Single Cell PBMC 2

Last updated: 2022-04-12

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library(tidyverse)
library(htmltools)
source('code/utils.R')
source('code/logistic_susie_vb.R')
source('code/logistic_susie_veb_boost.R')
source('code/load_gene_sets.R')
source('code/enrichment_pipeline.R')

Setup

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

names(deseq)

#> [1] "CD19+ B"        "CD56+ NK"       "T cell"         "CD14+ Monocyte"
#> [5] "CD34+"

de <- map_dfr(names(deseq), ~ deseq[[.x]] %>%
    as.data.frame %>%
    rownames_to_column(var = 'gene') %>% mutate(celltype = .x))

hs <- org.Hs.eg.db::org.Hs.eg.db
gene_symbols <- unique(de$gene)
symbol2entrez <- AnnotationDbi::select(
  hs, keys=gene_symbols,
  columns=c('ENTREZID', 'ENSEMBL'),
  keytype = 'ENSEMBL')

add_names = function(l, n){
  names(l) <- n
  return(l)
}

data <- de %>%
  dplyr::rename('ENSEMBL' = gene) %>%
  left_join(symbol2entrez, by='ENSEMBL') %>%
  relocate(ENTREZID, .after=ENSEMBL) %>%
  mutate(  # set default columns
    beta = log2FoldChange,
    se = lfcSE,
    threshold.on = padj
  ) %>%
  group_by(celltype) %>%
  group_map(~ .x, .keep = T) %>%
  add_names(map_chr(., ~pluck(.x, 'celltype')[1]))

Fit

# fit logistic susie
do_logistic_susie_cached = function(data,
                                    db,
                                    thresh,
                                    prefix=''){
  res <- xfun::cache_rds({
    purrr::map_dfr(
      names(data),
      ~do_logistic_susie(.x, db, thresh, genesets, data))
  },
  dir = params$cache_dir,
  file=paste0(prefix, 'logistic_susie_', db, '_', thresh),
  hash = list(data, db, thresh, prefix))
}

params.genesets <- eval(parse(text=params$genesets))
params.thresh <- eval(parse(text=params$thresh))
fits <- map_dfr(params.genesets, ~do_logistic_susie_cached(data, .x, params.thresh))

# fit ora
do_ora_cached = function(data, db, thresh, prefix='', ...){
  res <- xfun::cache_rds({
    purrr::map_dfr(names(data), ~do_ora(.x, db, thresh, genesets, data))
  }, dir = params$cache_dir, file=paste0(prefix, 'ora_', db, '_', thresh), ...)
}
ora <- map_dfr(params.genesets, ~do_ora_cached(data, .x, params.thresh))

Overview

Threshold sensitivity

mean.gene.prop = function(l){
  purrr::map_dbl(3:10, ~get_y(l, 10^(-.x)) %>% mean())
}

thresh <- map_dbl(1:10, ~10**-.x)

.prop.ones = function(experiment){
  map_dbl(thresh, ~ prep_binary_data(
  genesets[['gobp']], data[[experiment]], thresh=.x)$y %>% mean())
}

prop.ones <- xfun::cache_rds({map_dfc(names(data), ~.prop.ones(.x))},
                             dir=params$cache_dir,
                             file='threshold_sensitivity')
colnames(prop.ones) <- names(data)
prop.ones <- prop.ones %>% mutate(thresh = thresh)

prop.ones %>%
  pivot_longer(one_of(names(data))) %>%
  group_by(name) %>%
  mutate(value = value) %>%
  ggplot(aes(x=factor(-log10(thresh)), y=value)) +
  geom_boxplot() +
  labs(
    y = 'Proportions of genes in gene list',
    title = 'Sensitivity to thresholding'
  )

Big volcano plot

Colors represent enrichment/depletion detected by Fishers exact test (Benjamini Hochberg corrected p-values < \(0.05\)). Gene sets that belong to a SuSiE credible set are circled.

get_ora_enrichments = function(tbl){
   tbl %>% mutate(
    padj = p.adjust(pFishersExact),
    result = case_when(
      padj < 0.05 & oddsRatio < 1 ~ 'depleted',
      padj < 0.05 & oddsRatio > 1 ~ 'enriched',
      TRUE ~ 'not significant'
    )
  )
}

