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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')

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)) %>%
  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 pValueHypergeometric
gobp CD19+ B L1 GO:0002376 immune system process <span style=" color: green !important;" >0.999957465451611</span> 2.526664e-269
gobp CD19+ B L2 GO:0045047, GO:0006613, GO:0072599, GO:0006614 protein targeting to ER , cotranslational protein targeting to membrane , establishment of protein localization to endoplasmic reticulum, SRP-dependent cotranslational protein targeting to membrane <span style=" color: green !important;" >0.962052077569581</span>, <span style=" color: red !important;" >0.0216561609975944</span> , <span style=" color: red !important;" >0.0145368812974931</span> , <span style=" color: red !important;" >0.00410197009826074</span> 2.532661e-36, 1.984360e-34, 8.259486e-35, 9.432379e-33
gobp CD19+ B L3 GO:0042773, GO:0042775, GO:0006119 ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport, oxidative phosphorylation <span style=" color: red !important;" >0.624496308507348</span> , <span style=" color: red !important;" >0.360022211508933</span> , <span style=" color: red !important;" >0.0175238678609325</span> 1.605842e-25, 4.064871e-25, 2.075548e-29
gobp CD19+ B L5 GO:0001775, GO:0045321, GO:0002366, GO:0002263 cell activation , leukocyte activation , leukocyte activation involved in immune response, cell activation involved in immune response <span style=" color: green !important;" >0.978054175097094</span> , <span style=" color: red !important;" >0.0218972720769344</span> , <span style=" color: red !important;" >0.000595713062097269</span>, <span style=" color: red !important;" >0.000577006708652683</span> 4.428372e-165, 7.685551e-152, 1.405750e-97, 8.244815e-98
gobp CD19+ B L6 GO:0008380, GO:0000377, GO:0000398, GO:0000375, GO:0006397, GO:0050684, GO:0043484, GO:0000380, GO:0048024, GO:0016071 RNA splicing , RNA splicing, via transesterification reactions with bulged adenosine as nucleophile, mRNA splicing, via spliceosome , RNA splicing, via transesterification reactions , mRNA processing , regulation of mRNA processing , regulation of RNA splicing , alternative mRNA splicing, via spliceosome , regulation of mRNA splicing, via spliceosome , mRNA metabolic process <span style=" color: red !important;" >0.822736133183297</span> , <span style=" color: red !important;" >0.049644134105862</span> , <span style=" color: red !important;" >0.049644134105862</span> , <span style=" color: red !important;" >0.0330051165719797</span> , <span style=" color: red !important;" >0.0172340532174977</span> , <span style=" color: red !important;" >0.0094172042437507</span> , <span style=" color: red !important;" >0.00722067130606185</span>, <span style=" color: red !important;" >0.00293948333200866</span>, <span style=" color: red !important;" >0.00183491753300979</span>, <span style=" color: red !important;" >0.00105163745213244</span> 2.990867e-36, 3.387925e-28, 3.387925e-28, 6.887275e-28, 4.148046e-35, 6.486732e-18, 1.878944e-17, 7.772036e-12, 1.226187e-12, 1.879865e-61
gobp_nr CD19+ B L1 GO:0002446, GO:0036230 neutrophil mediated immunity, granulocyte activation <span style=" color: red !important;" >0.515144038268755</span>, <span style=" color: red !important;" >0.485735788920244</span> 4.775951e-71, 2.936426e-71
gobp_nr CD19+ B L2 GO:0070972 protein localization to endoplasmic reticulum <span style=" color: green !important;" >0.999958026971368</span> 7.382525e-33
gobp_nr CD19+ B L4 GO:0009123, GO:0009141 nucleoside monophosphate metabolic process, nucleoside triphosphate metabolic process <span style=" color: green !important;" >0.984497563614406</span>, <span style=" color: red !important;" >0.0164867485447392</span> 7.371703e-40, 2.011998e-35
gobp_nr CD19+ B L5 GO:0002764 immune response-regulating signaling pathway <span style=" color: green !important;" >0.996185347850837</span> 8.086259e-55
gomf CD19+ B L1 GO:0003723 RNA binding <span style=" color: green !important;" >0.999743954825178</span> 3.707404e-127
gomf CD19+ B L2 GO:0000981, GO:0003700 DNA-binding transcription factor activity, RNA polymerase II-specific, DNA-binding transcription factor activity <span style=" color: green !important;" >0.995003782967434</span>, <span style=" color: red !important;" >0.00505824116754672</span> 1.942472e-16, 2.738455e-20
gomf CD19+ B L3 GO:0000977, GO:0001012, GO:0000987, GO:0000978, GO:0000976, GO:0003690, GO:1990837, GO:0001067, GO:0044212 RNA polymerase II regulatory region sequence-specific DNA binding, RNA polymerase II regulatory region DNA binding , proximal promoter sequence-specific DNA binding , RNA polymerase II proximal promoter sequence-specific DNA binding, transcription regulatory region sequence-specific DNA binding , double-stranded DNA binding , sequence-specific double-stranded DNA binding , regulatory region nucleic acid binding , transcription regulatory region DNA binding <span style=" color: red !important;" >0.487251391312216</span> , <span style=" color: red !important;" >0.431399316819835</span> , <span style=" color: red !important;" >0.0365953412200314</span> , <span style=" color: red !important;" >0.0243679373454444</span> , <span style=" color: red !important;" >0.0132413813040726</span> , <span style=" color: red !important;" >0.00592789564076235</span> , <span style=" color: red !important;" >0.00136790369019235</span> , <span style=" color: red !important;" >0.00046527212966796</span> , <span style=" color: red !important;" >0.000355705894771408</span> 2.822624e-34, 2.658045e-34, 8.331683e-30, 2.661740e-29, 5.231202e-34, 8.306797e-44, 1.071864e-35, 1.990230e-36, 5.770724e-36
gomf CD19+ B L6 GO:0003735 structural constituent of ribosome <span style=" color: green !important;" >0.995344082600683</span> 2.994289e-32
