Single-cell PBMC Example
karltayeb
2022-03-16
Last updated: 2022-03-29
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Knit directory: logistic-susie-gsea/
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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)
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')
}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. ### Overview
pbmc_res_set_summary %>%
filter(active_set, thresh==1e-4) %>%
group_by(db, celltype, top_component) %>%
arrange(db, celltype, top_component) %>%
select(geneSet, description) %>% chop(c(geneSet, description)) %>%
knitr::kable()Adding missing grouping variables: `db`, `celltype`, `top_component`| db | celltype | top_component | geneSet | description |
|---|---|---|---|---|
| gobp | CD14+ Monocyte | L1 | GO:0001775, GO:0045321 | cell activation , leukocyte activation |
| gobp | CD14+ Monocyte | L2 | GO:0070972, GO:0045047, GO:0072599, GO:0006613, GO:0006614 | protein localization to endoplasmic reticulum , protein targeting to ER , establishment of protein localization to endoplasmic reticulum, cotranslational protein targeting to membrane , SRP-dependent cotranslational protein targeting to membrane |
| gobp | CD14+ Monocyte | L3 | GO:0006119, GO:0042773, GO:0042775 | oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport |
| gobp | CD14+ Monocyte | L4 | GO:0006810, GO:0006887, GO:0016192, GO:0045055, GO:0051234, GO:0002376, GO:0006955, GO:0042119 | transport , exocytosis , vesicle-mediated transport , regulated exocytosis , establishment of localization, immune system process , immune response , neutrophil activation |
| gobp | CD14+ Monocyte | L5 | GO:0050896, GO:0006950, GO:0048518, GO:0048519, GO:0048523, GO:0050790, GO:0051716, GO:0070887, GO:0048522, GO:0010033, GO:0006915, GO:0008219, GO:0010941, GO:0012501, GO:0042981, GO:0043066, GO:0043067, GO:0043069, GO:0060548, GO:0097190, GO:0010942, GO:0043065, GO:0043068, GO:2001233 | response to stimulus , response to stress , positive regulation of biological process , negative regulation of biological process , negative regulation of cellular process , regulation of catalytic activity , cellular response to stimulus , cellular response to chemical stimulus , positive regulation of cellular process , response to organic substance , apoptotic process , cell death , regulation of cell death , programmed cell death , regulation of apoptotic process , negative regulation of apoptotic process , regulation of programmed cell death , negative regulation of programmed cell death, negative regulation of cell death , apoptotic signaling pathway , positive regulation of cell death , positive regulation of apoptotic process , positive regulation of programmed cell death, regulation of apoptotic signaling pathway |
| gobp | CD14+ Monocyte | L6 | GO:0043603, GO:0043604, GO:0006412, GO:0006518, GO:0043043 | cellular amide metabolic process, amide biosynthetic process , translation , peptide metabolic process , peptide biosynthetic process |
| gobp | CD14+ Monocyte | L7 | GO:0006397, GO:0016071, GO:0008380, GO:0000375, GO:0000377, GO:0000398 | mRNA processing , mRNA metabolic process , RNA splicing , RNA splicing, via transesterification reactions , RNA splicing, via transesterification reactions with bulged adenosine as nucleophile, mRNA splicing, via spliceosome |
| gobp | CD19+ B | L1 | GO:0002376 | immune system process |
| gobp | CD19+ B | L2 | GO:0045047, GO:0072599, GO:0006613, GO:0006614 | protein targeting to ER , establishment of protein localization to endoplasmic reticulum, cotranslational protein targeting to membrane , SRP-dependent cotranslational protein targeting to membrane |