# plot all enrichments, highlight gene sets in credible set
csdat <- res2 %>% 
  filter(in_cs, active_cs)

res %>% 
  group_by(experiment, db) %>%
  get_ora_enrichments %>%
  ggplot(aes(x=log10(oddsRatio), y=-log10(pFishersExact), color=result)) +
  geom_point() +
  geom_point(
    csdat, 
    mapping=aes(x=log10(oddsRatio), y=-log10(pFishersExact)),
    color='black', pch=21, size=5) +
  scale_color_manual(values = c('depleted' = 'coral',
                                'enriched' = 'dodgerblue',
                                'not significant' = 'grey')) +
  facet_wrap(vars(db))

Enrichment results

Glossary

alpha is the posterior probability of SuSiE including this gene set in this component which is different from PIP (probability of SuSiE including this gene set in ANY component)
beta posterior mean/standard error of posterior mean for effect size. Standard errors are likely too small.
oddsRatio, pHypergeometric, pFishersExact construct a contingency table (gene list membersip) x (gene set membership), estimate the oddsRatio gives the odds of being in the gene list conditional on being in the gene set / odds of being in the gene list conditional on NOT being in the gene set. pHypergeometric and pFishersExact are pvalues from 1 and 2 sided test respectively.

experiments <- unique(res$experiment)

do.experiment.volcano = function(this_experiment){
  res %>% 
    filter(experiment == this_experiment) %>%
    group_by(db) %>%
    get_ora_enrichments %>%
    ggplot(aes(x=log10(oddsRatio), y=-log10(pFishersExact), color=result)) +
    geom_point() +
    geom_point(
      csdat %>% filter(experiment == this_experiment), 
      mapping=aes(x=log10(oddsRatio), y=-log10(pFishersExact)),
      color='black', pch=21, size=5) +
    scale_color_manual(values = c('depleted' = 'coral',
                                  'enriched' = 'dodgerblue',
                                  'not significant' = 'grey')) +
    facet_wrap(vars(db)) +
    labs(title = this_experiment)
}

for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  do.experiment.volcano(this_experiment) %>% print()
  cat("\n\n") 

  for(db in names(html_tables[[this_experiment]])){
    cat("####", db, "\n") # Create second level headings with the names.
    to_print <- html_tables[[this_experiment]][[db]] %>% distinct()
    to_print %>% report_susie_credible_sets() %>% htmltools::HTML() %>% print()
    cat("\n")
  }}

CD14+ Monocyte

gobp

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0045321	leukocyte activation	0.876	0.785	0.0658	3.61e-42	6.64e-42	760	1020	5.98
GO:0001775	cell activation	0.124	0.733	0.0622	3.97e-41	6.2e-41	828	1120	5.64
L2
GO:0045047	protein targeting to ER	0.842	2.15	0.238	2.99e-18	6.12e-18	98	105	25.8
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.067	2.22	0.254	1.35e-17	1.57e-17	88	93	32.4
GO:0006613	cotranslational protein targeting to membrane	0.0569	2.16	0.247	1.93e-17	3e-17	91	97	27.9
GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0337	2.02	0.233	5.91e-17	8.07e-17	99	108	20.3
L3
GO:0006119	oxidative phosphorylation	0.999	1.8	0.208	4.54e-14	8.46e-14	103	118	12.6
L4
GO:0006518	peptide metabolic process	0.772	0.477	0.0776	5.5e-16	1.11e-15	490	705	4.39
GO:0006412	translation	0.131	0.501	0.0859	3.42e-14	5.29e-14	403	575	4.46
GO:0043043	peptide biosynthetic process	0.0857	0.487	0.0845	7.72e-14	1.23e-13	413	593	4.37
GO:0070125	mitochondrial translational elongation	0.00383	0.996	0.198	1.95e-06	3.57e-06	69	87	7.02
L6
GO:0008380	RNA splicing	0.4	0.581	0.103	3.28e-07	5.52e-07	261	387	3.87
GO:0000375	RNA splicing, via transesterification reactions	0.206	0.635	0.115	9.79e-07	1.67e-06	210	307	4.02
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.186	0.636	0.116	1.07e-06	1.97e-06	208	304	4.03
GO:0000398	mRNA splicing, via spliceosome	0.186	0.636	0.116	1.07e-06	1.97e-06	208	304	4.03
GO:0006397	mRNA processing	0.0195	0.488	0.0955	5.82e-06	9.7e-06	291	446	3.52
L7
GO:0016192	vesicle-mediated transport	0.976	0.314	0.0505	3.11e-20	5.22e-20	1050	1610	3.92
GO:0002376	immune system process	0.00856	0.234	0.0431	6.37e-37	1.1e-36	1490	2230	4.47
GO:0045055	regulated exocytosis	0.00343	0.41	0.0797	8.65e-28	1.5e-27	487	647	5.88
GO:0006887	exocytosis	0.00222	0.379	0.0748	4.83e-25	7.66e-25	536	734	5.26

