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Overview

We report gene set enrichment analysis of the topics from Jason’s NMF and SNMF of the Deng et al. data set.

For each topic we construct a binary gene list by thresholding on local false sign rates output from flash. Here, I pick \(lfsr <- 1e-5\).

library(tidyverse)
library(htmltools)
source('code/utils.R')
source('code/load_gene_sets.R')
source('code/load_data.R')
data <- load_deng_topics()
genesets <- load_gene_sets()
source('code/logistic_susie_vb.R')
source('code/logistic_susie_veb_boost.R')
source('code/enrichment_pipeline.R')

# fix params
params.genesets <- eval(parse(text=params$genesets))
params.thresh <- eval(parse(text=params$thresh))
params.rerun <- eval(parse(text=params$rerun))

do_logistic_susie_cached = function(data, db, thresh, .sign=c(1, -1), prefix=''){
  res <- xfun::cache_rds({
    purrr::map_dfr(
      names(data),
      ~do_logistic_susie(.x, db, thresh, genesets, data, .sign=.sign))},
    dir = params$cache_dir,
    file=paste0(prefix, 'logistic_susie_', db, '_', thresh),
    hash = list(data, db, thresh, prefix),
    rerun = params.rerun)
}

fits <- map_dfr(params.genesets, ~do_logistic_susie_cached(data, .x, params.thresh))

snmf.data <- data[grep('^SNMF*', names(data))]
positive.fits <- map_dfr(
  params.genesets,
  ~do_logistic_susie_cached(snmf.data, .x, params.thresh, c(1), 'positive'))
negative.fits <- map_dfr(
  params.genesets,
  ~do_logistic_susie_cached(snmf.data, .x, params.thresh, c(1), 'negative'))

do_ora_cached = function(data, db, thresh, .sign=c(1, -1), prefix=''){
  res <- xfun::cache_rds({
    purrr::map_dfr(names(data), ~do_ora(.x, db, thresh, genesets, data, .sign=.sign))
  },
  dir = params$cache_dir,
  file=paste0(prefix, 'ora_', db, '_', thresh),
  rerun=params.rerun)
}

ora <- map_dfr(params.genesets, ~do_ora_cached(data, .x, params.thresh))
positive.ora <- map_dfr(
  params.genesets,
  ~do_ora_cached(snmf.data, .x, params.thresh, c(1), 'positive'))
negative.ora <- map_dfr(
  params.genesets,
  ~do_ora_cached(snmf.data, .x, params.thresh, c(-1), 'negative'))
# take credible set summary, return "best" row for each gene set
get_cs_summary_condensed = function(fit){
  fit %>%
    get_credible_set_summary() %>%
    group_by(geneSet) %>%
    arrange(desc(alpha)) %>%
    filter(row_number() == 1)
}
# generate table for making gene-set plots
get_plot_tbl = function(fits, ora){
  res <- fits %>%
    left_join(ora) %>%
    mutate(
      gs_summary = map(fit, get_gene_set_summary),
      cs_summary = map(fit, get_cs_summary_condensed),
      res = map2(gs_summary, cs_summary, ~ left_join(.x, .y, by='geneSet')),
      res = map2(res, ora, ~ possibly(left_join, NULL)(.x, .y))
    ) %>%
    select(-c(fit, susie.args, ora, gs_summary, cs_summary)) %>%
    unnest(res)
  return(res)
}

# split tibble into a list using 'col'
split_tibble = function(tibble, col = 'col'){
  tibble %>% split(., .[, col])
}
  
# Get summary of credible sets with gene set descriptions
get_table_tbl = function(fits, ora){
  res2 <- fits %>%
    left_join(ora) %>%
    mutate(res = map(fit, get_credible_set_summary)) %>%
    mutate(res = map2(res, ora, ~ left_join(.x, .y))) %>%
    select(-c(fit, ora)) %>%
    unnest(res)

  descriptions <- map_dfr(genesets, ~pluck(.x, 'geneSet', 'geneSetDes'))
  tbl <- res2 %>% 
    filter(active_cs) %>%
    left_join(descriptions)
  tbl_split <- split_tibble(tbl, 'experiment')
  html_tables <- map(tbl_split, ~split_tibble(.x, 'db'))
  return(html_tables)
}
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'
    )
  )
}

do.volcano = function(res){
  res %>% 
    get_ora_enrichments %>%
    ggplot(aes(x=log10(oddsRatio), y=-log10(pFishersExact), color=result)) +
    geom_point() +
    geom_point(
      res %>% filter(in_cs, active_cs), 
      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'))
}

NMF

Threshold sensitivity

thresh <- map_dbl(1:20, ~10**-.x)

