	<span style=" color: red !important;" >0.00361414870965138</span>
reactome	CD19+ B	L6	R-HSA-1234174	Regulation of Hypoxia-inducible Factor (HIF) by oxygen	<span style=" color: red !important;" >0.00305797077052683</span>
reactome	CD19+ B	L6	R-HSA-2262749	Cellular response to hypoxia	<span style=" color: red !important;" >0.00305797077052683</span>
reactome	CD19+ B	L6	R-HSA-983705	Signaling by the B Cell Receptor (BCR)	<span style=" color: red !important;" >0.00286836400043933</span>
reactome	CD19+ B	L6	R-HSA-174113	SCF-beta-TrCP mediated degradation of Emi1	<span style=" color: red !important;" >0.0024109403813769</span>
reactome	CD19+ B	L6	R-HSA-450408	AUF1 (hnRNP D0) binds and destabilizes mRNA	<span style=" color: red !important;" >0.00171267983373247</span>
reactome	CD19+ B	L6	R-HSA-69563	p53-Dependent G1 DNA Damage Response	<span style=" color: red !important;" >0.00150097375541414</span>
reactome	CD19+ B	L6	R-HSA-69580	p53-Dependent G1/S DNA damage checkpoint	<span style=" color: red !important;" >0.00150097375541414</span>
reactome	CD19+ B	L6	R-HSA-174184	Cdc20:Phospho-APC/C mediated degradation of Cyclin A	<span style=" color: red !important;" >0.00133190881117529</span>
reactome	CD19+ B	L6	R-HSA-351202	Metabolism of polyamines	<span style=" color: red !important;" >0.00131731594365259</span>
reactome	CD19+ B	L6	R-HSA-68867	Assembly of the pre-replicative complex	<span style=" color: red !important;" >0.00121050465862294</span>
reactome	CD19+ B	L6	R-HSA-176409	APC/C:Cdc20 mediated degradation of mitotic proteins	<span style=" color: red !important;" >0.00116496309289926</span>
reactome	CD19+ B	L6	R-HSA-350562	Regulation of ornithine decarboxylase (ODC)	<span style=" color: red !important;" >0.00102467992167676</span>
reactome	CD19+ B	L6	R-HSA-69615	G1/S DNA Damage Checkpoints	<span style=" color: red !important;" >0.000957829552408529</span>
reactome	CD19+ B	L6	R-HSA-5362768	Hh mutants that don’t undergo autocatalytic processing are degraded by ERAD	<span style=" color: red !important;" >0.00095140800156257</span>
reactome	CD19+ B	L6	R-HSA-174178	APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1	<span style=" color: red !important;" >0.000862233445453997</span>
reactome	CD19+ B	L6	R-HSA-179419	APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint	<span style=" color: red !important;" >0.000720719571974726</span>
reactome	CD19+ B	L6	R-HSA-5610780	Degradation of GLI1 by the proteasome	<span style=" color: red !important;" >0.000661022828454261</span>
reactome	CD19+ B	L7	R-HSA-72163	mRNA Splicing - Major Pathway	<span style=" color: red !important;" >0.545788750456562</span>
reactome	CD19+ B	L7	R-HSA-72172	mRNA Splicing	<span style=" color: red !important;" >0.443954636390887</span>
reactome	CD19+ B	L7	R-HSA-109688	Cleavage of Growing Transcript in the Termination Region	<span style=" color: red !important;" >0.00214822879004417</span>
reactome	CD19+ B	L7	R-HSA-73856	RNA Polymerase II Transcription Termination	<span style=" color: red !important;" >0.00214822879004417</span>
reactome	CD19+ B	L7	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	<span style=" color: red !important;" >0.00064614111580874</span>
reactome	CD19+ B	L8	R-HSA-76005	Response to elevated platelet cytosolic Ca2+	<span style=" color: red !important;" >0.706384848748338</span>
reactome	CD19+ B	L8	R-HSA-114608	Platelet degranulation	<span style=" color: red !important;" >0.231432202567839</span>
reactome	CD19+ B	L8	R-HSA-76002	Platelet activation, signaling and aggregation	<span style=" color: red !important;" >0.0252623002452426</span>
reactome	CD19+ B	L8	R-HSA-109582	Hemostasis	<span style=" color: red !important;" >0.000407534393526032</span>
wikipathway	CD19+ B	L1	WP477	Cytoplasmic Ribosomal Proteins	<span style=" color: green !important;" >0.999999999999907</span>
wikipathway	CD19+ B	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	<span style=" color: green !important;" >0.999918859916203</span>
wikipathway_cancer	CD19+ B	L1	WP619	Type II interferon signaling (IFNG)	<span style=" color: green !important;" >0.999863579914409</span>