gomf

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0003723	RNA binding	1	0.419	0.053	3.28e-22	6.31e-22	986	1480	4.07
L2
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	1	-0.629	0.059	1	1.13e-09	540	1160	1.63
L3
GO:0001012	RNA polymerase II regulatory region DNA binding	0.657	0.882	0.0896	0.000104	0.000186	321	509	3.21
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.293	0.88	0.0901	0.000123	0.000244	317	503	3.2
GO:0000987	proximal promoter sequence-specific DNA binding	0.0381	0.997	0.105	1.01e-05	1.72e-05	245	372	3.6
GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	0.0081	0.993	0.106	1.62e-05	2.74e-05	238	362	3.58
L4
GO:0003735	structural constituent of ribosome	1	1.61	0.188	1.79e-20	2.88e-20	136	152	15.8
L5
GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	0.827	1.87	0.301	1.9e-08	2.5e-08	51	57	15.6
GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.0776	1.97	0.339	1.51e-07	2.01e-07	41	45	18.7
GO:0050136	NADH dehydrogenase (quinone) activity	0.0776	1.97	0.339	1.51e-07	2.01e-07	41	45	18.7
GO:0003954	NADH dehydrogenase activity	0.0176	1.85	0.335	6.45e-07	8.09e-07	41	46	15
L6
GO:0045296	cadherin binding	0.762	0.618	0.12	1.65e-09	2.72e-09	206	286	4.8
GO:0050839	cell adhesion molecule binding	0.203	0.503	0.102	1.55e-08	2.8e-08	269	392	4.1
GO:0005515	protein binding	0.00157	0.0886	0.0212	1.42e-16	2.73e-16	5160	9020	7.2
GO:0042802	identical protein binding	0.00146	0.218	0.0553	6.83e-06	1.35e-05	796	1310	3.05
GO:0044877	protein-containing complex binding	0.00089	0.255	0.068	5.8e-07	1.04e-06	548	871	3.27
GO:0019899	enzyme binding	0.000707	0.175	0.0462	5.4e-07	1.06e-06	1140	1890	3.1
GO:0051082	unfolded protein binding	0.000595	0.635	0.19	3.55e-05	5.44e-05	76	102	5.36
GO:0003823	antigen binding	0.000499	0.863	0.271	0.000176	0.000352	36	44	8.22
GO:0019199	transmembrane receptor protein kinase activity	0.000403	-0.788	0.251	1	0.000133	15	53	0.717
GO:0140098	catalytic activity, acting on RNA	0.000402	-0.369	0.109	0.981	0.0444	165	333	1.81

kegg

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
hsa03010	Ribosome	1	1.75	0.202	7.88e-14	1.06e-13	115	129	14.2
L2
hsa05012	Parkinson disease	1	1.7	0.205	4.1e-13	7.31e-13	111	125	13.7

CD19+ B

gobp

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0002376	immune system process	1	0.685	0.0436	2.02e-47	3.5e-47	1580	2230	5.15
L2
GO:0045047	protein targeting to ER	0.96	2.55	0.243	8.02e-18	1.19e-17	99	105	29.2
GO:0006613	cotranslational protein targeting to membrane	0.0214	2.54	0.251	3.83e-17	5.69e-17	92	97	32.6
GO:0072599	establishment of protein localization to endoplasmic reticulum	0.0151	2.4	0.238	1.91e-16	3.26e-16	100	108	22.2
L3
GO:0042773	ATP synthesis coupled electron transport	0.622	2.12	0.26	6.38e-12	9.05e-12	75	82	18.9
GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.359	2.12	0.262	1.03e-11	1.53e-11	74	81	18.7
GO:0006119	oxidative phosphorylation	0.0185	1.6	0.206	5.47e-12	7.4e-12	102	118	11.3
L5
GO:0008380	RNA splicing	0.811	0.527	0.102	1.76e-05	3.5e-05	261	387	3.72
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.049	0.523	0.114	0.000218	0.000412	204	304	3.64
GO:0000398	mRNA splicing, via spliceosome	0.049	0.523	0.114	0.000218	0.000412	204	304	3.64
GO:0000375	RNA splicing, via transesterification reactions	0.0328	0.51	0.114	0.000321	0.000555	205	307	3.59
GO:0006397	mRNA processing	0.0154	0.413	0.095	0.000516	0.000906	289	446	3.31
GO:0050684	regulation of mRNA processing	0.00745	0.711	0.176	3.53e-05	5.77e-05	90	120	5.3
GO:0043484	regulation of RNA splicing	0.00738	0.729	0.181	3.6e-05	5.62e-05	86	114	5.42
GO:0006338	chromatin remodeling	0.00115	0.589	0.166	1.43e-05	2.29e-05	101	135	5.26
GO:0016071	mRNA metabolic process	0.00079	0.282	0.0771	1.65e-07	2.78e-07	470	708	3.63
GO:0048024	regulation of mRNA splicing, via spliceosome	0.000772	0.7	0.208	0.000684	0.00114	62	83	5.2