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

prop.ones <- map_dfc(names(data[grep('^NMF*', names(data))]), ~.prop.ones(.x))

new.names = paste0('Topic', str_pad(2:20, 2, pad='0'))
colnames(prop.ones) <- new.names
prop.ones <- prop.ones %>% mutate(thresh = thresh)

prop.ones %>%
  pivot_longer(one_of(new.names)) %>%
  filter(thresh <= 1e-3) %>%
  group_by(name) %>%
  mutate(value = value / (sort(value, decreasing = T)[1])) %>%
  ggplot(aes(x=-log10(thresh), y=value, color=name)) +
  geom_point() + geom_line() +
  labs(
    y = 'prop.ones relative to 1e-3 threshold',
    title = 'Sensitivity of lfsr to threshold'
  )

Version Author Date
72fad28 karltayeb 2022-04-09

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.
res <- fits %>%
  filter(str_detect(experiment, '^NMF*')) %>%
  get_plot_tbl(., ora)

html_tables <- fits %>%
  filter(str_detect(experiment, '^NMF*')) %>%
  get_table_tbl(., ora)

experiments <- unique(res$experiment)

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

  cat("\n\n") 

  # print table
  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")
  }}

NMF_Topic2

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0044772 mitotic cell cycle phase transition 0.97 0.518 0.0949 4.1e-11 7.71e-11 231 435 3.1
GO:0048285 organelle fission 0.0136 0.47 0.102 1.91e-10 3.52e-10 202 376 3.17
GO:1901987 regulation of cell cycle phase transition 0.0052 0.469 0.107 5.79e-08 9.78e-08 176 338 2.95
GO:0007059 chromosome segregation 0.00303 0.52 0.123 3.27e-09 5.82e-09 142 254 3.43
L3
GO:0040029 regulation of gene expression, epigenetic 0.937 0.816 0.137 5e-10 6.8e-10 124 211 3.84
GO:0016458 gene silencing 0.0624 0.853 0.156 6.49e-09 9.52e-09 97 161 4.07
L4
GO:0006399 tRNA metabolic process 0.957 -1.02 0.185 1 3.34e-08 22 136 0.506
GO:0034470 ncRNA processing 0.0394 -0.59 0.118 1 1.43e-06 76 304 0.876
L5
GO:0070646 protein modification by small protein removal 0.954 0.619 0.125 9.91e-08 1.45e-07 135 249 3.19
GO:0000209 protein polyubiquitination 0.0048 0.487 0.131 7.08e-07 1.19e-06 123 229 3.12
GO:0016311 dephosphorylation 0.0015 0.353 0.102 9.77e-06 1.76e-05 187 385 2.56
GO:0016569 covalent chromatin modification 0.00148 0.352 0.101 1.54e-07 2.63e-07 196 387 2.79
GO:0030522 intracellular receptor signaling pathway 0.00138 0.429 0.127 2.37e-05 4.27e-05 124 244 2.78
GO:0140053 mitochondrial gene expression 0.00137 -0.556 0.169 1 1.34e-07 24 139 0.547
GO:0071166 ribonucleoprotein complex localization 0.00127 0.581 0.178 1.03e-05 1.45e-05 68 118 3.63
GO:0009755 hormone-mediated signaling pathway 0.00101 0.467 0.143 3.3e-05 5.5e-05 99 189 2.95
GO:0007265 Ras protein signal transduction 0.000958 0.345 0.103 6.18e-08 1.12e-07 191 372 2.87
GO:0018210 peptidyl-threonine modification 0.000929 0.603 0.192 3.48e-05 4.65e-05 58 100 3.68

NMF_Topic3

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.85 0.156 5.76e-52 5.76e-52 112 177 13
L10
GO:0070646 protein modification by small protein removal 1 0.922 0.132 3.23e-08 5.52e-08 68 249 2.73
L2
GO:0006414 translational elongation 1 2.67 0.187 2.06e-39 2.06e-39 80 121 14.5
L3
GO:0033108 mitochondrial respiratory chain complex assembly 0.903 2.27 0.262 2.09e-24 2.09e-24 45 64 17.2
GO:0010257 NADH dehydrogenase complex assembly 0.0973 2.59 0.309 8.33e-24 8.33e-24 37 46 29.7
L4
GO:0006605 protein targeting 1 1.2 0.109 1.04e-40 1.04e-40 154 364 5.64
L5
GO:0009123 nucleoside monophosphate metabolic process 0.985 1.2 0.13 2.49e-22 2.49e-22 98 255 4.64
GO:0009141 nucleoside triphosphate metabolic process 0.0145 1.18 0.134 2.16e-23 2.16e-23 97 244 4.9
L6
GO:0022613 ribonucleoprotein complex biogenesis 1 0.96 0.107 7.21e-28 7.21e-28 140 391 4.23
L7
GO:0006457 protein folding 1 1.16 0.154 1.08e-11 1.18e-11 61 179 3.76
L8
GO:0036230 granulocyte activation 0.52 0.798 0.108 7.46e-09 1e-08 96 384 2.44
GO:0002446 neutrophil mediated immunity 0.48 0.796 0.108 9.89e-09 1.65e-08 96 386 2.42
L9
GO:0006399 tRNA metabolic process 1 1.17 0.177 4.79e-08 6.72e-08 44 136 3.44