CD56+ NK

pbmc_res_set_summary %>%
  filter(celltype == 'CD56+ NK') %>%
  filter(active_set, thresh==1e-4) %>%
  db_component_kable

Adding missing grouping variables: `db`, `celltype`, `top_component`

db	celltype	top_component	geneSet	description	pip
gobp	CD56+ NK	L1	GO:0002376	immune system process	<span style=" color: green !important;" >0.999998415304339</span>
gobp	CD56+ NK	L2	GO:0045047	protein targeting to ER	<span style=" color: red !important;" >0.682786144147153</span>
gobp	CD56+ NK	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.209785127668247</span>
gobp	CD56+ NK	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.0712305252918061</span>
gobp	CD56+ NK	L2	GO:0006613	cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.0382267562392382</span>
gobp	CD56+ NK	L4	GO:0006119	oxidative phosphorylation	<span style=" color: green !important;" >0.981575408284152</span>
gobp	CD56+ NK	L4	GO:0009123	nucleoside monophosphate metabolic process	<span style=" color: red !important;" >0.00751725679613058</span>
gobp	CD56+ NK	L4	GO:0042773	ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.00504616694105076</span>
gobp	CD56+ NK	L4	GO:0042775	mitochondrial ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.00356583700729807</span>
gobp	CD56+ NK	L4	GO:0009161	ribonucleoside monophosphate metabolic process	<span style=" color: red !important;" >0.00314627190684258</span>
gobp	CD56+ NK	L4	GO:0009126	purine nucleoside monophosphate metabolic process	<span style=" color: red !important;" >0.00184701119525377</span>
gobp	CD56+ NK	L4	GO:0009167	purine ribonucleoside monophosphate metabolic process	<span style=" color: red !important;" >0.00184701119525377</span>
gobp	CD56+ NK	L4	GO:0022900	electron transport chain	<span style=" color: red !important;" >0.0017166414433879</span>
gobp	CD56+ NK	L4	GO:0022904	respiratory electron transport chain	<span style=" color: red !important;" >0.00153917641145329</span>
gobp	CD56+ NK	L4	GO:0046034	ATP metabolic process	<span style=" color: red !important;" >0.000947236633707993</span>
gobp	CD56+ NK	L5	GO:0008380	RNA splicing	<span style=" color: red !important;" >0.590744524371383</span>
gobp	CD56+ NK	L5	GO:0006397	mRNA processing	<span style=" color: red !important;" >0.222524709416129</span>
gobp	CD56+ NK	L5	GO:0000375	RNA splicing, via transesterification reactions	<span style=" color: red !important;" >0.0582561122282698</span>
gobp	CD56+ NK	L5	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	<span style=" color: red !important;" >0.0544142179241016</span>
gobp	CD56+ NK	L5	GO:0000398	mRNA splicing, via spliceosome	<span style=" color: red !important;" >0.0544142179241016</span>
gobp	CD56+ NK	L5	GO:0016071	mRNA metabolic process	<span style=" color: red !important;" >0.0145223502033037</span>
gobp_nr	CD56+ NK	L1	GO:0036230	granulocyte activation	<span style=" color: red !important;" >0.665507403243785</span>
gobp_nr	CD56+ NK	L1	GO:0002446	neutrophil mediated immunity	<span style=" color: red !important;" >0.335442878271956</span>
gobp_nr	CD56+ NK	L2	GO:0006413	translational initiation	<span style=" color: green !important;" >0.99548773368734</span>
gobp_nr	CD56+ NK	L3	GO:0042110	T cell activation	<span style=" color: green !important;" >0.985660130026994</span>
gobp_nr	CD56+ NK	L3	GO:0007159	leukocyte cell-cell adhesion	<span style=" color: red !important;" >0.00817191764319258</span>
gobp_nr	CD56+ NK	L4	GO:0009123	nucleoside monophosphate metabolic process	<span style=" color: green !important;" >0.981592710152146</span>
gobp_nr	CD56+ NK	L4	GO:0009141	nucleoside triphosphate metabolic process	<span style=" color: red !important;" >0.0159047739538065</span>
gobp_nr	CD56+ NK	L4	GO:0009259	ribonucleotide metabolic process	<span style=" color: red !important;" >0.00137244907750789</span>
gobp_nr	CD56+ NK	L5	GO:0042113	B cell activation	<span style=" color: green !important;" >0.99727245196416</span>
gomf	CD56+ NK	L1	GO:0003735	structural constituent of ribosome	<span style=" color: green !important;" >0.999999999999999</span>
gomf	CD56+ NK	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	<span style=" color: green !important;" >0.996770584349283</span>
gomf	CD56+ NK	L2	GO:0003700	DNA-binding transcription factor activity	<span style=" color: red !important;" >0.00335654880277059</span>