| gobp | CD19+ B | L3 | GO:0006119, GO:0042773, GO:0042775 | oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport |
| gobp | CD19+ B | L5 | GO:0001775, GO:0002263, GO:0002366, GO:0045321 | cell activation , cell activation involved in immune response , leukocyte activation involved in immune response, leukocyte activation |
| gobp | CD19+ B | L6 | GO:0006397, GO:0016071, GO:0050684, GO:0008380, GO:0043484, GO:0000375, GO:0000377, GO:0000398, GO:0048024, GO:0000380 | mRNA processing , mRNA metabolic process , regulation of mRNA processing , RNA splicing , regulation of RNA splicing , RNA splicing, via transesterification reactions , RNA splicing, via transesterification reactions with bulged adenosine as nucleophile, mRNA splicing, via spliceosome , regulation of mRNA splicing, via spliceosome , alternative mRNA splicing, via spliceosome |
| gobp | CD34+ | L1 | GO:0001775, GO:0045321 | cell activation , leukocyte activation |
| gobp | CD34+ | L2 | GO:0045047, GO:0072599, GO:0006613, GO:0006614 | protein targeting to ER , establishment of protein localization to endoplasmic reticulum, cotranslational protein targeting to membrane , SRP-dependent cotranslational protein targeting to membrane |
| gobp | CD34+ | L3 | GO:0006119, GO:0042773, GO:0042775 | oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport |
| gobp | CD34+ | L4 | GO:0016032, GO:0044403, GO:0044419 | viral process , symbiont process , interspecies interaction between organisms |
| gobp | CD56+ NK | L1 | GO:0002376 | immune system process |
| gobp | CD56+ NK | L2 | GO:0045047, GO:0072599, GO:0006613, GO:0006614 | protein targeting to ER , establishment of protein localization to endoplasmic reticulum, cotranslational protein targeting to membrane , SRP-dependent cotranslational protein targeting to membrane |
| gobp | CD56+ NK | L4 | GO:0009123, GO:0009126, GO:0009161, GO:0009167, GO:0046034, GO:0006119, GO:0022900, GO:0022904, GO:0042773, GO:0042775 | nucleoside monophosphate metabolic process , purine nucleoside monophosphate metabolic process , ribonucleoside monophosphate metabolic process , purine ribonucleoside monophosphate metabolic process , ATP metabolic process , oxidative phosphorylation , electron transport chain , respiratory electron transport chain , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport |
| gobp | CD56+ NK | L5 | GO:0006397, GO:0016071, GO:0008380, GO:0000375, GO:0000377, GO:0000398 | mRNA processing , mRNA metabolic process , RNA splicing , RNA splicing, via transesterification reactions , RNA splicing, via transesterification reactions with bulged adenosine as nucleophile, mRNA splicing, via spliceosome |
| gobp | T cell | L1 | GO:0001775, GO:0045321 | cell activation , leukocyte activation |
| gobp | T cell | L2 | GO:0006119, GO:0042773, GO:0042775 | oxidative phosphorylation , ATP synthesis coupled electron transport , mitochondrial ATP synthesis coupled electron transport |
| gobp | T cell | L3 | GO:0048518, GO:0048519, GO:0048522, GO:0006915, GO:0008219, GO:0010941, GO:0012501, GO:0042981, GO:0043067, GO:0097190, GO:0010942, GO:0043065, GO:0043068 | positive regulation of biological process , negative regulation of biological process , positive regulation of cellular process , apoptotic process , cell death , regulation of cell death , programmed cell death , regulation of apoptotic process , regulation of programmed cell death , apoptotic signaling pathway , positive regulation of cell death , positive regulation of apoptotic process , positive regulation of programmed cell death |