NMF_Topic4

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0022613 ribonucleoprotein complex biogenesis 1 1.57 0.111 5.24e-63 8.47e-63 316 391 11.2
L2
GO:0044772 mitotic cell cycle phase transition 1 1.07 0.0979 8.84e-26 1.53e-25 281 435 4.79
L3
GO:0006397 mRNA processing 0.991 1.02 0.102 2.68e-38 3.18e-38 300 425 6.34
L4
GO:0043062 extracellular structure organization 1 -0.871 0.119 1 5.11e-16 63 325 0.593
L5
GO:0016569 covalent chromatin modification 1 0.865 0.103 3.74e-19 5.28e-19 241 387 4.29
L6
GO:0070972 protein localization to endoplasmic reticulum 0.996 1.69 0.191 9.03e-22 1.07e-21 106 131 10.8
L7
GO:0061919 process utilizing autophagic mechanism 1 0.75 0.1 3.83e-11 6.73e-11 226 403 3.3
L8
GO:0034765 regulation of ion transmembrane transport 0.992 -0.865 0.116 1 1.92e-13 73 339 0.678
L9
GO:0098781 ncRNA transcription 0.99 1.7 0.233 1.08e-15 1.74e-15 72 88 11.4
GO:0016073 snRNA metabolic process 0.0101 1.6 0.242 2.81e-16 3.88e-16 67 79 14.1

NMF_Topic5

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0016197 endosomal transport 0.981 0.86 0.152 1.79e-11 2.92e-11 86 170 3.93
GO:0016482 cytosolic transport 0.016 0.854 0.176 1.24e-08 1.51e-08 64 128 3.82
L2
GO:0061919 process utilizing autophagic mechanism 0.996 0.555 0.0992 7.39e-11 1.21e-10 166 403 2.73
L3
GO:0006091 generation of precursor metabolites and energy 0.989 0.566 0.103 2.31e-07 3.3e-07 143 371 2.43
GO:0009123 nucleoside monophosphate metabolic process 0.00462 0.544 0.125 1.16e-05 2.05e-05 99 255 2.43

NMF_Topic6

NMF_Topic7

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006397 mRNA processing 0.902 0.985 0.0984 4.02e-22 5.49e-22 275 425 4.59
GO:0008380 RNA splicing 0.0984 1.03 0.106 2.57e-20 3.47e-20 240 367 4.71
L10
GO:0048193 Golgi vesicle transport 1 0.765 0.113 5.69e-10 1.11e-09 185 314 3.53
L2
GO:0034470 ncRNA processing 1 1.09 0.117 2.65e-20 4.71e-20 206 304 5.21
L3
GO:0034765 regulation of ion transmembrane transport 1 -0.961 0.116 1 4.65e-16 72 339 0.638
L4
GO:0061919 process utilizing autophagic mechanism 1 0.757 0.1 2.65e-12 4.95e-12 237 403 3.54
L5
GO:0044772 mitotic cell cycle phase transition 0.987 0.663 0.0971 1.12e-17 2.01e-17 269 435 4.05
GO:0044839 cell cycle G2/M phase transition 0.00606 0.885 0.148 6.1e-15 9.5e-15 129 184 5.73
L6
GO:0031023 microtubule organizing center organization 1 1.36 0.199 5.23e-15 9.82e-15 88 113 8.55
L7
GO:0140053 mitochondrial gene expression 0.999 1.12 0.174 2.21e-11 2.9e-11 97 139 5.61
L8
GO:0006260 DNA replication 0.984 0.877 0.133 2.08e-13 3.72e-13 152 232 4.66
GO:0006289 nucleotide-excision repair 0.00808 1.12 0.194 3.05e-13 5.79e-13 80 104 8.08

NMF_Topic8

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.59 0.154 1.39e-48 1.39e-48 95 177 12.5
L2
GO:0070972 protein localization to endoplasmic reticulum 1 1.34 0.181 6.8e-38 6.8e-38 72 131 12.9
L3
GO:1990823 response to leukemia inhibitory factor 1 1.55 0.216 1.14e-09 1.14e-09 30 89 5.15
L4
GO:0022613 ribonucleoprotein complex biogenesis 1 0.844 0.108 1.87e-22 1.87e-22 106 391 3.97