gomf CD19+ B L7 GO:0003954, GO:0008137, GO:0050136, GO:0016655, GO:0016651 NADH dehydrogenase activity , NADH dehydrogenase (ubiquinone) activity , NADH dehydrogenase (quinone) activity , oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor, oxidoreductase activity, acting on NAD(P)H <span style=" color: red !important;" >0.325953617177259</span> , <span style=" color: red !important;" >0.218583180359325</span> , <span style=" color: red !important;" >0.218583180359325</span> , <span style=" color: red !important;" >0.177265521649769</span> , <span style=" color: red !important;" >0.0387976083993536</span> 1.385073e-13, 3.413042e-13, 3.413042e-13, 1.315866e-14, 2.200053e-17
kegg CD19+ B L1 hsa00190, hsa05012 Oxidative phosphorylation, Parkinson disease <span style=" color: green !important;" >0.997990176564082</span>, <span style=" color: red !important;" >0.0125303037367086</span> 5.027625e-29, 3.697096e-27
kegg CD19+ B L2 hsa04640 Hematopoietic cell lineage <span style=" color: green !important;" >0.999795101338638</span> 8.551153e-21
kegg CD19+ B L3 hsa03010 Ribosome <span style=" color: green !important;" >0.999999982887443</span> 3.24636e-30
reactome CD19+ B L1 R-HSA-168256 Immune System <span style=" color: green !important;" >1</span> 7.929629e-180
reactome CD19+ B L2 R-HSA-156842 , R-HSA-156902 , R-HSA-192823 , R-HSA-2408557, R-HSA-72764 , R-HSA-72689 , R-HSA-1799339, R-HSA-72706 , R-HSA-156827 Eukaryotic Translation Elongation , Peptide chain elongation , Viral mRNA Translation , Selenocysteine synthesis , Eukaryotic Translation Termination , Formation of a pool of free 40S subunits , SRP-dependent cotranslational protein targeting to membrane , GTP hydrolysis and joining of the 60S ribosomal subunit , L13a-mediated translational silencing of Ceruloplasmin expression <span style=" color: red !important;" >0.760651463839203</span> , <span style=" color: red !important;" >0.12438973980464</span> , <span style=" color: red !important;" >0.0671329230529306</span> , <span style=" color: red !important;" >0.0260066810882063</span> , <span style=" color: red !important;" >0.0172676775018812</span> , <span style=" color: red !important;" >0.00330537630812389</span>, <span style=" color: red !important;" >0.00313197971436374</span>, <span style=" color: red !important;" >0.00122676226108998</span>, <span style=" color: red !important;" >0.00100083013030172</span> 7.985692e-32, 1.394445e-30, 1.394445e-30, 9.148401e-31, 9.148401e-31, 2.883586e-31, 2.254688e-34, 4.386878e-33, 1.096100e-32
reactome CD19+ B L3 R-HSA-74160 , R-HSA-212436, R-HSA-73857 Gene expression (Transcription), Generic Transcription Pathway , RNA Polymerase II Transcription <span style=" color: red !important;" >0.885679352792777</span> , <span style=" color: red !important;" >0.0726625717379175</span>, <span style=" color: red !important;" >0.041834760675025</span> 8.299766e-30, 2.296229e-21, 4.497082e-27
reactome CD19+ B L4 R-HSA-163200 , R-HSA-1428517, R-HSA-611105 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., The citric acid (TCA) cycle and respiratory electron transport , Respiratory electron transport <span style=" color: red !important;" >0.845323000060671</span> , <span style=" color: red !important;" >0.14938336590149</span> , <span style=" color: red !important;" >0.00596574446721121</span> 9.259886e-26, 5.557534e-29, 1.019708e-20
reactome CD19+ B L5 R-HSA-983168, R-HSA-983169 Antigen processing: Ubiquitination & Proteasome degradation, Class I MHC mediated antigen processing & presentation <span style=" color: green !important;" >0.997049696139591</span>, <span style=" color: red !important;" >0.00311879186973374</span> 6.660057e-09, 4.421456e-14
reactome CD19+ B L6 R-HSA-180585 , R-HSA-1234176, R-HSA-211733 , R-HSA-69601 , R-HSA-69610 , R-HSA-69613 , R-HSA-69541 , R-HSA-69229 , R-HSA-75815 , R-HSA-180534 , R-HSA-169911 , R-HSA-349425 , R-HSA-9604323, R-HSA-8854050, R-HSA-1236978, R-HSA-174154 , R-HSA-1169091, R-HSA-174084 , R-HSA-1234174, R-HSA-2262749, R-HSA-983705 , R-HSA-174113 , R-HSA-450408 , R-HSA-69563 , R-HSA-69580 , R-HSA-174184 , R-HSA-351202 , R-HSA-68867 , R-HSA-176409 , R-HSA-350562 , R-HSA-69615 , R-HSA-5362768, R-HSA-174178 , R-HSA-179419 , R-HSA-5610780 Vif-mediated degradation of APOBEC3G , Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha , Regulation of activated PAK-2p34 by proteasome mediated degradation , Ubiquitin Mediated Degradation of Phosphorylated Cdc25A , p53-Independent DNA Damage Response , p53-Independent G1/S DNA damage checkpoint , Stabilization of p53 , Ubiquitin-dependent degradation of Cyclin D1 , Ubiquitin-dependent degradation of Cyclin D , Vpu mediated degradation of CD4 , Regulation of Apoptosis , Autodegradation of the E3 ubiquitin ligase COP1 , Negative regulation of NOTCH4 signaling , FBXL7 down-regulates AURKA during mitotic entry and in early mitosis , Cross-presentation of soluble exogenous antigens (endosomes) , APC/C:Cdc20 mediated degradation of Securin , Activation of NF-kappaB in B cells , Autodegradation of Cdh1 by Cdh1:APC/C , Regulation of Hypoxia-inducible Factor (HIF) by oxygen , Cellular response to hypoxia , Signaling by the B Cell Receptor (BCR) , SCF-beta-TrCP mediated degradation of Emi1 , AUF1 (hnRNP D0) binds and destabilizes mRNA , p53-Dependent G1 DNA Damage Response , p53-Dependent G1/S DNA damage checkpoint , Cdc20:Phospho-APC/C mediated degradation of Cyclin A , Metabolism of polyamines , Assembly of the pre-replicative complex , APC/C:Cdc20 mediated degradation of mitotic proteins , Regulation of ornithine decarboxylase (ODC) , G1/S DNA Damage Checkpoints , Hh mutants that don’t undergo autocatalytic processing are degraded by ERAD , APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1, APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint , Degradation of GLI1 by the proteasome <span style=" color: red !important;" >0.749039310761527</span> , <span style=" color: red !important;" >0.0319137208638701</span> , <span