| gobp | T cell | L4 | GO:0070972, GO:0045047, GO:0072599, GO:0006613, GO:0006614 | protein localization to endoplasmic reticulum , protein targeting to ER , establishment of protein localization to endoplasmic reticulum, cotranslational protein targeting to membrane , SRP-dependent cotranslational protein targeting to membrane |
| gobp | T cell | L5 | GO:0002376, GO:0006955 | immune system process, immune response |
| gobp_nr | CD14+ Monocyte | L1 | GO:0002446, GO:0036230 | neutrophil mediated immunity, granulocyte activation |
| gobp_nr | CD14+ Monocyte | L2 | GO:0006413 | translational initiation |
| gobp_nr | CD14+ Monocyte | L3 | GO:0009123, GO:0009141 | nucleoside monophosphate metabolic process, nucleoside triphosphate metabolic process |
| gobp_nr | CD14+ Monocyte | L4 | GO:0002521, GO:0002694, GO:0042110, GO:1903706 | leukocyte differentiation , regulation of leukocyte activation, T cell activation , regulation of hemopoiesis |
| gobp_nr | CD14+ Monocyte | L5 | GO:0006397, GO:0008380, GO:1903311 | mRNA processing , RNA splicing , regulation of mRNA metabolic process |
| gobp_nr | CD14+ Monocyte | L6 | GO:0006605, GO:0070972, GO:0090150 | protein targeting , protein localization to endoplasmic reticulum , establishment of protein localization to membrane |
| gobp_nr | CD19+ B | L1 | GO:0002446, GO:0036230 | neutrophil mediated immunity, granulocyte activation |
| gobp_nr | CD19+ B | L2 | GO:0070972 | protein localization to endoplasmic reticulum |
| gobp_nr | CD19+ B | L4 | GO:0009123, GO:0009141 | nucleoside monophosphate metabolic process, nucleoside triphosphate metabolic process |
| gobp_nr | CD19+ B | L5 | GO:0002764 | immune response-regulating signaling pathway |
| gobp_nr | CD34+ | L1 | GO:0002446, GO:0036230 | neutrophil mediated immunity, granulocyte activation |
| gobp_nr | CD34+ | L2 | GO:0006413 | translational initiation |
| gobp_nr | CD56+ NK | L1 | GO:0002446, GO:0036230 | neutrophil mediated immunity, granulocyte activation |
| gobp_nr | CD56+ NK | L2 | GO:0006413 | translational initiation |
| gobp_nr | CD56+ NK | L3 | GO:0007159, GO:0042110 | leukocyte cell-cell adhesion, T cell activation |
| gobp_nr | CD56+ NK | L4 | GO:0009123, GO:0009141, GO:0009259 | nucleoside monophosphate metabolic process, nucleoside triphosphate metabolic process , ribonucleotide metabolic process |
| gobp_nr | CD56+ NK | L5 | GO:0042113 | B cell activation |
| gobp_nr | T cell | L1 | GO:0002446, GO:0036230 | neutrophil mediated immunity, granulocyte activation |
| gobp_nr | T cell | L2 | GO:0042110 | T cell activation |
| gobp_nr | T cell | L3 | GO:0070972 | protein localization to endoplasmic reticulum |
| gomf | CD14+ Monocyte | L1 | GO:0003723 | RNA binding |
| gomf | CD14+ Monocyte | L2 | GO:0000981, GO:0003700 | DNA-binding transcription factor activity, RNA polymerase II-specific, DNA-binding transcription factor activity |
| gomf | CD14+ Monocyte | L3 | GO:0000976, GO:0000977, GO:0000978, GO:0000987, GO:0001012, GO:0043565, GO:0044212, GO:1990837 | transcription regulatory region sequence-specific DNA binding , RNA polymerase II regulatory region sequence-specific DNA binding, RNA polymerase II proximal promoter sequence-specific DNA binding, proximal promoter sequence-specific DNA binding , RNA polymerase II regulatory region DNA binding , sequence-specific DNA binding , transcription regulatory region DNA binding , sequence-specific double-stranded DNA binding |