NMF_Topic9

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0002250 adaptive immune response 1 1.19 0.134 8.63e-21 8.63e-21 52 263 6.26
L2
GO:0002521 leukocyte differentiation 1 1.16 0.112 2.84e-22 2.84e-22 66 390 5.3

NMF_Topic10

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 1.56 0.178 9.82e-25 9.82e-25 86 131 8.35
L2
GO:0022613 ribonucleoprotein complex biogenesis 1 0.886 0.102 3.15e-23 3.83e-23 180 391 3.82
L3
GO:0070646 protein modification by small protein removal 1 0.827 0.126 1.03e-10 1.76e-10 104 249 3.13
L4
GO:0044282 small molecule catabolic process 0.999 -0.69 0.122 1 1.39e-07 41 336 0.582
L5
GO:0034504 protein localization to nucleus 0.954 0.642 0.132 1.81e-07 3.06e-07 88 227 2.74
GO:0006383 transcription by RNA polymerase III 0.00333 0.905 0.276 1.06e-05 1.37e-05 25 47 4.86
GO:0006457 protein folding 0.00246 0.514 0.153 4e-05 5.69e-05 66 179 2.52
GO:0006413 translational initiation 0.00194 0.5 0.152 4.89e-26 4.89e-26 107 177 6.72
GO:0071824 protein-DNA complex subunit organization 0.00188 0.498 0.151 2.59e-07 3.25e-07 73 180 2.95
GO:0016569 covalent chromatin modification 0.0017 0.353 0.105 2.14e-07 3.48e-07 135 387 2.34
GO:0018205 peptidyl-lysine modification 0.00162 0.404 0.122 1.22e-06 1.71e-06 102 283 2.45
GO:0006970 response to osmotic stress 0.000875 0.739 0.259 0.00147 0.00246 24 57 3.1
GO:0040029 regulation of gene expression, epigenetic 0.000865 0.431 0.141 7.41e-06 1.18e-05 78 211 2.53
GO:0007200 phospholipase C-activating G protein-coupled receptor signaling pathway 0.000804 -0.704 0.247 1 1.05e-05 2 64 0.136

NMF_Topic11

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0034976 response to endoplasmic reticulum stress 1 1.04 0.138 4.45e-10 4.45e-10 51 239 3.33
L2
GO:0002446 neutrophil mediated immunity 0.881 0.859 0.111 1.47e-09 1.95e-09 69 386 2.69
GO:0036230 granulocyte activation 0.119 0.833 0.111 7.16e-09 1.07e-08 67 384 2.61
L3
GO:0070085 glycosylation 0.999 0.893 0.15 2.63e-09 2.63e-09 44 200 3.44
L4
GO:0006643 membrane lipid metabolic process 0.999 0.984 0.167 2.85e-09 2.85e-09 38 159 3.82

NMF_Topic12

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 1.87 0.181 1.04e-40 1.04e-40 51 131 21
L2
GO:0006413 translational initiation 1 1.72 0.159 4.08e-40 4.08e-40 57 177 15.9

NMF_Topic13

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 1.88 0.185 1.48e-13 1.48e-13 29 131 7.03

NMF_Topic14

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 1.38 0.181 3.55e-10 3.55e-10 36 131 4.42
L2
GO:0002446 neutrophil mediated immunity 0.849 0.818 0.111 1.84e-08 2.34e-08 68 386 2.53
GO:0036230 granulocyte activation 0.151 0.795 0.111 7.98e-08 1.08e-07 66 384 2.45

NMF_Topic15

NMF_Topic16

NMF_Topic17

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0022613 ribonucleoprotein complex biogenesis 1 1.51 0.104 1.45e-48 1.45e-48 154 391 6.39
L10
GO:0009123 nucleoside monophosphate metabolic process 1 1.04 0.133 1.33e-07 1.99e-07 58 255 2.67
L2
GO:0006397 mRNA processing 0.999 0.994 0.101 2.61e-33 2.61e-33 139 425 4.7
L3
GO:0006414 translational elongation 1 1.76 0.185 1.96e-14 1.96e-14 46 121 5.57
L4
GO:0007059 chromosome segregation 1 1.11 0.131 5.27e-15 5.27e-15 74 254 3.79
L5
GO:0070646 protein modification by small protein removal 1 1.14 0.133 2.04e-12 2.1e-12 68 249 3.44
L6
GO:0006260 DNA replication 1 1.01 0.137 1.69e-13 1.69e-13 67 232 3.72
L7
GO:0006457 protein folding 1 1.26 0.156 2.37e-09 2.71e-09 49 179 3.41
L8
GO:0071166 ribonucleoprotein complex localization 0.999 1.23 0.188 3.93e-21 3.93e-21 54 118 7.72
L9
GO:0071824 protein-DNA complex subunit organization 1 1.13 0.155 1.05e-14 1.05e-14 59 180 4.46