style=" color: red !important;" >0.0256472437189241</span> , <span style=" color: red !important;" >0.0242873384108474</span> , <span style=" color: red !important;" >0.0242873384108474</span> , <span style=" color: red !important;" >0.0242873384108474</span> , <span style=" color: red !important;" >0.0225422403485689</span> , <span style=" color: red !important;" >0.0120133659466743</span> , <span style=" color: red !important;" >0.0120133659466743</span> , <span style=" color: red !important;" >0.0119846232558787</span> , <span style=" color: red !important;" >0.0108046763000044</span> , <span style=" color: red !important;" >0.0101911528157629</span> , <span style=" color: red !important;" >0.0071579855747933</span> , <span style=" color: red !important;" >0.00703778872278604</span> , <span style=" color: red !important;" >0.00406554835881989</span> , <span style=" color: red !important;" >0.00385891217123191</span> , <span style=" color: red !important;" >0.00376792382128477</span> , <span style=" color: red !important;" >0.00361414870965138</span> , <span style=" color: red !important;" >0.00305797077052683</span> , <span style=" color: red !important;" >0.00305797077052683</span> , <span style=" color: red !important;" >0.00286836400043933</span> , <span style=" color: red !important;" >0.0024109403813769</span> , <span style=" color: red !important;" >0.00171267983373247</span> , <span style=" color: red !important;" >0.00150097375541414</span> , <span style=" color: red !important;" >0.00150097375541414</span> , <span style=" color: red !important;" >0.00133190881117529</span> , <span style=" color: red !important;" >0.00131731594365259</span> , <span style=" color: red !important;" >0.00121050465862294</span> , <span style=" color: red !important;" >0.00116496309289926</span> , <span style=" color: red !important;" >0.00102467992167676</span> , <span style=" color: red !important;" >0.000957829552408529</span>, <span style=" color: red !important;" >0.00095140800156257</span> , <span style=" color: red !important;" >0.000862233445453997</span>, <span style=" color: red !important;" >0.000720719571974726</span>, <span style=" color: red !important;" >0.000661022828454261</span> 2.433018e-13, 1.735945e-13, 7.193688e-12, 5.424345e-12, 5.424345e-12, 5.424345e-12, 1.741572e-12, 1.238520e-11, 1.238520e-11, 1.238520e-11, 5.424345e-12, 1.238520e-11, 8.907071e-12, 4.486919e-11, 3.832536e-11, 1.884699e-12, 9.112376e-15, 2.855537e-12, 1.201408e-13, 1.201408e-13, 6.637218e-26, 6.786237e-11, 3.945748e-12, 8.833851e-12, 8.833851e-12, 3.601389e-12, 3.634256e-14, 8.655424e-13, 2.266767e-12, 2.223514e-10, 1.211591e-11, 6.786237e-11, 1.005329e-11, 1.005329e-11, 1.369024e-10
reactome CD19+ B L7 R-HSA-72163 , R-HSA-72172 , R-HSA-109688, R-HSA-73856 , R-HSA-72203 mRNA Splicing - Major Pathway , mRNA Splicing , Cleavage of Growing Transcript in the Termination Region, RNA Polymerase II Transcription Termination , Processing of Capped Intron-Containing Pre-mRNA <span style=" color: red !important;" >0.545788750456562</span> , <span style=" color: red !important;" >0.443954636390887</span> , <span style=" color: red !important;" >0.00214822879004417</span>, <span style=" color: red !important;" >0.00214822879004417</span>, <span style=" color: red !important;" >0.00064614111580874</span> 1.512823e-22, 6.075949e-23, 1.754344e-08, 1.754344e-08, 5.751685e-20
reactome CD19+ B L8 R-HSA-76005 , R-HSA-114608, R-HSA-76002 , R-HSA-109582 Response to elevated platelet cytosolic Ca2+ , Platelet degranulation , Platelet activation, signaling and aggregation, Hemostasis <span style=" color: red !important;" >0.706384848748338</span> , <span style=" color: red !important;" >0.231432202567839</span> , <span style=" color: red !important;" >0.0252623002452426</span> , <span style=" color: red !important;" >0.000407534393526032</span> 1.614308e-20, 3.964098e-19, 1.767108e-29, 2.862108e-43
wikipathway CD19+ B L1 WP477 Cytoplasmic Ribosomal Proteins <span style=" color: green !important;" >0.999999999999907</span> 1.254966e-28
wikipathway CD19+ B L2 WP111 Electron Transport Chain (OXPHOS system in mitochondria) <span style=" color: green !important;" >0.999918859916203</span> 4.726328e-27
wikipathway_cancer CD19+ B L1 WP619 Type II interferon signaling (IFNG) <span style=" color: green !important;" >0.999863579914409</span> 2.260695e-11

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 pValueHypergeometric
gobp CD56+ NK L1 GO:0002376 immune system process <span style=" color: green !important;" >0.999998415304339</span> 2.947781e-276
gobp CD56+ NK L2 GO:0045047, GO:0072599, GO:0006614, GO:0006613 protein targeting to ER , establishment of protein localization to endoplasmic reticulum, SRP-dependent cotranslational protein targeting to membrane , cotranslational protein targeting to membrane <span style=" color: red !important;" >0.682786144147153</span> , <span style=" color: red !important;" >0.209785127668247</span> , <span style=" color: red !important;" >0.0712305252918061</span>, <span style=" color: red !important;" >0.0382267562392382</span> 9.495193e-34, 1.280004e-33, 1.085035e-31, 6.691900e-32
gobp CD56+ NK L4 GO:0006119, GO:0009123, GO:0042773, GO:0042775, GO:0009161, GO:0009126, GO:0009167, GO:0022900, GO:0022904, GO:0046034 oxidative phosphorylation , nucleoside monophosphate metabolic process , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport, ribonucleoside monophosphate metabolic process , purine nucleoside monophosphate metabolic process , purine ribonucleoside monophosphate metabolic process , electron transport chain , respiratory electron transport chain , ATP metabolic process <span style=" color: green !important;" >0.981575408284152</span> , <span style=" color: red !important;" >0.00751725679613058</span> , <span style=" color: red !important;" >0.00504616694105076</span> , <span style=" color: red !important;" >0.00356583700729807</span> , <span style=" color: red !important;" >0.00314627190684258</span> , <span style=" color: red !important;" >0.00184701119525377</span> , <span style=" color: red !important;" >0.00184701119525377</span> , <span style=" color: red !important;" >0.0017166414433879</span> , <span style=" color: red !important;" >0.00153917641145329</span> , <span style=" color: red !important;" >0.000947236633707993</span> 2.922476e-26, 3.203909e-41, 3.830697e-19, 8.794047e-19, 6.509045e-39, 2.429909e-37, 2.429909e-37, 8.544784e-26, 1.986936e-19, 5.926956e-33