| gomf | CD14+ Monocyte | L4 | GO:0003735 | structural constituent of ribosome |
| gomf | CD14+ Monocyte | L5 | GO:0016651, GO:0016655, GO:0003954, GO:0008137, GO:0050136 | oxidoreductase activity, acting on NAD(P)H , oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor, NADH dehydrogenase activity , NADH dehydrogenase (ubiquinone) activity , NADH dehydrogenase (quinone) activity |
| gomf | CD14+ Monocyte | L6 | GO:0050839, GO:0045296 | cell adhesion molecule binding, cadherin binding |
| gomf | CD19+ B | L1 | GO:0003723 | RNA binding |
| gomf | CD19+ B | L2 | GO:0000981, GO:0003700 | DNA-binding transcription factor activity, RNA polymerase II-specific, DNA-binding transcription factor activity |
| gomf | CD19+ B | L3 | GO:0000976, GO:0000977, GO:0000978, GO:0000987, GO:0001012, GO:0001067, GO:0003690, GO:0044212, GO:1990837 | transcription regulatory region sequence-specific DNA binding , RNA polymerase II regulatory region sequence-specific DNA binding, RNA polymerase II proximal promoter sequence-specific DNA binding, proximal promoter sequence-specific DNA binding , RNA polymerase II regulatory region DNA binding , regulatory region nucleic acid binding , double-stranded DNA binding , transcription regulatory region DNA binding , sequence-specific double-stranded DNA binding |
| gomf | CD19+ B | L6 | GO:0003735 | structural constituent of ribosome |
| gomf | CD19+ B | L7 | GO:0016651, GO:0016655, GO:0003954, GO:0008137, GO:0050136 | oxidoreductase activity, acting on NAD(P)H , oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor, NADH dehydrogenase activity , NADH dehydrogenase (ubiquinone) activity , NADH dehydrogenase (quinone) activity |
| gomf | CD34+ | L1 | GO:0003735 | structural constituent of ribosome |
| gomf | CD34+ | L2 | GO:0005515 | protein binding |
| gomf | CD56+ NK | L1 | GO:0003735 | structural constituent of ribosome |
| gomf | CD56+ NK | L2 | GO:0000981, GO:0003700 | DNA-binding transcription factor activity, RNA polymerase II-specific, DNA-binding transcription factor activity |
| gomf | CD56+ NK | L3 | GO:0000976, GO:0000977, GO:0000987, GO:0001012, GO:0001067, GO:0003690, GO:0043565, GO:0044212, GO:1990837 | transcription regulatory region sequence-specific DNA binding , RNA polymerase II regulatory region sequence-specific DNA binding, proximal promoter sequence-specific DNA binding , RNA polymerase II regulatory region DNA binding , regulatory region nucleic acid binding , double-stranded DNA binding , sequence-specific DNA binding , transcription regulatory region DNA binding , sequence-specific double-stranded DNA binding |
| gomf | T cell | L1 | GO:0005515 | protein binding |
| kegg | CD14+ Monocyte | L1 | hsa03010 | Ribosome |
| kegg | CD14+ Monocyte | L2 | hsa05012 | Parkinson disease |
| kegg | CD19+ B | L1 | hsa00190, hsa05012 | Oxidative phosphorylation, Parkinson disease |
| kegg | CD19+ B | L2 | hsa04640 | Hematopoietic cell lineage |
| kegg | CD19+ B | L3 | hsa03010 | Ribosome |
| kegg | CD34+ | L1 | hsa00190, hsa05012 | Oxidative phosphorylation, Parkinson disease |
| kegg | CD34+ | L2 | hsa03010 | Ribosome |
| kegg | CD56+ NK | L1 | hsa03010 | Ribosome |
| kegg | CD56+ NK | L2 | hsa05012 | Parkinson disease |
| kegg | CD56+ NK | L3 | hsa04640 | Hematopoietic cell lineage |
| kegg | T cell | L1 | hsa05010 | Alzheimer disease |
| reactome | CD14+ Monocyte | L1 | R-HSA-6798695 | Neutrophil degranulation |
| reactome | CD14+ Monocyte | L2 | R-HSA-72766 | Translation |
| 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 |