NMF_Topic18

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 2 0.156 1.5e-52 1.5e-52 75 177 17.7
L2
GO:0070972 protein localization to endoplasmic reticulum 1 1.79 0.181 4.58e-47 4.58e-47 62 131 21.1
L3
GO:0009141 nucleoside triphosphate metabolic process 1 1.66 0.14 1.66e-14 1.66e-14 44 244 4.9

NMF_Topic19

NMF_Topic20

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0002446 neutrophil mediated immunity 0.91 1.33 0.116 2.16e-12 2.16e-12 47 386 3.89
GO:0036230 granulocyte activation 0.0903 1.31 0.117 6.76e-12 6.76e-12 46 384 3.81
L2
GO:0006413 translational initiation 1 1.58 0.167 9.48e-10 9.48e-10 27 177 4.88

SNMF

res <- fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_plot_tbl(., ora)

html_tables <- fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_table_tbl(., ora)

experiments <- unique(res$experiment)
for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  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")
  }}

SNMF_Topic2

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 0.993 1.21 0.156 1.14e-16 2.15e-16 131 177 6.7

SNMF_Topic3

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.49 0.153 5.33e-35 5.33e-35 104 177 8.48
L2
GO:0009141 nucleoside triphosphate metabolic process 0.998 0.975 0.13 1.71e-16 2.09e-16 97 244 3.88
L3
GO:0070646 protein modification by small protein removal 1 1.04 0.128 5.44e-13 7.07e-13 91 249 3.38
L4
GO:0070972 protein localization to endoplasmic reticulum 0.992 1.12 0.178 4.78e-27 4.78e-27 78 131 8.65
L5
GO:0010257 NADH dehydrogenase complex assembly 0.976 1.67 0.299 1.18e-13 1.18e-13 31 46 11.9
GO:0033108 mitochondrial respiratory chain complex assembly 0.0234 1.27 0.258 2.2e-11 2.2e-11 35 64 6.94
L6
GO:0006414 translational elongation 0.991 0.962 0.183 1.77e-06 2.95e-06 43 121 3.17

SNMF_Topic4

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 0.988 1.04 0.15 4.52e-12 5.04e-12 76 177 3.81
GO:0070972 protein localization to endoplasmic reticulum 0.0122 1.11 0.177 3.3e-11 3.67e-11 60 131 4.26

SNMF_Topic5

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.71 0.151 2.26e-31 2.26e-31 100 177 7.64

SNMF_Topic6

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0002521 leukocyte differentiation 1 1.19 0.113 9.51e-22 9.51e-22 64 390 5.3
L2
GO:0002250 adaptive immune response 1 1.19 0.135 5.99e-20 5.99e-20 50 263 6.18

SNMF_Topic7

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0022613 ribonucleoprotein complex biogenesis 1 1.41 0.104 1.63e-71 1.63e-71 236 391 8.45
L10
GO:0098781 ncRNA transcription 0.929 1.25 0.221 4.02e-15 4.02e-15 51 88 7.05
GO:0016073 snRNA metabolic process 0.0509 1.17 0.23 3.94e-13 3.94e-13 45 79 6.75
GO:0006383 transcription by RNA polymerase III 0.0102 1.43 0.304 1.59e-08 1.59e-08 27 47 6.84
L2
GO:0006413 translational initiation 1 1.67 0.156 2.13e-39 2.13e-39 115 177 9.77
L3
GO:0006397 mRNA processing 1 0.965 0.0992 1.03e-42 1.03e-42 208 425 5.21
L4
GO:0070646 protein modification by small protein removal 1 0.983 0.128 5.73e-12 9.41e-12 96 249 3.25
L5
GO:0006360 transcription by RNA polymerase I 0.998 1.72 0.292 4.62e-17 4.62e-17 39 53 14.2
L6
GO:0007059 chromosome segregation 1 0.938 0.128 8.49e-12 9.99e-12 97 254 3.2
L7
GO:0009123 nucleoside monophosphate metabolic process 0.731 0.813 0.128 2.19e-06 3.4e-06 82 255 2.43
GO:0009141 nucleoside triphosphate metabolic process 0.261 0.811 0.131 1.24e-06 2.01e-06 80 244 2.5
L8
GO:0006403 RNA localization 0.99 0.886 0.141 8.39e-26 8.39e-26 110 211 5.7
GO:0051169 nuclear transport 0.00854 0.659 0.12 8.28e-21 9.79e-21 133 310 3.95
L9
GO:0006338 chromatin remodeling 0.962 0.986 0.175 1.73e-10 2.29e-10 59 134 4.03
GO:0006260 DNA replication 0.0117 0.678 0.14 1.84e-09 3.17e-09 85 232 2.98
GO:0071824 protein-DNA complex subunit organization 0.0112 0.748 0.156 5.24e-14 5.54e-14 80 180 4.13
GO:0016569 covalent chromatin modification 0.0065 0.518 0.109 4.55e-11 5.77e-11 131 387 2.67