gomf	CD56+ NK	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	<span style=" color: red !important;" >0.52466380080945</span>
gomf	CD56+ NK	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	<span style=" color: red !important;" >0.281690588134962</span>
gomf	CD56+ NK	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	<span style=" color: red !important;" >0.176078508119199</span>
gomf	CD56+ NK	L3	GO:1990837	sequence-specific double-stranded DNA binding	<span style=" color: red !important;" >0.0110809288112284</span>
gomf	CD56+ NK	L3	GO:0003690	double-stranded DNA binding	<span style=" color: red !important;" >0.00671717319054521</span>
gomf	CD56+ NK	L3	GO:0043565	sequence-specific DNA binding	<span style=" color: red !important;" >0.000626085792263753</span>
gomf	CD56+ NK	L3	GO:0000987	proximal promoter sequence-specific DNA binding	<span style=" color: red !important;" >0.00036790679417642</span>
gomf	CD56+ NK	L3	GO:0001067	regulatory region nucleic acid binding	<span style=" color: red !important;" >0.000251707443836069</span>
gomf	CD56+ NK	L3	GO:0044212	transcription regulatory region DNA binding	<span style=" color: red !important;" >0.000226812998128212</span>
kegg	CD56+ NK	L1	hsa03010	Ribosome	<span style=" color: green !important;" >0.99999999999974</span>
kegg	CD56+ NK	L2	hsa05012	Parkinson disease	<span style=" color: green !important;" >0.999997842304999</span>
kegg	CD56+ NK	L3	hsa04640	Hematopoietic cell lineage	<span style=" color: green !important;" >0.997854126506646</span>
reactome	CD56+ NK	L1	R-HSA-168256	Immune System	<span style=" color: green !important;" >0.999999999999966</span>
reactome	CD56+ NK	L2	R-HSA-156842	Eukaryotic Translation Elongation	<span style=" color: red !important;" >0.864742536856063</span>
reactome	CD56+ NK	L2	R-HSA-156902	Peptide chain elongation	<span style=" color: red !important;" >0.106897566460362</span>
reactome	CD56+ NK	L2	R-HSA-192823	Viral mRNA Translation	<span style=" color: red !important;" >0.0271582604054716</span>
reactome	CD56+ NK	L2	R-HSA-72764	Eukaryotic Translation Termination	<span style=" color: red !important;" >0.00241317499950555</span>
reactome	CD56+ NK	L2	R-HSA-72689	Formation of a pool of free 40S subunits	<span style=" color: red !important;" >0.00141870838965241</span>
reactome	CD56+ NK	L3	R-HSA-212436	Generic Transcription Pathway	<span style=" color: red !important;" >0.68127739585357</span>
reactome	CD56+ NK	L3	R-HSA-74160	Gene expression (Transcription)	<span style=" color: red !important;" >0.296792949917508</span>
reactome	CD56+ NK	L3	R-HSA-73857	RNA Polymerase II Transcription	<span style=" color: red !important;" >0.0222263519097332</span>
reactome	CD56+ NK	L4	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	<span style=" color: green !important;" >0.993324533392242</span>
reactome	CD56+ NK	L4	R-HSA-1428517	The citric acid (TCA) cycle and respiratory electron transport	<span style=" color: red !important;" >0.00603401657316116</span>
reactome	CD56+ NK	L4	R-HSA-611105	Respiratory electron transport	<span style=" color: red !important;" >0.00157556665476488</span>
reactome	CD56+ NK	L5	R-HSA-8878171	Transcriptional regulation by RUNX1	<span style=" color: green !important;" >0.97128180665404</span>
reactome	CD56+ NK	L5	R-HSA-157118	Signaling by NOTCH	<span style=" color: red !important;" >0.0439386134612366</span>
reactome	CD56+ NK	L5	R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs	<span style=" color: red !important;" >0.0199801192168844</span>
reactome	CD56+ NK	L6	R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	<span style=" color: red !important;" >0.880824832409136</span>
reactome	CD56+ NK	L6	R-HSA-983169	Class I MHC mediated antigen processing & presentation	<span style=" color: red !important;" >0.118994963852104</span>
reactome	CD56+ NK	L6	R-HSA-8951664	Neddylation	<span style=" color: red !important;" >0.000972083746535013</span>
wikipathway	CD56+ NK	L1	WP477	Cytoplasmic Ribosomal Proteins	<span style=" color: green !important;" >1</span>
wikipathway	CD56+ NK	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	<span style=" color: green !important;" >0.990862019433003</span>
wikipathway	CD56+ NK	L2	WP623	Oxidative phosphorylation	<span style=" color: red !important;" >0.0189766446579098</span>