gomf

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0003723	RNA binding	1	0.359	0.0526	1.6e-13	3.07e-13	977	1480	3.76
L2
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.995	-0.657	0.0589	1	1.87e-11	555	1160	1.65
L3
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.485	0.778	0.0899	0.00452	0.00869	316	503	3.05
GO:0001012	RNA polymerase II regulatory region DNA binding	0.429	0.772	0.0893	0.00529	0.0104	319	509	3.03
GO:0000987	proximal promoter sequence-specific DNA binding	0.0386	0.869	0.104	0.000916	0.00167	242	372	3.34
GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	0.0258	0.875	0.106	0.000883	0.00173	236	362	3.36
GO:0000976	transcription regulatory region sequence-specific DNA binding	0.0133	0.713	0.0866	0.0144	0.0263	334	541	2.92
L6
GO:0003735	structural constituent of ribosome	0.995	0.966	0.175	8.89e-12	1.39e-11	126	152	8.62
L7
GO:0003954	NADH dehydrogenase activity	0.325	1.62	0.325	2.4e-06	3.45e-06	41	46	14.4
GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.218	1.61	0.328	3.78e-06	5.7e-06	40	45	14.1
GO:0050136	NADH dehydrogenase (quinone) activity	0.218	1.61	0.328	3.78e-06	5.7e-06	40	45	14.1
GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	0.177	1.41	0.288	2.74e-06	5.02e-06	49	57	10.8
GO:0016651	oxidoreductase activity, acting on NAD(P)H	0.0386	0.999	0.216	6.08e-06	9.32e-06	75	95	6.63
GO:0009055	electron transfer activity	0.00116	0.775	0.203	4.5e-05	8.11e-05	75	98	5.76
GO:0003823	antigen binding	0.000779	1.06	0.294	1.29e-05	1.76e-05	40	46	11.7
GO:0016491	oxidoreductase activity	0.000776	0.332	0.0844	4.29e-05	8.32e-05	374	575	3.39
GO:0016860	intramolecular oxidoreductase activity	0.000678	1.1	0.31	2.24e-05	4.31e-05	36	41	12.7
GO:0005070	SH3/SH2 adaptor activity	0.000445	0.965	0.279	3.18e-05	4.85e-05	43	51	9.46

kegg

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
hsa00190	Oxidative phosphorylation	0.998	1.46	0.205	8.72e-10	1.31e-09	105	120	11.5
L2
hsa04640	Hematopoietic cell lineage	1	1.51	0.253	9.95e-08	1.61e-07	72	81	13
L3
hsa03010	Ribosome	1	1.41	0.197	6.83e-10	9.38e-10	112	129	10.8

CD34+

gobp

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0001775	cell activation	0.987	0.743	0.0647	9.5e-26	1.65e-25	930	1130	7.43
GO:0045321	leukocyte activation	0.0129	0.755	0.0681	1.93e-24	3.29e-24	843	1020	7.54
L2
GO:0006613	cotranslational protein targeting to membrane	0.814	2.05	0.253	3.67e-10	5.93e-10	92	97	26.9
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.152	2.04	0.259	1.31e-09	2.36e-09	88	93	25.7
GO:0045047	protein targeting to ER	0.0274	1.82	0.238	1.41e-09	3.08e-09	98	105	20.4
L3
GO:0006119	oxidative phosphorylation	0.999	1.57	0.217	4.64e-09	8.3e-09	108	118	15.8
L4
GO:0044419	interspecies interaction between organisms	0.419	0.445	0.0797	3.58e-10	6.64e-10	558	703	5.88
GO:0016032	viral process	0.384	0.463	0.0834	1.3e-09	2.4e-09	509	640	5.91
GO:0044403	symbiont process	0.194	0.439	0.0808	1.86e-09	3.43e-09	541	684	5.77