SNMF_Topic8

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 0.996 1.08 0.183 2.12e-41 2.12e-41 84 131 14
L2
GO:0022613 ribonucleoprotein complex biogenesis 1 0.881 0.106 1.96e-24 2.03e-24 130 391 3.94
L3
GO:0006414 translational elongation 1 1.52 0.183 3.07e-14 3.07e-14 50 121 5.35
L4
GO:0009141 nucleoside triphosphate metabolic process 0.999 0.979 0.133 4.81e-09 6.22e-09 67 244 2.88
L5
GO:0006413 translational initiation 1 1.12 0.157 3.87e-40 3.87e-40 98 177 9.76
L6
GO:0006605 protein targeting 1 0.865 0.11 6.81e-34 6.81e-34 140 364 5

SNMF_Topic9

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006401 RNA catabolic process 0.999 0.694 0.114 2.96e-09 4.51e-09 121 304 2.75
L2
GO:0006520 cellular amino acid metabolic process 0.999 0.707 0.125 6.39e-08 8.74e-08 101 254 2.74

SNMF_Topic10

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 0.962 1.14 0.174 7.35e-10 1.26e-09 55 131 3.91
GO:0090150 establishment of protein localization to membrane 0.0299 0.775 0.128 2.63e-10 3.2e-10 93 266 2.94
L2
GO:0048013 ephrin receptor signaling pathway 0.998 1.26 0.229 2.21e-09 2.21e-09 37 75 5.23
L3
GO:0038127 ERBB signaling pathway 0.971 0.893 0.181 1.02e-07 1.32e-07 48 122 3.49
GO:0070671 response to interleukin-12 0.00272 1.04 0.305 1.28e-05 1.28e-05 21 44 4.88
GO:1990823 response to leukemia inhibitory factor 0.00161 0.737 0.221 1.53e-05 1.71e-05 34 89 3.31
GO:0034109 homotypic cell-cell adhesion 0.00152 0.836 0.255 1.96e-05 2.08e-05 27 65 3.8
GO:0007015 actin filament organization 0.00131 0.404 0.117 6.55e-09 1.05e-08 105 329 2.56
GO:0046847 filopodium assembly 0.00118 0.933 0.296 4.46e-05 4.46e-05 21 47 4.31
GO:0034330 cell junction organization 0.000818 0.442 0.134 1.32e-06 2.33e-06 78 249 2.47
GO:0002446 neutrophil mediated immunity 0.000789 0.362 0.108 1.08e-06 1.6e-06 111 386 2.2
GO:0008544 epidermis development 0.000718 0.433 0.133 1.6e-05 2.3e-05 76 256 2.28
GO:0072337 modified amino acid transport 0.000602 1.16 0.412 0.000954 0.000954 11 22 5.32

SNMF_Topic11

SNMF_Topic12

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.4 0.157 1.67e-14 1.67e-14 48 177 4.87
L2
GO:0006414 translational elongation 0.999 1.61 0.187 1.68e-12 1.68e-12 36 121 5.48
L3
GO:0006403 RNA localization 0.998 1.15 0.146 5.16e-12 5.16e-12 49 211 3.95
L4
GO:0071824 protein-DNA complex subunit organization 1 1.2 0.158 1.92e-09 1.92e-09 40 180 3.7

SNMF_Topic13

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 4.29 0.18 7.55e-52 7.55e-52 40 131 75.8

SNMF_Topic14

SNMF_Topic15

SNMF_Topic16

SNMF_Topic17

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0034976 response to endoplasmic reticulum stress 1 1.38 0.143 2.37e-11 2.37e-11 39 239 4.22
L2
GO:0002446 neutrophil mediated immunity 0.959 1.14 0.115 6.63e-11 6.63e-11 51 386 3.33
GO:0036230 granulocyte activation 0.0405 1.11 0.116 5.47e-10 5.47e-10 49 384 3.19

SNMF_Topic18

SNMF_Topic19

SNMF_Topic20

SNMF - Positive loadings

res <- positive.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_plot_tbl(., positive.ora)

html_tables <- positive.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_table_tbl(., positive.ora)

experiments <- unique(res$experiment)
for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  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")
  }}

SNMF_Topic2

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0022613 ribonucleoprotein complex biogenesis 1 -1.15 0.115 1 7.26e-20 48 391 0.432
L2
GO:0140053 mitochondrial gene expression 1 -1.66 0.206 1 2.62e-12 10 139 0.241
L3
GO:0009123 nucleoside monophosphate metabolic process 0.906 -0.781 0.135 1 1.27e-07 44 255 0.651
GO:0009141 nucleoside triphosphate metabolic process 0.0891 -0.735 0.137 1 6.37e-07 43 244 0.668
L5
GO:0002446 neutrophil mediated immunity 0.805 -0.571 0.107 1 3.48e-06 82 386 0.844
GO:0036230 granulocyte activation 0.192 -0.542 0.107 1 1.27e-05 84 384 0.876