T cell

pbmc_res_set_summary %>%
  filter(celltype == 'T cell') %>%
  filter(active_set, thresh==1e-4) %>%
  db_component_kable

Adding missing grouping variables: `db`, `celltype`, `top_component`

db	celltype	top_component	geneSet	description	pip
gobp	T cell	L1	GO:0001775	cell activation	<span style=" color: green !important;" >0.998243490581058</span>
gobp	T cell	L1	GO:0045321	leukocyte activation	<span style=" color: red !important;" >0.00286420092825412</span>
gobp	T cell	L2	GO:0006119	oxidative phosphorylation	<span style=" color: green !important;" >0.998867320720395</span>
gobp	T cell	L2	GO:0042773	ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.0023066924918852</span>
gobp	T cell	L2	GO:0042775	mitochondrial ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.00209073341052279</span>
gobp	T cell	L3	GO:0010941	regulation of cell death	<span style=" color: red !important;" >0.404035437148868</span>
gobp	T cell	L3	GO:0008219	cell death	<span style=" color: red !important;" >0.367067203128673</span>
gobp	T cell	L3	GO:0043067	regulation of programmed cell death	<span style=" color: red !important;" >0.0598125813344138</span>
gobp	T cell	L3	GO:0042981	regulation of apoptotic process	<span style=" color: red !important;" >0.0595901782002641</span>
gobp	T cell	L3	GO:0012501	programmed cell death	<span style=" color: red !important;" >0.0428480095786762</span>
gobp	T cell	L3	GO:0006915	apoptotic process	<span style=" color: red !important;" >0.0385478112991525</span>
gobp	T cell	L3	GO:0097190	apoptotic signaling pathway	<span style=" color: red !important;" >0.0206934598276991</span>
gobp	T cell	L3	GO:0048518	positive regulation of biological process	<span style=" color: red !important;" >0.00970233532368381</span>
gobp	T cell	L3	GO:0010942	positive regulation of cell death	<span style=" color: red !important;" >0.00624600959039168</span>
gobp	T cell	L3	GO:0048522	positive regulation of cellular process	<span style=" color: red !important;" >0.00603763209058406</span>
gobp	T cell	L3	GO:0048519	negative regulation of biological process	<span style=" color: red !important;" >0.00546887738370505</span>
gobp	T cell	L3	GO:0043068	positive regulation of programmed cell death	<span style=" color: red !important;" >0.00209014350358461</span>
gobp	T cell	L3	GO:0043065	positive regulation of apoptotic process	<span style=" color: red !important;" >0.00193399448533771</span>
gobp	T cell	L4	GO:0045047	protein targeting to ER	<span style=" color: red !important;" >0.422517754846463</span>
gobp	T cell	L4	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.370059387377491</span>
gobp	T cell	L4	GO:0072599	establishment of protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.138094584905281</span>
gobp	T cell	L4	GO:0070972	protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.0438561363685445</span>
gobp	T cell	L4	GO:0006613	cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.0317425197962778</span>
gobp	T cell	L5	GO:0002376	immune system process	<span style=" color: green !important;" >0.998468900817696</span>
gobp	T cell	L5	GO:0006955	immune response	<span style=" color: red !important;" >0.00288124340072227</span>
gobp_nr	T cell	L1	GO:0036230	granulocyte activation	<span style=" color: red !important;" >0.732429735587743</span>
gobp_nr	T cell	L1	GO:0002446	neutrophil mediated immunity	<span style=" color: red !important;" >0.270336034815327</span>
gobp_nr	T cell	L2	GO:0042110	T cell activation	<span style=" color: green !important;" >0.999990596278583</span>
gobp_nr	T cell	L3	GO:0070972	protein localization to endoplasmic reticulum	<span style=" color: green !important;" >0.999855861356505</span>
gomf	T cell	L1	GO:0005515	protein binding	<span style=" color: green !important;" >0.999999999999996</span>
kegg	T cell	L1	hsa05010	Alzheimer disease	<span style=" color: green !important;" >0.999999276670234</span>
reactome	T cell	L1	R-HSA-6798695	Neutrophil degranulation	<span style=" color: green !important;" >0.999999999999371</span>
reactome	T cell	L2	R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	<span style=" color: red !important;" >0.586005479354723</span>
reactome	T cell	L2	R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	<span style=" color: red !important;" >0.400596683089486</span>
reactome	T cell	L2	R-HSA-72689	Formation of a pool of free 40S subunits	<span style=" color: red !important;" >0.00918003962007052</span>
reactome	T cell	L2	R-HSA-72613	Eukaryotic Translation Initiation	<span style=" color: red !important;" >0.00466852361335934</span>
reactome	T cell	L2	R-HSA-72737	Cap-dependent Translation Initiation	<span style=" color: red !important;" >0.00466852361335934</span>
reactome	T cell	L2	R-HSA-192823	Viral mRNA Translation	<span style=" color: red !important;" >0.00349644548656469</span>
reactome	T cell	L2	R-HSA-156902	Peptide chain elongation	<span style=" color: red !important;" >0.00317407099445022</span>