gomf

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0003735	structural constituent of ribosome	1	1.76	0.196	7.32e-13	1.25e-12	141	152	18.9
L2
GO:0005515	protein binding	1	0.336	0.0217	2e-14	3.4e-14	6410	9040	11.5

kegg

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
hsa00190	Oxidative phosphorylation	0.992	1.52	0.218	2.2e-08	3.89e-08	111	120	17.5
L2
hsa03010	Ribosome	1	1.52	0.21	1.04e-08	2.01e-08	119	129	17

CD56+ NK

gobp

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0002376	immune system process	1	0.654	0.0439	1.62e-41	3.08e-41	1610	2230	5.31
L2
GO:0045047	protein targeting to ER	0.684	2.22	0.237	5.01e-15	6.91e-15	98	105	23.7
GO:0072599	establishment of protein localization to endoplasmic reticulum	0.211	2.15	0.233	1.13e-14	1.81e-14	100	108	21.2
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.0689	2.29	0.253	1.21e-14	1.95e-14	88	93	29.7
GO:0006613	cotranslational protein targeting to membrane	0.0368	2.21	0.246	2e-14	3.49e-14	91	97	25.6
L3
GO:0006357	regulation of transcription by RNA polymerase II	0.18	-0.205	0.0438	1	8.46e-05	1110	1990	2.32
GO:0006366	transcription by RNA polymerase II	0.149	-0.198	0.0426	1	0.000155	1190	2120	2.37
GO:0016070	RNA metabolic process	0.0932	-0.152	0.0331	0.962	0.0816	2130	3620	2.94
GO:0090304	nucleic acid metabolic process	0.0828	-0.143	0.0312	0.982	0.0377	2390	4090	3.03
GO:0019219	regulation of nucleobase-containing compound metabolic process	0.0541	-0.159	0.0356	0.993	0.0155	1800	3100	2.74
GO:0010468	regulation of gene expression	0.0503	-0.153	0.0343	0.918	0.172	1990	3380	2.92
GO:2000112	regulation of cellular macromolecule biosynthetic process	0.044	-0.16	0.0362	0.998	0.00453	1720	2990	2.67
GO:0010556	regulation of macromolecule biosynthetic process	0.0345	-0.156	0.0357	0.996	0.00885	1780	3080	2.72
GO:0051252	regulation of RNA metabolic process	0.0336	-0.16	0.0369	0.994	0.0129	1660	2870	2.68
GO:0006351	transcription, DNA-templated	0.0276	-0.161	0.0376	0.998	0.00468	1590	2760	2.62
L4
GO:0006119	oxidative phosphorylation	0.975	1.33	0.202	3.47e-09	6.57e-09	100	118	9.4
GO:0009123	nucleoside monophosphate metabolic process	0.00819	0.727	0.124	2.68e-09	4.8e-09	218	286	5.49
GO:0042773	ATP synthesis coupled electron transport	0.00547	1.37	0.24	4.48e-07	6.66e-07	70	82	9.83
GO:0042775	mitochondrial ATP synthesis coupled electron transport	0.00364	1.36	0.241	6.44e-07	1.02e-06	69	81	9.69
L5
GO:0097237	cellular response to toxic substance	0.938	0.825	0.158	5.29e-09	8.86e-09	144	180	6.8
GO:0071236	cellular response to antibiotic	0.0262	0.866	0.195	1.18e-07	2.39e-07	95	115	8.03
GO:1990748	cellular detoxification	0.0061	0.952	0.234	9.38e-06	1.85e-05	64	77	8.29
GO:0098869	cellular oxidant detoxification	0.00464	0.959	0.24	1.08e-05	1.9e-05	61	73	8.56
GO:0098754	detoxification	0.00169	0.83	0.221	4.44e-05	8.84e-05	69	86	6.84
GO:0006338	chromatin remodeling	0.00104	0.63	0.171	8.53e-05	0.000135	102	135	5.22
GO:0006333	chromatin assembly or disassembly	0.000951	0.636	0.174	0.000173	0.000281	97	129	5.12
GO:0002576	platelet degranulation	0.000864	0.731	0.204	8.06e-07	1.41e-06	79	95	8.33
GO:0046677	response to antibiotic	0.000736	0.483	0.132	4.88e-07	9.56e-07	184	246	5.06
GO:0001775	cell activation	0.000439	0.23	0.0617	1.88e-35	3.02e-35	865	1130	6.06
L6
GO:0008380	RNA splicing	0.593	0.547	0.103	1.59e-05	2.96e-05	271	387	4.02
GO:0006397	mRNA processing	0.23	0.493	0.0956	4.03e-05	7.89e-05	307	446	3.81
GO:0000375	RNA splicing, via transesterification reactions	0.0533	0.554	0.115	0.000116	0.000197	215	307	3.99
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0495	0.555	0.115	0.000119	0.000228	213	304	4
GO:0000398	mRNA splicing, via spliceosome	0.0495	0.555	0.115	0.000119	0.000228	213	304	4
GO:0016071	mRNA metabolic process	0.0165	0.361	0.0773	4.28e-09	7.24e-09	496	708	4.12