gobp CD56+ NK L5 GO:0008380, GO:0006397, GO:0000375, GO:0000377, GO:0000398, GO:0016071 RNA splicing , mRNA processing , RNA splicing, via transesterification reactions , RNA splicing, via transesterification reactions with bulged adenosine as nucleophile, mRNA splicing, via spliceosome , mRNA metabolic process <span style=" color: red !important;" >0.590744524371383</span> , <span style=" color: red !important;" >0.222524709416129</span> , <span style=" color: red !important;" >0.0582561122282698</span>, <span style=" color: red !important;" >0.0544142179241016</span>, <span style=" color: red !important;" >0.0544142179241016</span>, <span style=" color: red !important;" >0.0145223502033037</span> 1.141014e-39, 2.284529e-42, 9.013714e-32, 1.546092e-31, 1.546092e-31, 3.470305e-72
gobp_nr CD56+ NK L1 GO:0036230, GO:0002446 granulocyte activation , neutrophil mediated immunity <span style=" color: red !important;" >0.665507403243785</span>, <span style=" color: red !important;" >0.335442878271956</span> 8.805074e-72, 8.544872e-71
gobp_nr CD56+ NK L2 GO:0006413 translational initiation <span style=" color: green !important;" >0.99548773368734</span> 9.230939e-37
gobp_nr CD56+ NK L3 GO:0042110, GO:0007159 T cell activation , leukocyte cell-cell adhesion <span style=" color: green !important;" >0.985660130026994</span>, <span style=" color: red !important;" >0.00817191764319258</span> 3.058385e-58, 4.198497e-42
gobp_nr CD56+ NK L4 GO:0009123, GO:0009141, GO:0009259 nucleoside monophosphate metabolic process, nucleoside triphosphate metabolic process , ribonucleotide metabolic process <span style=" color: green !important;" >0.981592710152146</span>, <span style=" color: red !important;" >0.0159047739538065</span> , <span style=" color: red !important;" >0.00137244907750789</span> 5.279727e-40, 6.177407e-35, 6.209394e-41
gobp_nr CD56+ NK L5 GO:0042113 B cell activation <span style=" color: green !important;" >0.99727245196416</span> 9.375193e-38
gomf CD56+ NK L1 GO:0003735 structural constituent of ribosome <span style=" color: green !important;" >0.999999999999999</span> 1.182382e-44
gomf CD56+ NK L2 GO:0000981, GO:0003700 DNA-binding transcription factor activity, RNA polymerase II-specific, DNA-binding transcription factor activity <span style=" color: green !important;" >0.996770584349283</span>, <span style=" color: red !important;" >0.00335654880277059</span> 3.240357e-18, 3.414777e-22
gomf CD56+ NK L3 GO:0000977, GO:0000976, GO:0001012, GO:1990837, GO:0003690, GO:0043565, GO:0000987, GO:0001067, GO:0044212 RNA polymerase II regulatory region sequence-specific DNA binding, transcription regulatory region sequence-specific DNA binding , RNA polymerase II regulatory region DNA binding , sequence-specific double-stranded DNA binding , double-stranded DNA binding , sequence-specific DNA binding , proximal promoter sequence-specific DNA binding , regulatory region nucleic acid binding , transcription regulatory region DNA binding <span style=" color: red !important;" >0.52466380080945</span> , <span style=" color: red !important;" >0.281690588134962</span> , <span style=" color: red !important;" >0.176078508119199</span> , <span style=" color: red !important;" >0.0110809288112284</span> , <span style=" color: red !important;" >0.00671717319054521</span> , <span style=" color: red !important;" >0.000626085792263753</span>, <span style=" color: red !important;" >0.00036790679417642</span> , <span style=" color: red !important;" >0.000251707443836069</span>, <span style=" color: red !important;" >0.000226812998128212</span> 6.617810e-37, 8.879108e-39, 2.222485e-36, 3.657740e-40, 6.115445e-47, 6.947558e-44, 1.156041e-28, 1.529375e-38, 4.443215e-38
kegg CD56+ NK L1 hsa03010 Ribosome <span style=" color: green !important;" >0.99999999999974</span> 9.217956e-36
kegg CD56+ NK L2 hsa05012 Parkinson disease <span style=" color: green !important;" >0.999997842304999</span> 2.585983e-32
kegg CD56+ NK L3 hsa04640 Hematopoietic cell lineage <span style=" color: green !important;" >0.997854126506646</span> 4.769128e-19
reactome CD56+ NK L1 R-HSA-168256 Immune System <span style=" color: green !important;" >0.999999999999966</span> 9.313458e-193
reactome CD56+ NK L2 R-HSA-156842, R-HSA-156902, R-HSA-192823, R-HSA-72764 , R-HSA-72689 Eukaryotic Translation Elongation , Peptide chain elongation , Viral mRNA Translation , Eukaryotic Translation Termination , Formation of a pool of free 40S subunits <span style=" color: red !important;" >0.864742536856063</span> , <span style=" color: red !important;" >0.106897566460362</span> , <span style=" color: red !important;" >0.0271582604054716</span> , <span style=" color: red !important;" >0.00241317499950555</span>, <span style=" color: red !important;" >0.00141870838965241</span> 6.208280e-34, 1.059151e-32, 1.059151e-32, 1.163653e-32, 2.528922e-34
reactome CD56+ NK L3 R-HSA-212436, R-HSA-74160 , R-HSA-73857 Generic Transcription Pathway , Gene expression (Transcription), RNA Polymerase II Transcription <span style=" color: red !important;" >0.68127739585357</span> , <span style=" color: red !important;" >0.296792949917508</span> , <span style=" color: red !important;" >0.0222263519097332</span> 1.321222e-30, 3.097765e-41, 2.085936e-37