CD14+ Monocyte

pbmc_res_set_summary %>%
  filter(celltype == 'CD14+ Monocyte') %>%
  filter(active_set, thresh==1e-4) %>%
  db_component_kable

Adding missing grouping variables: `db`, `celltype`, `top_component`

db	celltype	top_component	geneSet	description	pip	pValueHypergeometric
gobp	CD14+ Monocyte	L1	GO:0045321	leukocyte activation	<span style=" color: red !important;" >0.913955996656784</span>	0.0000000
gobp	CD14+ Monocyte	L1	GO:0001775	cell activation	<span style=" color: red !important;" >0.0861038961576571</span>	0.0000000
gobp	CD14+ Monocyte	L2	GO:0045047	protein targeting to ER	<span style=" color: red !important;" >0.861539198812174</span>	0.0000000
gobp	CD14+ Monocyte	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.0574691369768895</span>	0.0000000
gobp	CD14+ Monocyte	L2	GO:0006613	cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.0477713854410204</span>	0.0000000
gobp	CD14+ Monocyte	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.0336165786420544</span>	0.0000000
gobp	CD14+ Monocyte	L2	GO:0070972	protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.000401591156238168</span>	0.0000000
gobp	CD14+ Monocyte	L3	GO:0006119	oxidative phosphorylation	<span style=" color: green !important;" >0.999048492769061</span>	0.0000000
gobp	CD14+ Monocyte	L3	GO:0042773	ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.00061526966849168</span>	0.0000000
gobp	CD14+ Monocyte	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.000437951615106402</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0016192	vesicle-mediated transport	<span style=" color: green !important;" >0.985143389925145</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0002376	immune system process	<span style=" color: red !important;" >0.0210152324386211</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0006955	immune response	<span style=" color: red !important;" >0.00598414884177589</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0045055	regulated exocytosis	<span style=" color: red !important;" >0.00105846105456608</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0006810	transport	<span style=" color: red !important;" >0.000928956786439117</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0042119	neutrophil activation	<span style=" color: red !important;" >0.000810401236960523</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0006887	exocytosis	<span style=" color: red !important;" >0.000757076172462012</span>	0.0000000
gobp	CD14+ Monocyte	L4	GO:0051234	establishment of localization	<span style=" color: red !important;" >0.000747810324681297</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0006915	apoptotic process	<span style=" color: red !important;" >0.272017554202987</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0012501	programmed cell death	<span style=" color: red !important;" >0.194857583380731</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0043067	regulation of programmed cell death	<span style=" color: red !important;" >0.194088173818995</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0042981	regulation of apoptotic process	<span style=" color: red !important;" >0.158326414667851</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0010941	regulation of cell death	<span style=" color: red !important;" >0.10083762777805</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0008219	cell death	<span style=" color: red !important;" >0.0513299924130467</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0097190	apoptotic signaling pathway	<span style=" color: red !important;" >0.00254918838420504</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0006950	response to stress	<span style=" color: red !important;" >0.000930732251314792</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0010942	positive regulation of cell death	<span style=" color: red !important;" >0.000657647931395888</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0050790	regulation of catalytic activity	<span style=" color: red !important;" >0.000573508659057254</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0048518	positive regulation of biological process	<span style=" color: red !important;" >0.000545987494292133</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0010033	response to organic substance	<span style=" color: red !important;" >0.000481190817748667</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0070887	cellular response to chemical stimulus	<span style=" color: red !important;" >0.000450649515349011</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:2001233	regulation of apoptotic signaling pathway	<span style=" color: red !important;" >0.000349195404672376</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0043065	positive regulation of apoptotic process	<span style=" color: red !important;" >0.00032984108689027</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0043068	positive regulation of programmed cell death	<span style=" color: red !important;" >0.000290053025053139</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0043069	negative regulation of programmed cell death	<span style=" color: red !important;" >0.000181772401672053</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0043066	negative regulation of apoptotic process	<span style=" color: red !important;" >0.000147644072101105</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0051716	cellular response to stimulus	<span style=" color: red !important;" >0.000136512713189374</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0048522	positive regulation of cellular process	<span style=" color: red !important;" >0.000135936601124764</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0060548	negative regulation of cell death	<span style=" color: red !important;" >0.000122829004029934</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0050896	response to stimulus	<span style=" color: red !important;" >0.00011255017314471</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0048523	negative regulation of cellular process	<span style=" color: red !important;" >7.49396073772557e-05</span>	0.0000000
gobp	CD14+ Monocyte	L5	GO:0048519	negative regulation of biological process	<span style=" color: red !important;" >6.92053062711917e-05</span>	0.0000000
gobp	CD14+ Monocyte	L6	GO:0006518	peptide metabolic process	<span style=" color: red !important;" >0.790995030090949</span>	0.0000000
gobp	CD14+ Monocyte	L6	GO:0006412	translation	<span style=" color: red !important;" >0.119614037058977</span>	0.0000000
gobp	CD14+ Monocyte	L6	GO:0043043	peptide biosynthetic process	<span style=" color: red !important;" >0.0828579448699818</span>	0.0000000
gobp	CD14+ Monocyte	L6	GO:0043603	cellular amide metabolic process	<span style=" color: red !important;" >0.00254329546224519</span>	0.0000000
gobp	CD14+ Monocyte	L6	GO:0043604	amide biosynthetic process	<span style=" color: red !important;" >0.00124595731038435</span>	0.0000000
gobp	CD14+ Monocyte	L7	GO:0008380	RNA splicing	<span style=" color: red !important;" >0.422448316361525</span>	0.0000000
gobp	CD14+ Monocyte	L7	GO:0000375	RNA splicing, via transesterification reactions	<span style=" color: red !important;" >0.19679459335928</span>	0.0000000
gobp	CD14+ Monocyte	L7	GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	<span style=" color: red !important;" >0.178759471245491</span>	0.0000000
gobp	CD14+ Monocyte	L7	GO:0000398	mRNA splicing, via spliceosome	<span style=" color: red !important;" >0.178759471245491</span>	0.0000000
gobp	CD14+ Monocyte	L7	GO:0006397	mRNA processing	<span style=" color: red !important;" >0.0212448579074473</span>	0.0000000
gobp	CD14+ Monocyte	L7	GO:0016071	mRNA metabolic process	<span style=" color: red !important;" >0.00160999577015686</span>	0.0000000
gobp_nr	CD14+ Monocyte	L1	GO:0036230	granulocyte activation	<span style=" color: green !important;" >0.975928025123381</span>	0.0000000
gobp_nr	CD14+ Monocyte	L1	GO:0002446	neutrophil mediated immunity	<span style=" color: red !important;" >0.0246951417690048</span>	0.0000000
gobp_nr	CD14+ Monocyte	L2	GO:0006413	translational initiation	<span style=" color: green !important;" >0.999994018876987</span>	0.0000000
gobp_nr	CD14+ Monocyte	L3	GO:0009123	nucleoside monophosphate metabolic process	<span style=" color: green !important;" >0.988352798616283</span>	0.0000000
gobp_nr	CD14+ Monocyte	L3	GO:0009141	nucleoside triphosphate metabolic process	<span style=" color: red !important;" >0.0125932371081144</span>	0.0000000
gobp_nr	CD14+ Monocyte	L4	GO:0002521	leukocyte differentiation	<span style=" color: red !important;" >0.619222288628166</span>	0.0000000
gobp_nr	CD14+ Monocyte	L4	GO:0042110	T cell activation	<span style=" color: red !important;" >0.358464783041196</span>	0.0000000
gobp_nr	CD14+ Monocyte	L4	GO:0002694	regulation of leukocyte activation	<span style=" color: red !important;" >0.00793501697430843</span>	0.0000000
gobp_nr	CD14+ Monocyte	L4	GO:1903706	regulation of hemopoiesis	<span style=" color: red !important;" >0.00445659052005509</span>	0.0000000
gobp_nr	CD14+ Monocyte	L5	GO:0008380	RNA splicing	<span style=" color: red !important;" >0.876773132747017</span>	0.0000000
gobp_nr	CD14+ Monocyte	L5	GO:0006397	mRNA processing	<span style=" color: red !important;" >0.0896324054247939</span>	0.0000000
gobp_nr	CD14+ Monocyte	L5	GO:1903311	regulation of mRNA metabolic process	<span style=" color: red !important;" >0.00430389549836563</span>	0.0000000
gobp_nr	CD14+ Monocyte	L6	GO:0090150	establishment of protein localization to membrane	<span style=" color: red !important;" >0.756201036295744</span>	0.0000000