| reactome | CD14+ Monocyte | L5 | R-HSA-72163, R-HSA-72172, R-HSA-72203 | mRNA Splicing - Major Pathway , mRNA Splicing , Processing of Capped Intron-Containing Pre-mRNA |
| reactome | CD14+ Monocyte | L6 | R-HSA-198933 | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |
| reactome | CD14+ Monocyte | L7 | R-HSA-379726 | Mitochondrial tRNA aminoacylation |
| reactome | CD19+ B | L1 | R-HSA-168256 | Immune System |
| reactome | CD19+ B | L2 | R-HSA-156827 , R-HSA-72689 , R-HSA-72706 , R-HSA-1799339, R-HSA-156842 , R-HSA-156902 , R-HSA-192823 , R-HSA-2408557, R-HSA-72764 | L13a-mediated translational silencing of Ceruloplasmin expression, Formation of a pool of free 40S subunits , GTP hydrolysis and joining of the 60S ribosomal subunit , SRP-dependent cotranslational protein targeting to membrane , Eukaryotic Translation Elongation , Peptide chain elongation , Viral mRNA Translation , Selenocysteine synthesis , Eukaryotic Translation Termination |
| reactome | CD19+ B | L3 | R-HSA-212436, R-HSA-73857 , R-HSA-74160 | Generic Transcription Pathway , RNA Polymerase II Transcription, Gene expression (Transcription) |
| reactome | CD19+ B | L4 | R-HSA-1428517, R-HSA-163200 , R-HSA-611105 | The citric acid (TCA) cycle and respiratory electron transport , Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., Respiratory electron transport |
| reactome | CD19+ B | L5 | R-HSA-983168, R-HSA-983169 | Antigen processing: Ubiquitination & Proteasome degradation, Class I MHC mediated antigen processing & presentation |
| reactome | CD19+ B | L6 | R-HSA-983705 , R-HSA-351202 , R-HSA-69563 , R-HSA-69580 , R-HSA-69615 , R-HSA-69229 , R-HSA-75815 , R-HSA-1169091, R-HSA-1234174, R-HSA-1234176, R-HSA-1236978, R-HSA-169911 , R-HSA-174084 , R-HSA-174113 , R-HSA-174154 , R-HSA-174178 , R-HSA-174184 , R-HSA-176409 , R-HSA-179419 , R-HSA-180534 , R-HSA-180585 , R-HSA-211733 , R-HSA-2262749, R-HSA-349425 , R-HSA-350562 , R-HSA-450408 , R-HSA-5362768, R-HSA-5610780, R-HSA-68867 , R-HSA-69541 , R-HSA-69601 , R-HSA-69610 , R-HSA-69613 , R-HSA-8854050, R-HSA-9604323 | Signaling by the B Cell Receptor (BCR) , Metabolism of polyamines , p53-Dependent G1 DNA Damage Response , p53-Dependent G1/S DNA damage checkpoint , G1/S DNA Damage Checkpoints , Ubiquitin-dependent degradation of Cyclin D1 , Ubiquitin-dependent degradation of Cyclin D , Activation of NF-kappaB in B cells , Regulation of Hypoxia-inducible Factor (HIF) by oxygen , Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha , Cross-presentation of soluble exogenous antigens (endosomes) , Regulation of Apoptosis , Autodegradation of Cdh1 by Cdh1:APC/C , SCF-beta-TrCP mediated degradation of Emi1 , APC/C:Cdc20 mediated degradation of Securin , APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1, Cdc20:Phospho-APC/C mediated degradation of Cyclin A , APC/C:Cdc20 mediated degradation of mitotic proteins , APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint , Vpu mediated degradation of CD4 , Vif-mediated degradation of APOBEC3G , Regulation of activated PAK-2p34 by proteasome mediated degradation , Cellular response to hypoxia , Autodegradation of the E3 ubiquitin ligase COP1 , Regulation of ornithine decarboxylase (ODC) , AUF1 (hnRNP D0) binds and destabilizes mRNA , Hh mutants that don’t undergo autocatalytic processing are degraded by ERAD , Degradation of GLI1 by the proteasome , Assembly of the pre-replicative complex , Stabilization of p53 , Ubiquitin Mediated Degradation of Phosphorylated Cdc25A , p53-Independent DNA Damage Response , p53-Independent G1/S DNA damage checkpoint , FBXL7 down-regulates AURKA during mitotic entry and in early mitosis , Negative regulation of NOTCH4 signaling |