reactome CD56+ NK L4 R-HSA-163200 , R-HSA-1428517, R-HSA-611105 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., The citric acid (TCA) cycle and respiratory electron transport , Respiratory electron transport <span style=" color: green !important;" >0.993324533392242</span>, <span style=" color: red !important;" >0.00603401657316116</span>, <span style=" color: red !important;" >0.00157556665476488</span> 1.782486e-25, 1.148730e-26, 7.189017e-19
reactome CD56+ NK L5 R-HSA-8878171, R-HSA-157118 , R-HSA-8939236 Transcriptional regulation by RUNX1 , Signaling by NOTCH , RUNX1 regulates transcription of genes involved in differentiation of HSCs <span style=" color: green !important;" >0.97128180665404</span>, <span style=" color: red !important;" >0.0439386134612366</span>, <span style=" color: red !important;" >0.0199801192168844</span> 4.649106e-25, 1.638239e-27, 2.982359e-17
reactome CD56+ NK L6 R-HSA-983168 , R-HSA-983169 , R-HSA-8951664 Antigen processing: Ubiquitination & Proteasome degradation, Class I MHC mediated antigen processing & presentation , Neddylation <span style=" color: red !important;" >0.880824832409136</span> , <span style=" color: red !important;" >0.118994963852104</span> , <span style=" color: red !important;" >0.000972083746535013</span> 4.596003e-14, 1.163224e-19, 1.837871e-09
wikipathway CD56+ NK L1 WP477 Cytoplasmic Ribosomal Proteins <span style=" color: green !important;" >1</span> 3.731258e-31
wikipathway CD56+ NK L2 WP111, WP623 Electron Transport Chain (OXPHOS system in mitochondria), Oxidative phosphorylation <span style=" color: green !important;" >0.990862019433003</span>, <span style=" color: red !important;" >0.0189766446579098</span> 3.364560e-24, 3.188613e-17

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 pValueHypergeometric
gobp T cell L1 GO:0001775, GO:0045321 cell activation , leukocyte activation <span style=" color: green !important;" >0.998243490581058</span>, <span style=" color: red !important;" >0.00286420092825412</span> 1.098801e-248, 2.328201e-226
gobp T cell L2 GO:0006119, GO:0042773, GO:0042775 oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport <span style=" color: green !important;" >0.998867320720395</span>, <span style=" color: red !important;" >0.0023066924918852</span> , <span style=" color: red !important;" >0.00209073341052279</span> 1.891240e-33, 9.259766e-25, 2.100714e-24
gobp T cell L3 GO:0010941, GO:0008219, GO:0043067, GO:0042981, GO:0012501, GO:0006915, GO:0097190, GO:0048518, GO:0010942, GO:0048522, GO:0048519, GO:0043068, GO:0043065 regulation of cell death , cell death , regulation of programmed cell death , regulation of apoptotic process , programmed cell death , apoptotic process , apoptotic signaling pathway , positive regulation of biological process , positive regulation of cell death , positive regulation of cellular process , negative regulation of biological process , positive regulation of programmed cell death, positive regulation of apoptotic process <span style=" color: red !important;" >0.404035437148868</span> , <span style=" color: red !important;" >0.367067203128673</span> , <span style=" color: red !important;" >0.0598125813344138</span> , <span style=" color: red !important;" >0.0595901782002641</span> , <span style=" color: red !important;" >0.0428480095786762</span> , <span style=" color: red !important;" >0.0385478112991525</span> , <span style=" color: red !important;" >0.0206934598276991</span> , <span style=" color: red !important;" >0.00970233532368381</span>, <span style=" color: red !important;" >0.00624600959039168</span>, <span style=" color: red !important;" >0.00603763209058406</span>, <span style=" color: red !important;" >0.00546887738370505</span>, <span style=" color: red !important;" >0.00209014350358461</span>, <span style=" color: red !important;" >0.00193399448533771</span> 2.138535e-192, 7.032734e-238, 3.661703e-176, 1.383501e-174, 1.127119e-219, 4.508930e-213, 1.876837e-89, 0.000000e+00, 7.689401e-95, 0.000000e+00, 0.000000e+00, 3.313749e-84, 5.541783e-83
gobp T cell L4 GO:0045047, GO:0006614, GO:0072599, GO:0070972, GO:0006613 protein targeting to ER , SRP-dependent cotranslational protein targeting to membrane , establishment of protein localization to endoplasmic reticulum, protein localization to endoplasmic reticulum , cotranslational protein targeting to membrane <span style=" color: red !important;" >0.422517754846463</span> , <span style=" color: red !important;" >0.370059387377491</span> , <span style=" color: red !important;" >0.138094584905281</span> , <span style=" color: red !important;" >0.0438561363685445</span>, <span style=" color: red !important;" >0.0317425197962778</span> 6.738692e-29, 2.697911e-27, 1.069848e-28, 2.389817e-33, 4.015516e-26
gobp T cell L5 GO:0002376, GO:0006955 immune system process, immune response <span style=" color: green !important;" >0.998468900817696</span>, <span style=" color: red !important;" >0.00288124340072227</span> 0.000000e+00, 2.059792e-293
gobp_nr T cell L1 GO:0036230, GO:0002446 granulocyte activation , neutrophil mediated immunity <span style=" color: red !important;" >0.732429735587743</span>, <span style=" color: red !important;" >0.270336034815327</span> 8.893801e-111, 9.709562e-110
gobp_nr T cell L2 GO:0042110 T cell activation <span style=" color: green !important;" >0.999990596278583</span> 2.423836e-82
gobp_nr T cell L3 GO:0070972 protein localization to endoplasmic reticulum <span style=" color: green !important;" >0.999855861356505</span> 7.082395e-33
gomf T cell L1 GO:0005515 protein binding <span style=" color: green !important;" >0.999999999999996</span> 0
kegg T cell L1 hsa05010 Alzheimer disease <span style=" color: green !important;" >0.999999276670234</span> 1.469698e-43
reactome T cell L1 R-HSA-6798695 Neutrophil degranulation <span style=" color: green !important;" >0.999999999999371</span> 4.546436e-106