gobp_nr	CD14+ Monocyte	L6	GO:0070972	protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.243465201424837</span>	0.0000000
gobp_nr	CD14+ Monocyte	L6	GO:0006605	protein targeting	<span style=" color: red !important;" >0.00495025186440967</span>	0.0000000
gomf	CD14+ Monocyte	L1	GO:0003723	RNA binding	<span style=" color: green !important;" >0.999999822304653</span>	0.0000000
gomf	CD14+ Monocyte	L2	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	<span style=" color: green !important;" >0.999827482454419</span>	0.0000000
gomf	CD14+ Monocyte	L2	GO:0003700	DNA-binding transcription factor activity	<span style=" color: red !important;" >0.000227989524673178</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0001012	RNA polymerase II regulatory region DNA binding	<span style=" color: red !important;" >0.660320565777245</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	<span style=" color: red !important;" >0.292436321580928</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0000987	proximal promoter sequence-specific DNA binding	<span style=" color: red !important;" >0.036062059217844</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	<span style=" color: red !important;" >0.00772449074681092</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0000976	transcription regulatory region sequence-specific DNA binding	<span style=" color: red !important;" >0.00308292567214929</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:1990837	sequence-specific double-stranded DNA binding	<span style=" color: red !important;" >0.00070252840459839</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0043565	sequence-specific DNA binding	<span style=" color: red !important;" >0.000386897461082891</span>	0.0000000
gomf	CD14+ Monocyte	L3	GO:0044212	transcription regulatory region DNA binding	<span style=" color: red !important;" >0.00010172217576454</span>	0.0000000
gomf	CD14+ Monocyte	L4	GO:0003735	structural constituent of ribosome	<span style=" color: green !important;" >0.999999999996356</span>	0.0000000
gomf	CD14+ Monocyte	L5	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	<span style=" color: red !important;" >0.827083558750439</span>	0.0000000
gomf	CD14+ Monocyte	L5	GO:0008137	NADH dehydrogenase (ubiquinone) activity	<span style=" color: red !important;" >0.0778621792476983</span>	0.0000000
gomf	CD14+ Monocyte	L5	GO:0050136	NADH dehydrogenase (quinone) activity	<span style=" color: red !important;" >0.0778621792476983</span>	0.0000000
gomf	CD14+ Monocyte	L5	GO:0003954	NADH dehydrogenase activity	<span style=" color: red !important;" >0.0178702201177219</span>	0.0000000
gomf	CD14+ Monocyte	L5	GO:0016651	oxidoreductase activity, acting on NAD(P)H	<span style=" color: red !important;" >0.00034694713121397</span>	0.0000000
gomf	CD14+ Monocyte	L6	GO:0045296	cadherin binding	<span style=" color: red !important;" >0.789080093597068</span>	0.0000000
gomf	CD14+ Monocyte	L6	GO:0050839	cell adhesion molecule binding	<span style=" color: red !important;" >0.188160373616359</span>	0.0000000
kegg	CD14+ Monocyte	L1	hsa03010	Ribosome	<span style=" color: green !important;" >0.999999999999889</span>	0.0000000
kegg	CD14+ Monocyte	L2	hsa05012	Parkinson disease	<span style=" color: green !important;" >0.999902118704163</span>	0.0000000
reactome	CD14+ Monocyte	L1	R-HSA-6798695	Neutrophil degranulation	<span style=" color: green !important;" >0.999995355573276</span>	0.0000000
reactome	CD14+ Monocyte	L2	R-HSA-72766	Translation	<span style=" color: green !important;" >0.99999999999981</span>	0.0000000
reactome	CD14+ Monocyte	L3	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	<span style=" color: green !important;" >0.99961105913657</span>	0.0000000
reactome	CD14+ Monocyte	L3	R-HSA-611105	Respiratory electron transport	<span style=" color: red !important;" >0.000839226913661562</span>	0.0000000
reactome	CD14+ Monocyte	L5	R-HSA-72172	mRNA Splicing	<span style=" color: red !important;" >0.674955580706303</span>	0.0000000
reactome	CD14+ Monocyte	L5	R-HSA-72163	mRNA Splicing - Major Pathway	<span style=" color: red !important;" >0.306411442261019</span>	0.0000000
reactome	CD14+ Monocyte	L5	R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	<span style=" color: red !important;" >0.0182645263922769</span>	0.0000000
reactome	CD14+ Monocyte	L6	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	<span style=" color: green !important;" >0.997487749726619</span>	0.0000000
reactome	CD14+ Monocyte	L7	R-HSA-379726	Mitochondrial tRNA aminoacylation	<span style=" color: green !important;" >0.99729860552702</span>	0.6931782
wikipathway	CD14+ Monocyte	L1	WP477	Cytoplasmic Ribosomal Proteins	<span style=" color: green !important;" >0.999999999999998</span>	0.0000000
wikipathway	CD14+ Monocyte	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	<span style=" color: green !important;" >0.999831154578974</span>	0.0000000