SNMF_Topic3

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 2.15 0.156 4.42e-57 4.42e-57 90 177 16.6
L2
GO:0010257 NADH dehydrogenase complex assembly 0.983 2.57 0.306 1.9e-25 1.9e-25 31 46 30.6
GO:0033108 mitochondrial respiratory chain complex assembly 0.0175 2.13 0.268 4.16e-24 4.16e-24 35 64 17.9
L3
GO:0070972 protein localization to endoplasmic reticulum 1 1.92 0.183 2.42e-51 2.42e-51 74 131 20.3
L4
GO:0009141 nucleoside triphosphate metabolic process 1 1.55 0.137 8.34e-28 8.34e-28 73 244 6.61
L5
GO:0006414 translational elongation 1 2.05 0.189 5.8e-15 5.8e-15 37 121 6.53
L6
GO:0070671 response to interleukin-12 1 2.41 0.306 2.64e-11 2.64e-11 19 44 11.1
L7
GO:0002446 neutrophil mediated immunity 0.795 0.997 0.114 1.36e-09 1.53e-09 61 386 2.81
GO:0036230 granulocyte activation 0.205 0.982 0.115 2.91e-09 3.11e-09 60 384 2.77
L8
GO:0070585 protein localization to mitochondrion 1 1.57 0.197 1.38e-09 1.38e-09 29 117 4.83
L9
GO:0043687 post-translational protein modification 1 1.03 0.128 2.38e-06 2.66e-06 45 310 2.5

SNMF_Topic4

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0016072 rRNA metabolic process 1 0.93 0.14 1.58e-11 2.05e-11 71 210 3.43
L2
GO:0006413 translational initiation 0.998 0.873 0.152 1.54e-09 2.31e-09 59 177 3.34

SNMF_Topic5

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.38 0.153 1.18e-32 1.18e-32 82 177 8.25
L2
GO:0070972 protein localization to endoplasmic reticulum 1 1.33 0.177 3.96e-30 3.96e-30 67 131 9.9

SNMF_Topic6

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0002521 leukocyte differentiation 1 1.19 0.113 8.42e-22 8.42e-22 64 390 5.32
L2
GO:0002250 adaptive immune response 1 1.19 0.135 5.43e-20 5.43e-20 50 263 6.2

SNMF_Topic7

SNMF_Topic8

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 1.8 0.182 1.74e-45 1.74e-45 83 131 15.8
L2
GO:0006414 translational elongation 1 1.65 0.184 3.5e-16 3.5e-16 49 121 6.05
L3
GO:0022613 ribonucleoprotein complex biogenesis 1 0.866 0.107 6.33e-24 6.33e-24 118 391 4
L4
GO:0010257 NADH dehydrogenase complex assembly 0.983 1.93 0.294 8.01e-09 8.01e-09 21 46 7.32
GO:0033108 mitochondrial respiratory chain complex assembly 0.0173 1.54 0.258 7.55e-08 7.55e-08 24 64 5.24
L5
GO:0006413 translational initiation 1 1.26 0.156 4.36e-43 4.36e-43 95 177 10.7
L6
GO:0070585 protein localization to mitochondrion 1 1.3 0.189 2.14e-08 2.14e-08 36 117 3.9

SNMF_Topic9

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006302 double-strand break repair 0.996 0.821 0.152 2.03e-07 2.68e-07 64 173 2.96
L2
GO:0006520 cellular amino acid metabolic process 0.994 0.697 0.126 1.89e-07 3.02e-07 86 254 2.59

SNMF_Topic10

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0007015 actin filament organization 1 0.781 0.113 3.54e-13 4.8e-13 102 329 3.05
L2
GO:0022613 ribonucleoprotein complex biogenesis 1 -1.31 0.13 1 3.1e-12 17 391 0.288
L3
GO:0048013 ephrin receptor signaling pathway 0.999 1.28 0.23 1.34e-10 1.34e-10 35 75 5.79

SNMF_Topic11

SNMF_Topic12

SNMF_Topic13

SNMF_Topic14

SNMF_Topic15

SNMF_Topic16

SNMF_Topic17

SNMF_Topic18

SNMF_Topic19

SNMF_Topic20

SNMF - Negative loadings

res <- negative.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_plot_tbl(., negative.ora)

html_tables <- negative.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_table_tbl(., negative.ora)

experiments <- unique(res$experiment)
for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  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")
  }}