reactome T cell L2 R-HSA-72706 , R-HSA-156827, R-HSA-72689 , R-HSA-72613 , R-HSA-72737 , R-HSA-192823, R-HSA-156902 GTP hydrolysis and joining of the 60S ribosomal subunit , L13a-mediated translational silencing of Ceruloplasmin expression, Formation of a pool of free 40S subunits , Eukaryotic Translation Initiation , Cap-dependent Translation Initiation , Viral mRNA Translation , Peptide chain elongation <span style=" color: red !important;" >0.586005479354723</span> , <span style=" color: red !important;" >0.400596683089486</span> , <span style=" color: red !important;" >0.00918003962007052</span>, <span style=" color: red !important;" >0.00466852361335934</span>, <span style=" color: red !important;" >0.00466852361335934</span>, <span style=" color: red !important;" >0.00349644548656469</span>, <span style=" color: red !important;" >0.00317407099445022</span> 4.807983e-34, 1.097988e-33, 4.127765e-30, 2.515433e-32, 2.515433e-32, 6.804717e-29, 6.804717e-29

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, GO:0001775 leukocyte activation, cell activation <span style=" color: red !important;" >0.913955996656784</span> , <span style=" color: red !important;" >0.0861038961576571</span> 1.266041e-152, 4.878344e-159
gobp CD14+ Monocyte L2 GO:0045047, GO:0006614, GO:0006613, GO:0072599, GO:0070972 protein targeting to ER , SRP-dependent cotranslational protein targeting to membrane , cotranslational protein targeting to membrane , establishment of protein localization to endoplasmic reticulum, protein localization to endoplasmic reticulum <span style=" color: red !important;" >0.861539198812174</span> , <span style=" color: red !important;" >0.0574691369768895</span> , <span style=" color: red !important;" >0.0477713854410204</span> , <span style=" color: red !important;" >0.0336165786420544</span> , <span style=" color: red !important;" >0.000401591156238168</span> 6.375283e-36, 1.173258e-33, 6.348075e-34, 1.637199e-34, 6.297308e-36
gobp CD14+ Monocyte L3 GO:0006119, GO:0042773, GO:0042775 oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport <span style=" color: green !important;" >0.999048492769061</span> , <span style=" color: red !important;" >0.00061526966849168</span> , <span style=" color: red !important;" >0.000437951615106402</span> 1.775985e-31, 7.453047e-24, 1.881893e-23
gobp CD14+ Monocyte L4 GO:0016192, GO:0002376, GO:0006955, GO:0045055, GO:0006810, GO:0042119, GO:0006887, GO:0051234 vesicle-mediated transport , immune system process , immune response , regulated exocytosis , transport , neutrophil activation , exocytosis , establishment of localization <span style=" color: green !important;" >0.985143389925145</span> , <span style=" color: red !important;" >0.0210152324386211</span> , <span style=" color: red !important;" >0.00598414884177589</span> , <span style=" color: red !important;" >0.00105846105456608</span> , <span style=" color: red !important;" >0.000928956786439117</span>, <span style=" color: red !important;" >0.000810401236960523</span>, <span style=" color: red !important;" >0.000757076172462012</span>, <span style=" color: red !important;" >0.000747810324681297</span> 2.927115e-145, 3.659065e-228, 8.733808e-175, 1.874116e-97, 3.322971e-280, 8.790244e-89, 1.301435e-98, 1.576263e-285
gobp CD14+ Monocyte L5 GO:0006915, GO:0012501, GO:0043067, GO:0042981, GO:0010941, GO:0008219, GO:0097190, GO:0006950, GO:0010942, GO:0050790, GO:0048518, GO:0010033, GO:0070887, GO:2001233, GO:0043065, GO:0043068, GO:0043069, GO:0043066, GO:0051716, GO:0048522, GO:0060548, GO:0050896, GO:0048523, GO:0048519 apoptotic process , programmed cell death , regulation of programmed cell death , regulation of apoptotic process , regulation of cell death , cell death , apoptotic signaling pathway , response to stress , positive regulation of cell death , regulation of catalytic activity , positive regulation of biological process , response to organic substance , cellular response to chemical stimulus , regulation of apoptotic signaling pathway , positive regulation of apoptotic process , positive regulation of programmed cell death, negative regulation of programmed cell death, negative regulation of apoptotic process , cellular response to stimulus , positive regulation of cellular process , negative regulation of cell death , response to stimulus , negative regulation of cellular process , negative regulation of biological process <span style=" color: red !important;" >0.272017554202987</span> , <span style=" color: red !important;" >0.194857583380731</span> , <span style=" color: red !important;" >0.194088173818995</span> , <span style=" color: red !important;" >0.158326414667851</span> , <span style=" color: red !important;" >0.10083762777805</span> , <span style=" color: red !important;" >0.0513299924130467</span> , <span style=" color: red !important;" >0.00254918838420504</span> , <span style=" color: red !important;" >0.000930732251314792</span>, <span style=" color: red !important;" >0.000657647931395888</span>, <span style=" color: red !important;" >0.000573508659057254</span>, <span style=" color: red !important;" >0.000545987494292133</span>, <span style=" color: red !important;" >0.000481190817748667</span>, <span style=" color: red !important;" >0.000450649515349011</span>, <span style=" color: red !important;" >0.000349195404672376</span>, <span style=" color: red !important;" >0.00032984108689027</span> , <span style=" color: red !important;" >0.000290053025053139</span>, <span style=" color: red !important;" >0.000181772401672053</span>, <span style=" color: red !important;" >0.000147644072101105</span>, <span style=" color: red !important;" >0.000136512713189374</span>, <span style=" color: red !important;" >0.000135936601124764</span>, <span style=" color: red !important;" >0.000122829004029934</span>, <span style=" color: red !important;" >0.00011255017314471</span> , <span style=" color: red !important;" >7.49396073772557e-05</span>, <span style=" color: red !important;" >6.92053062711917e-05</span> 4.451786e-113, 8.301835e-116, 7.895560e-95, 1.189669e-93, 3.999854e-100, 1.272117e-119, 1.841090e-46, 1.495543e-192, 1.854200e-49, 1.361590e-109, 1.578429e-290, 7.322372e-153, 5.666552e-149, 3.085467e-32, 1.847719e-44, 1.848623e-44, 2.655090e-54, 1.185635e-52, 7.682074e-311, 9.343174e-247, 5.466768e-57, 0.000000e+00, 3.391448e-204, 2.249264e-243