gomf

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0003735	structural constituent of ribosome	1	1.9	0.192	1.16e-18	1.56e-18	139	152	18.2
L2
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	0.997	-0.733	0.0589	1	1.22e-13	576	1160	1.7
L3
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	0.524	0.825	0.0902	0.00833	0.0157	327	503	3.2
GO:0000976	transcription regulatory region sequence-specific DNA binding	0.282	0.79	0.087	0.00977	0.0196	350	541	3.17
GO:0001012	RNA polymerase II regulatory region DNA binding	0.176	0.809	0.0897	0.0128	0.0237	329	509	3.15
GO:1990837	sequence-specific double-stranded DNA binding	0.0111	0.731	0.0838	0.0156	0.0304	374	583	3.1

kegg

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
hsa03010	Ribosome	1	1.79	0.208	2.53e-12	3.54e-12	118	129	17
L2
hsa05012	Parkinson disease	1	1.57	0.206	1.88e-10	2.7e-10	113	126	13.7
L3
hsa04640	Hematopoietic cell lineage	0.999	1.35	0.249	4.02e-06	5.62e-06	71	81	11.1
L4
hsa04650	Natural killer cell mediated cytotoxicity	0.997	1.15	0.221	4.11e-06	7.87e-06	84	98	9.39

T cell

gobp

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0001775	cell activation	0.999	0.763	0.0685	2.06e-42	4.43e-42	1000	1130	12.1
L2
GO:0006119	oxidative phosphorylation	0.999	1.8	0.228	3.29e-09	7.17e-09	111	118	22
L3
GO:0002376	immune system process	1	0.441	0.0467	9.41e-41	1.9e-40	1870	2230	8.71
L4
GO:0045047	protein targeting to ER	0.426	1.58	0.234	9.23e-08	1.92e-07	98	105	19.4
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.343	1.68	0.25	6.56e-08	1.12e-07	88	93	24.4
GO:0072599	establishment of protein localization to endoplasmic reticulum	0.139	1.52	0.23	2.12e-07	3.29e-07	100	108	17.3
GO:0070972	protein localization to endoplasmic reticulum	0.0615	1.32	0.203	5.41e-08	1e-07	121	132	15.3
GO:0006613	cotranslational protein targeting to membrane	0.0307	1.55	0.243	6.81e-07	1.46e-06	90	97	17.8

gomf

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0003723	RNA binding	0.987	0.328	0.0544	1.66e-07	3.31e-07	1160	1480	5.51
GO:0005515	protein binding	0.0128	0.119	0.0218	3.97e-17	7.27e-17	6760	9040	13.8

kegg

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
hsa05010	Alzheimer disease	1	1.68	0.202	3.79e-10	5.47e-10	146	154	24.8

sessionInfo()