| reactome | CD19+ B | L7 | R-HSA-72163 , R-HSA-72172 , R-HSA-72203 , R-HSA-109688, R-HSA-73856 | mRNA Splicing - Major Pathway , mRNA Splicing , Processing of Capped Intron-Containing Pre-mRNA , Cleavage of Growing Transcript in the Termination Region, RNA Polymerase II Transcription Termination |
| reactome | CD19+ B | L8 | R-HSA-109582, R-HSA-114608, R-HSA-76002 , R-HSA-76005 | Hemostasis , Platelet degranulation , Platelet activation, signaling and aggregation, Response to elevated platelet cytosolic Ca2+ |
| reactome | CD34+ | L1 | R-HSA-156842, R-HSA-156902, R-HSA-72764 | Eukaryotic Translation Elongation , Peptide chain elongation , Eukaryotic Translation Termination |
| reactome | CD34+ | L2 | R-HSA-168249 , R-HSA-6798695 | Innate Immune System , Neutrophil degranulation |
| 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 |
| reactome | CD34+ | L4 | R-HSA-198933 | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |
| reactome | CD56+ NK | L1 | R-HSA-168256 | Immune System |
| reactome | CD56+ NK | L2 | R-HSA-72689 , R-HSA-156842, R-HSA-156902, R-HSA-192823, R-HSA-72764 | Formation of a pool of free 40S subunits, Eukaryotic Translation Elongation , Peptide chain elongation , Viral mRNA Translation , Eukaryotic Translation Termination |
| reactome | CD56+ NK | L3 | R-HSA-212436, R-HSA-73857 , R-HSA-74160 | Generic Transcription Pathway , RNA Polymerase II Transcription, Gene expression (Transcription) |
| reactome | CD56+ NK | L4 | R-HSA-1428517, R-HSA-163200 , R-HSA-611105 | The citric acid (TCA) cycle and respiratory electron transport , Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., Respiratory electron transport |
| reactome | CD56+ NK | L5 | R-HSA-157118 , R-HSA-8878171, R-HSA-8939236 | Signaling by NOTCH , Transcriptional regulation by RUNX1 , RUNX1 regulates transcription of genes involved in differentiation of HSCs |
| reactome | CD56+ NK | L6 | R-HSA-8951664, R-HSA-983168 , R-HSA-983169 | Neddylation , Antigen processing: Ubiquitination & Proteasome degradation, Class I MHC mediated antigen processing & presentation |
| reactome | T cell | L1 | R-HSA-6798695 | Neutrophil degranulation |
| reactome | T cell | L2 | R-HSA-156827, R-HSA-72613 , R-HSA-72689 , R-HSA-72706 , R-HSA-72737 , R-HSA-156902, R-HSA-192823 | L13a-mediated translational silencing of Ceruloplasmin expression, Eukaryotic Translation Initiation , Formation of a pool of free 40S subunits , GTP hydrolysis and joining of the 60S ribosomal subunit , Cap-dependent Translation Initiation , Peptide chain elongation , Viral mRNA Translation |
| wikipathway | CD14+ Monocyte | L1 | WP477 | Cytoplasmic Ribosomal Proteins |
| wikipathway | CD14+ Monocyte | L2 | WP111 | Electron Transport Chain (OXPHOS system in mitochondria) |
| wikipathway | CD19+ B | L1 | WP477 | Cytoplasmic Ribosomal Proteins |
| wikipathway | CD19+ B | L2 | WP111 | Electron Transport Chain (OXPHOS system in mitochondria) |
| wikipathway | CD34+ | L1 | WP477 | Cytoplasmic Ribosomal Proteins |
| wikipathway | CD34+ | L2 | WP111 | Electron Transport Chain (OXPHOS system in mitochondria) |
| wikipathway | CD56+ NK | L1 | WP477 | Cytoplasmic Ribosomal Proteins |
| wikipathway | CD56+ NK | L2 | WP111, WP623 | Electron Transport Chain (OXPHOS system in mitochondria), Oxidative phosphorylation |
| wikipathway_cancer | CD19+ B | L1 | WP619 | Type II interferon signaling (IFNG) |
knitr::knit_exit()