gobp CD14+ Monocyte L6 GO:0006518, GO:0006412, GO:0043043, GO:0043603, GO:0043604 peptide metabolic process , translation , peptide biosynthetic process , cellular amide metabolic process, amide biosynthetic process <span style=" color: red !important;" >0.790995030090949</span> , <span style=" color: red !important;" >0.119614037058977</span> , <span style=" color: red !important;" >0.0828579448699818</span> , <span style=" color: red !important;" >0.00254329546224519</span>, <span style=" color: red !important;" >0.00124595731038435</span> 4.678462e-78, 1.088274e-65, 4.547896e-66, 2.326686e-80, 8.359365e-66
gobp CD14+ Monocyte L7 GO:0008380, GO:0000375, GO:0000377, GO:0000398, GO:0006397, GO:0016071 RNA splicing , RNA splicing, via transesterification reactions , RNA splicing, via transesterification reactions with bulged adenosine as nucleophile, mRNA splicing, via spliceosome , mRNA processing , mRNA metabolic process <span style=" color: red !important;" >0.422448316361525</span> , <span style=" color: red !important;" >0.19679459335928</span> , <span style=" color: red !important;" >0.178759471245491</span> , <span style=" color: red !important;" >0.178759471245491</span> , <span style=" color: red !important;" >0.0212448579074473</span> , <span style=" color: red !important;" >0.00160999577015686</span> 9.748365e-38, 7.437684e-32, 1.388978e-31, 1.388978e-31, 7.467478e-38, 2.423046e-69
gobp_nr CD14+ Monocyte L1 GO:0036230, GO:0002446 granulocyte activation , neutrophil mediated immunity <span style=" color: green !important;" >0.975928025123381</span>, <span style=" color: red !important;" >0.0246951417690048</span> 2.402996e-86, 1.745099e-83
gobp_nr CD14+ Monocyte L2 GO:0006413 translational initiation <span style=" color: green !important;" >0.999994018876987</span> 1.131814e-41
gobp_nr CD14+ Monocyte L3 GO:0009123, GO:0009141 nucleoside monophosphate metabolic process, nucleoside triphosphate metabolic process <span style=" color: green !important;" >0.988352798616283</span>, <span style=" color: red !important;" >0.0125932371081144</span> 5.790725e-44, 5.147747e-40
gobp_nr CD14+ Monocyte L4 GO:0002521, GO:0042110, GO:0002694, GO:1903706 leukocyte differentiation , T cell activation , regulation of leukocyte activation, regulation of hemopoiesis <span style=" color: red !important;" >0.619222288628166</span> , <span style=" color: red !important;" >0.358464783041196</span> , <span style=" color: red !important;" >0.00793501697430843</span>, <span style=" color: red !important;" >0.00445659052005509</span> 9.454964e-48, 2.311611e-47, 1.222276e-45, 1.243755e-35
gobp_nr CD14+ Monocyte L5 GO:0008380, GO:0006397, GO:1903311 RNA splicing , mRNA processing , regulation of mRNA metabolic process <span style=" color: red !important;" >0.876773132747017</span> , <span style=" color: red !important;" >0.0896324054247939</span> , <span style=" color: red !important;" >0.00430389549836563</span> 3.387665e-36, 3.352465e-36, 9.733062e-24
gobp_nr CD14+ Monocyte L6 GO:0090150, GO:0070972, GO:0006605 establishment of protein localization to membrane, protein localization to endoplasmic reticulum , protein targeting <span style=" color: red !important;" >0.756201036295744</span> , <span style=" color: red !important;" >0.243465201424837</span> , <span style=" color: red !important;" >0.00495025186440967</span> 9.080340e-44, 4.739729e-35, 6.381780e-43
gomf CD14+ Monocyte L1 GO:0003723 RNA binding <span style=" color: green !important;" >0.999999822304653</span> 1.173386e-141
gomf CD14+ Monocyte L2 GO:0000981, GO:0003700 DNA-binding transcription factor activity, RNA polymerase II-specific, DNA-binding transcription factor activity <span style=" color: green !important;" >0.999827482454419</span> , <span style=" color: red !important;" >0.000227989524673178</span> 1.396985e-15, 1.312394e-20
gomf CD14+ Monocyte L3 GO:0001012, GO:0000977, GO:0000987, GO:0000978, GO:0000976, GO:1990837, GO:0043565, GO:0044212 RNA polymerase II regulatory region DNA binding , RNA polymerase II regulatory region sequence-specific DNA binding, proximal promoter sequence-specific DNA binding , RNA polymerase II proximal promoter sequence-specific DNA binding, transcription regulatory region sequence-specific DNA binding , sequence-specific double-stranded DNA binding , sequence-specific DNA binding , transcription regulatory region DNA binding <span style=" color: red !important;" >0.660320565777245</span> , <span style=" color: red !important;" >0.292436321580928</span> , <span style=" color: red !important;" >0.036062059217844</span> , <span style=" color: red !important;" >0.00772449074681092</span> , <span style=" color: red !important;" >0.00308292567214929</span> , <span style=" color: red !important;" >0.00070252840459839</span> , <span style=" color: red !important;" >0.000386897461082891</span>, <span style=" color: red !important;" >0.00010172217576454</span> 1.246290e-37, 4.365922e-37, 2.762407e-33, 3.447619e-32, 2.150387e-36, 1.010515e-38, 5.047518e-44, 3.418838e-38
gomf CD14+ Monocyte L4 GO:0003735 structural constituent of ribosome <span style=" color: green !important;" >0.999999999996356</span> 4.918061e-44
gomf CD14+ Monocyte L5 GO:0016655, GO:0008137, GO:0050136, GO:0003954, GO:0016651 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor, NADH dehydrogenase (ubiquinone) activity , NADH dehydrogenase (quinone) activity , NADH dehydrogenase activity , oxidoreductase activity, acting on NAD(P)H <span style=" color: red !important;" >0.827083558750439</span> , <span style=" color: red !important;" >0.0778621792476983</span> , <span style=" color: red !important;" >0.0778621792476983</span> , <span style=" color: red !important;" >0.0178702201177219</span> , <span style=" color: red !important;" >0.00034694713121397</span> 2.846509e-17, 9.084810e-15, 9.084810e-15, 5.476813e-14, 1.127698e-15