CD34+

pbmc_res_set_summary %>%
  filter(celltype == 'CD34+') %>%
  filter(active_set, thresh==1e-4) %>%
  db_component_kable

Adding missing grouping variables: `db`, `celltype`, `top_component`

db	celltype	top_component	geneSet	description	pip
gobp	CD34+	L1	GO:0001775	cell activation	<span style=" color: green !important;" >0.987053979028693</span>
gobp	CD34+	L1	GO:0045321	leukocyte activation	<span style=" color: red !important;" >0.0137772991951518</span>
gobp	CD34+	L2	GO:0006613	cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.813781011088962</span>
gobp	CD34+	L2	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	<span style=" color: red !important;" >0.153626340011531</span>
gobp	CD34+	L2	GO:0045047	protein targeting to ER	<span style=" color: red !important;" >0.0290629664314263</span>
gobp	CD34+	L2	GO:0072599	establishment of protein localization to endoplasmic reticulum	<span style=" color: red !important;" >0.00852780905068462</span>
gobp	CD34+	L3	GO:0006119	oxidative phosphorylation	<span style=" color: green !important;" >0.998941297041509</span>
gobp	CD34+	L3	GO:0042773	ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.00219768696027844</span>
gobp	CD34+	L3	GO:0042775	mitochondrial ATP synthesis coupled electron transport	<span style=" color: red !important;" >0.00204003835356481</span>
gobp	CD34+	L4	GO:0044419	interspecies interaction between organisms	<span style=" color: red !important;" >0.420351724582621</span>
gobp	CD34+	L4	GO:0016032	viral process	<span style=" color: red !important;" >0.383314261542707</span>
gobp	CD34+	L4	GO:0044403	symbiont process	<span style=" color: red !important;" >0.195249491605503</span>
gobp_nr	CD34+	L1	GO:0002446	neutrophil mediated immunity	<span style=" color: red !important;" >0.607843923572364</span>
gobp_nr	CD34+	L1	GO:0036230	granulocyte activation	<span style=" color: red !important;" >0.394659620593896</span>
gobp_nr	CD34+	L2	GO:0006413	translational initiation	<span style=" color: green !important;" >0.999660829824325</span>
gomf	CD34+	L1	GO:0003735	structural constituent of ribosome	<span style=" color: green !important;" >0.999999999995723</span>
gomf	CD34+	L2	GO:0005515	protein binding	<span style=" color: green !important;" >0.999999999999647</span>
kegg	CD34+	L1	hsa00190	Oxidative phosphorylation	<span style=" color: green !important;" >0.992175886824888</span>
kegg	CD34+	L1	hsa05012	Parkinson disease	<span style=" color: red !important;" >0.0333607954124152</span>
kegg	CD34+	L2	hsa03010	Ribosome	<span style=" color: green !important;" >0.999999994840815</span>
reactome	CD34+	L1	R-HSA-72764	Eukaryotic Translation Termination	<span style=" color: green !important;" >0.99305623315484</span>
reactome	CD34+	L1	R-HSA-156902	Peptide chain elongation	<span style=" color: red !important;" >0.00637721696595694</span>
reactome	CD34+	L1	R-HSA-156842	Eukaryotic Translation Elongation	<span style=" color: red !important;" >0.00406036803807552</span>
reactome	CD34+	L2	R-HSA-6798695	Neutrophil degranulation	<span style=" color: green !important;" >0.986271609979922</span>
reactome	CD34+	L2	R-HSA-168249	Innate Immune System	<span style=" color: red !important;" >0.0166937283411153</span>
reactome	CD34+	L3	R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	<span style=" color: green !important;" >0.997732525415435</span>
reactome	CD34+	L3	R-HSA-611105	Respiratory electron transport	<span style=" color: red !important;" >0.00375852255366282</span>
reactome	CD34+	L4	R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	<span style=" color: green !important;" >0.999950260516898</span>
wikipathway	CD34+	L1	WP477	Cytoplasmic Ribosomal Proteins	<span style=" color: green !important;" >1</span>
wikipathway	CD34+	L2	WP111	Electron Transport Chain (OXPHOS system in mitochondria)	<span style=" color: green !important;" >0.999997114937164</span>

knitr::knit_exit()