SNMF_Topic2

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0022613 ribonucleoprotein complex biogenesis 1 -1.15 0.115 1.24e-53 1.24e-53 163 391 6.86
L2
GO:0140053 mitochondrial gene expression 1 -1.66 0.206 2.53e-17 2.53e-17 55 139 5.8
L3
GO:0009123 nucleoside monophosphate metabolic process 0.906 -0.781 0.135 1.45e-18 1.45e-18 82 255 4.26
GO:0009141 nucleoside triphosphate metabolic process 0.0891 -0.735 0.137 5.64e-17 5.64e-17 77 244 4.12
L5
GO:0002446 neutrophil mediated immunity 0.805 -0.571 0.107 3.72e-09 6.04e-09 85 386 2.51
GO:0036230 granulocyte activation 0.192 -0.542 0.107 2.86e-09 3.56e-09 85 384 2.53

SNMF_Topic3

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 2.15 0.156 0.909 0.269 14 177 0.806
L2
GO:0010257 NADH dehydrogenase complex assembly 0.983 2.57 0.306 0.994 0.0131 0 46 0
GO:0033108 mitochondrial respiratory chain complex assembly 0.0175 2.13 0.268 0.999 0.00157 0 64 0
L3
GO:0070972 protein localization to endoplasmic reticulum 1 1.92 0.183 1 0.00239 4 131 0.294
L4
GO:0009141 nucleoside triphosphate metabolic process 1 1.55 0.137 0.688 0.753 24 244 1.03
L5
GO:0006414 translational elongation 1 2.05 0.189 0.991 0.0378 6 121 0.488
L6
GO:0070671 response to interleukin-12 1 2.41 0.306 0.993 0.0832 1 44 0.218
L7
GO:0002446 neutrophil mediated immunity 0.795 0.997 0.114 0.991 0.0284 28 386 0.73
GO:0036230 granulocyte activation 0.205 0.982 0.115 0.994 0.0181 27 384 0.705
L8
GO:0070585 protein localization to mitochondrion 1 1.57 0.197 0.972 0.129 7 117 0.596
L9
GO:0043687 post-translational protein modification 1 1.03 0.128 0.523 1 33 310 1.12

SNMF_Topic4

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0016072 rRNA metabolic process 1 0.93 0.14 0.994 0.0358 4 210 0.389
L2
GO:0006413 translational initiation 0.998 0.873 0.152 0.00653 0.00777 17 177 2.19

SNMF_Topic5

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006413 translational initiation 1 1.38 0.153 0.0488 0.0676 18 177 1.71
L2
GO:0070972 protein localization to endoplasmic reticulum 1 1.33 0.177 0.781 0.723 7 131 0.843

SNMF_Topic6

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0002521 leukocyte differentiation 1 1.19 0.113 0.0362 1 0 390 0
L2
GO:0002250 adaptive immune response 1 1.19 0.135 0.0244 1 0 263 0

SNMF_Topic7

SNMF_Topic8

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0070972 protein localization to endoplasmic reticulum 1 1.8 0.182 0.919 0.523 1 131 0.403
L2
GO:0006414 translational elongation 1 1.65 0.184 0.902 0.731 1 121 0.437
L3
GO:0022613 ribonucleoprotein complex biogenesis 1 0.866 0.107 0.068 0.0874 12 391 1.71
L4
GO:0010257 NADH dehydrogenase complex assembly 0.983 1.93 0.294 0.586 1 0 46 0
GO:0033108 mitochondrial respiratory chain complex assembly 0.0173 1.54 0.258 0.707 0.636 0 64 0
L5
GO:0006413 translational initiation 1 1.26 0.156 0.655 1 3 177 0.91
L6
GO:0070585 protein localization to mitochondrion 1 1.3 0.189 0.653 1 2 117 0.918

SNMF_Topic9

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0006302 double-strand break repair 0.996 0.821 0.152 0.997 0.0254 2 173 0.256
L2
GO:0006520 cellular amino acid metabolic process 0.994 0.697 0.126 0.174 0.281 15 254 1.4

SNMF_Topic10

gobp_nr

geneSet description alpha beta beta.se pHypergeometric pFishersExact overlap geneSetSize oddsRatio
L1
GO:0007015 actin filament organization 1 0.781 0.113 0.999 0.00543 3 329 0.257
L2
GO:0022613 ribonucleoprotein complex biogenesis 1 -1.31 0.13 3.72e-17 3.72e-17 52 391 4.93
L3
GO:0048013 ephrin receptor signaling pathway 0.999 1.28 0.23 0.744 1 2 75 0.782

SNMF_Topic11

SNMF_Topic12

SNMF_Topic13

SNMF_Topic14

SNMF_Topic15

SNMF_Topic16

SNMF_Topic17

SNMF_Topic18

SNMF_Topic19

SNMF_Topic20

knitr::knit_exit()