gomf CD14+ Monocyte L6 GO:0045296, GO:0050839 cadherin binding , cell adhesion molecule binding <span style=" color: red !important;" >0.789080093597068</span>, <span style=" color: red !important;" >0.188160373616359</span> 4.054477e-37, 1.113159e-41
kegg CD14+ Monocyte L1 hsa03010 Ribosome <span style=" color: green !important;" >0.999999999999889</span> 7.453734e-35
kegg CD14+ Monocyte L2 hsa05012 Parkinson disease <span style=" color: green !important;" >0.999902118704163</span> 2.609968e-33
reactome CD14+ Monocyte L1 R-HSA-6798695 Neutrophil degranulation <span style=" color: green !important;" >0.999995355573276</span> 3.105498e-81
reactome CD14+ Monocyte L2 R-HSA-72766 Translation <span style=" color: green !important;" >0.99999999999981</span> 5.172352e-59
reactome CD14+ Monocyte L3 R-HSA-163200, R-HSA-611105 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., Respiratory electron transport <span style=" color: green !important;" >0.99961105913657</span> , <span style=" color: red !important;" >0.000839226913661562</span> 1.294295e-30, 2.557783e-24
reactome CD14+ Monocyte L5 R-HSA-72172, R-HSA-72163, R-HSA-72203 mRNA Splicing , mRNA Splicing - Major Pathway , Processing of Capped Intron-Containing Pre-mRNA <span style=" color: red !important;" >0.674955580706303</span> , <span style=" color: red !important;" >0.306411442261019</span> , <span style=" color: red !important;" >0.0182645263922769</span> 2.542532e-25, 3.287091e-24, 2.103706e-25
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> 5.102985e-21
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> 1.207268e-29
wikipathway CD14+ Monocyte L2 WP111 Electron Transport Chain (OXPHOS system in mitochondria) <span style=" color: green !important;" >0.999831154578974</span> 9.058329e-28

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 pValueHypergeometric
gobp CD34+ L1 GO:0001775, GO:0045321 cell activation , leukocyte activation <span style=" color: green !important;" >0.987053979028693</span>, <span style=" color: red !important;" >0.0137772991951518</span> 2.633476e-189, 3.972660e-173
gobp CD34+ L2 GO:0006613, GO:0006614, GO:0045047, GO:0072599 cotranslational protein targeting to membrane , SRP-dependent cotranslational protein targeting to membrane , protein targeting to ER , establishment of protein localization to endoplasmic reticulum <span style=" color: red !important;" >0.813781011088962</span> , <span style=" color: red !important;" >0.153626340011531</span> , <span style=" color: red !important;" >0.0290629664314263</span> , <span style=" color: red !important;" >0.00852780905068462</span> 7.184084e-30, 2.122256e-28, 4.082612e-30, 6.229293e-30
gobp CD34+ L3 GO:0006119, GO:0042773, GO:0042775 oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport <span style=" color: green !important;" >0.998941297041509</span>, <span style=" color: red !important;" >0.00219768696027844</span>, <span style=" color: red !important;" >0.00204003835356481</span> 4.557019e-31, 6.681278e-22, 1.502267e-21
gobp CD34+ L4 GO:0044419, GO:0016032, GO:0044403 interspecies interaction between organisms, viral process , symbiont process <span style=" color: red !important;" >0.420351724582621</span>, <span style=" color: red !important;" >0.383314261542707</span>, <span style=" color: red !important;" >0.195249491605503</span> 2.033013e-99, 3.869982e-91, 3.235558e-95
gobp_nr CD34+ L1 GO:0002446, GO:0036230 neutrophil mediated immunity, granulocyte activation <span style=" color: red !important;" >0.607843923572364</span>, <span style=" color: red !important;" >0.394659620593896</span> 1.592450e-76, 1.318184e-76
gobp_nr CD34+ L2 GO:0006413 translational initiation <span style=" color: green !important;" >0.999660829824325</span> 1.64713e-38
gomf CD34+ L1 GO:0003735 structural constituent of ribosome <span style=" color: green !important;" >0.999999999995723</span> 4.128375e-42
gomf CD34+ L2 GO:0005515 protein binding <span style=" color: green !important;" >0.999999999999647</span> 0
kegg CD34+ L1 hsa00190, hsa05012 Oxidative phosphorylation, Parkinson disease <span style=" color: green !important;" >0.992175886824888</span>, <span style=" color: red !important;" >0.0333607954124152</span> 4.886096e-32, 6.352523e-33
kegg CD34+ L2 hsa03010 Ribosome <span style=" color: green !important;" >0.999999994840815</span> 5.679335e-34
reactome CD34+ L1 R-HSA-72764 , R-HSA-156902, R-HSA-156842 Eukaryotic Translation Termination, Peptide chain elongation , Eukaryotic Translation Elongation <span style=" color: green !important;" >0.99305623315484</span> , <span style=" color: red !important;" >0.00637721696595694</span>, <span style=" color: red !important;" >0.00406036803807552</span> 2.275039e-33, 7.764526e-32, 5.500776e-33
reactome CD34+ L2 R-HSA-6798695, R-HSA-168249 Neutrophil degranulation, Innate Immune System <span style=" color: green !important;" >0.986271609979922</span>, <span style=" color: red !important;" >0.0166937283411153</span> 1.517922e-75, 6.465420e-123
reactome CD34+ L3 R-HSA-163200, R-HSA-611105 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., Respiratory electron transport <span style=" color: green !important;" >0.997732525415435</span>, <span style=" color: red !important;" >0.00375852255366282</span> 8.425069e-32, 2.834000e-25
reactome CD34+ L4 R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell <span style=" color: green !important;" >0.999950260516898</span> 1.147541e-26
wikipathway CD34+ L1 WP477 Cytoplasmic Ribosomal Proteins <span style=" color: green !important;" >1</span> 1.328872e-30
wikipathway CD34+ L2 WP111 Electron Transport Chain (OXPHOS system in mitochondria) <span style=" color: green !important;" >0.999997114937164</span> 1.517475e-31 
knitr::knit_exit()