#> R version 4.1.2 (2021-11-01)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices datasets  utils     methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] kableExtra_1.3.4            DESeq2_1.34.0              
#>  [3] SummarizedExperiment_1.24.0 Biobase_2.54.0             
#>  [5] MatrixGenerics_1.6.0        matrixStats_0.61.0         
#>  [7] GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
#>  [9] IRanges_2.28.0              S4Vectors_0.32.3           
#> [11] BiocGenerics_0.40.0         htmltools_0.5.2            
#> [13] forcats_0.5.1               stringr_1.4.0              
#> [15] dplyr_1.0.8                 purrr_0.3.4                
#> [17] readr_2.1.2                 tidyr_1.2.0                
#> [19] tibble_3.1.6                ggplot2_3.3.5              
#> [21] tidyverse_1.3.1            
#> 
#> loaded via a namespace (and not attached):
#>   [1] colorspace_2.0-3       ellipsis_0.3.2         rprojroot_2.0.2       
#>   [4] XVector_0.34.0         fs_1.5.2               rstudioapi_0.13       
#>   [7] farver_2.1.0           bit64_4.0.5            AnnotationDbi_1.56.2  
#>  [10] fansi_1.0.2            lubridate_1.8.0        xml2_1.3.3            
#>  [13] splines_4.1.2          codetools_0.2-18       doParallel_1.0.17     
#>  [16] cachem_1.0.6           geneplotter_1.72.0     knitr_1.38            
#>  [19] jsonlite_1.8.0         workflowr_1.7.0        apcluster_1.4.9       
#>  [22] WebGestaltR_0.4.4      broom_0.7.12           annotate_1.72.0       
#>  [25] dbplyr_2.1.1           png_0.1-7              BiocManager_1.30.16   
#>  [28] compiler_4.1.2         httr_1.4.2             backports_1.4.1       
#>  [31] assertthat_0.2.1       Matrix_1.4-0           fastmap_1.1.0         
#>  [34] cli_3.2.0              later_1.3.0            tools_4.1.2           
#>  [37] igraph_1.2.11          gtable_0.3.0           glue_1.6.2            
#>  [40] GenomeInfoDbData_1.2.7 doRNG_1.8.2            Rcpp_1.0.8.2          
#>  [43] cellranger_1.1.0       jquerylib_0.1.4        Biostrings_2.62.0     
#>  [46] vctrs_0.3.8            svglite_2.1.0          iterators_1.0.14      
#>  [49] xfun_0.30              rvest_1.0.2            lifecycle_1.0.1       
#>  [52] renv_0.15.4            rngtools_1.5.2         XML_3.99-0.9          
#>  [55] org.Hs.eg.db_3.14.0    zlibbioc_1.40.0        scales_1.1.1          
#>  [58] vroom_1.5.7            hms_1.1.1              promises_1.2.0.1      
#>  [61] parallel_4.1.2         RColorBrewer_1.1-2     yaml_2.3.5            
#>  [64] curl_4.3.2             memoise_2.0.1          sass_0.4.0            
#>  [67] RSQLite_2.2.10         stringi_1.7.6          highr_0.9             
#>  [70] genefilter_1.76.0      foreach_1.5.2          BiocParallel_1.28.3   
#>  [73] rlang_1.0.2            pkgconfig_2.0.3        systemfonts_1.0.4     
#>  [76] bitops_1.0-7           evaluate_0.15          lattice_0.20-45       
#>  [79] labeling_0.4.2         bit_4.0.4              tidyselect_1.1.2      
#>  [82] magrittr_2.0.2         R6_2.5.1               generics_0.1.2        
#>  [85] DelayedArray_0.20.0    DBI_1.1.2              pillar_1.7.0          
#>  [88] haven_2.4.3            whisker_0.4            withr_2.5.0           
#>  [91] survival_3.3-1         KEGGREST_1.34.0        RCurl_1.98-1.6        
#>  [94] modelr_0.1.8           crayon_1.5.0           utf8_1.2.2            
#>  [97] tzdb_0.2.0             rmarkdown_2.13         locfit_1.5-9.5        
#> [100] grid_4.1.2             readxl_1.3.1           blob_1.2.2            
#> [103] git2r_0.29.0           webshot_0.5.2          reprex_2.0.1          
#> [106] digest_0.6.29          xtable_1.8-4           httpuv_1.6.5          
#> [109] munsell_0.5.0          viridisLite_0.4.0      bslib_0.3.1

Single Cell PBMC 2

karltayeb

2022-04-12

Setup

Fit

Overview

Threshold sensitivity

Big volcano plot

Enrichment results

Glossary

CD14+ Monocyte

gobp

gomf

kegg

CD19+ B

gobp

gomf

kegg

CD34+

gobp

gomf

kegg

CD56+ NK

gobp

gomf

kegg

T cell

gobp

gomf

kegg