Deng et al. Logistic SuSiE GSEA

<<<<<<< HEAD Last updated: 2022-04-11 ======= Last updated: 2022-04-13 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

Checks: 6 1

Knit directory: logistic-susie-gsea/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20220105)

The command set.seed(20220105) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: absolute

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute	relative
/project2/gilad/ktayeb/logistic-susie-gsea/	.

<<<<<<< HEAD Repository version: 8e9dff0

======= Repository version: 9d6fcad

>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

<<<<<<< HEAD The results in this page were generated with repository version 8e9dff0. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files. ======= The results in this page were generated with repository version 9d6fcad. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files. >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    data/data/
    Ignored:    library/
    Ignored:    renv/library/
    Ignored:    renv/staging/
    Ignored:    staging/
    Ignored:    summary_stat_gsea_univariate_simulations_cache/

Untracked files:
    Untracked:  .test.R.swp
    Untracked:  _targets.R
    Untracked:  _targets.md
    Untracked:  _targets/
    Untracked:  _targets_r/
<<<<<<< HEAD
=======
    Untracked:  analysis/de_droplet_noshrink.Rmd
    Untracked:  analysis/de_droplet_noshrink_logistic_susie.Rmd
    Untracked:  analysis/fetal_reference_cellid_gsea.Rmd
    Untracked:  analysis/fixed_intercept.Rmd
    Untracked:  analysis/iDEA_examples.Rmd
    Untracked:  analysis/latent_gene_list.Rmd
    Untracked:  analysis/libra_setup.Rmd
    Untracked:  analysis/linear_method_failure_modes.Rmd
    Untracked:  analysis/linear_regression_failure_regime.Rmd
    Untracked:  analysis/logistic_susie_veb_boost_vs_vb.Rmd
    Untracked:  analysis/logistic_susie_vis.Rmd
    Untracked:  analysis/references.bib
    Untracked:  analysis/scale_v_standardize_v_raw.Rmd
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
    Untracked:  analysis/simulations.Rmd
    Untracked:  cache/
<<<<<<< HEAD
    Untracked:  data/adipose_2yr_topsnp.txt
    Untracked:  data/chimp_human_eb_de/
    Untracked:  data/de-droplet-noshrink.RData
=======
    Untracked:  code/html_tables.R
    Untracked:  code/latent_logistic_susie.R
    Untracked:  code/load_data.R
    Untracked:  code/logistic_susie_data_driver.R
    Untracked:  code/marginal_sumstat_gsea_collapsed.R
    Untracked:  code/sumstat_gsea.py
    Untracked:  code/susie_gsea_queries.R
    Untracked:  data/adipose_2yr_topsnp.txt
    Untracked:  data/de-droplet/
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
    Untracked:  data/deng/
    Untracked:  data/fetal_reference_cellid_gene_sets.RData
    Untracked:  data/human_chimp_eb/
    Untracked:  data/pbmc-purified/
    Untracked:  data/wenhe_baboon_diet/
    Untracked:  deng_example.md
    Untracked:  deng_example_cache/
<<<<<<< HEAD
    Untracked:  figure/
    Untracked:  renv/settings.dcf
    Untracked:  simulation_targets/
    Untracked:  target_components/.factories.R.swp
=======
    Untracked:  docs.zip
    Untracked:  export/
    Untracked:  human_chimp_eb_de_example_cache/
    Untracked:  index.md
    Untracked:  latent_logistic_susie_cache/
    Untracked:  simulation_targets/
    Untracked:  single_cell_pbmc_cache/
    Untracked:  single_cell_pbmc_l1_cache/
    Untracked:  summary_stat_gsea_exploration_cache/
    Untracked:  summary_stat_gsea_sim_cache/

Unstaged changes:
    Modified:   _simulation_targets.R
    Modified:   _targets.Rmd
    Modified:   analysis/alpha_for_single_cell.Rmd
    Modified:   analysis/baboon_diet.Rmd
    Modified:   analysis/gseabenchmark_tcga.Rmd
    Modified:   analysis/human_chimp_eb_de_example.Rmd
    Modified:   analysis/single_cell_pbmc.Rmd
    Modified:   analysis/single_cell_pbmc_l1.Rmd
    Deleted:    analysis/summary_stat_gsea_univariate_simulations.Rmd
    Modified:   code/enrichment_pipeline.R
    Modified:   code/fit_baselines.R
    Modified:   code/fit_logistic_susie.R
    Modified:   code/fit_mr_ash.R
    Modified:   code/fit_susie.R
    Modified:   code/load_gene_sets.R
    Modified:   code/logistic_susie_vb.R
    Modified:   code/marginal_sumstat_gsea.R
    Modified:   code/simulate_gene_lists.R
    Modified:   target_components/factories.R
    Modified:   target_components/methods.R
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/deng_example.Rmd) and HTML (docs/deng_example.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	<<<<<<< HEAD 8e9dff0	Karl Tayeb	2022-04-11	wflow_publish(“analysis/deng_example.Rmd”, verbose = T) ======= 9d6fcad	karltayeb	2022-04-13	wflow_publish(“analysis/deng_example.Rmd”)
html	a102c2d	karltayeb	2022-04-13	Build site. >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
Rmd	<<<<<<< HEAD 48561c8	Karl Tayeb	2022-04-09	Merge branch ‘master’ of https://github.com/karltayeb/logistic-susie-gsea ======= 862ad9b	karltayeb	2022-04-13	wflow_publish(“analysis/deng_example.Rmd”) >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
html	72fad28	karltayeb	2022-04-09	Build site.
Rmd	419aadc	karltayeb	2022-04-09	wflow_publish(“analysis/deng_example.Rmd”)

Overview

<<<<<<< HEAD

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

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

#source('code/latent_logistic_susie.R')

# load nmf models
nmf <- readRDS('data/deng/nmf.rds')
snmf <- readRDS('data/deng/snmf.rds')

# load genesets
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
)

convert_labels <- function(y, from='SYMBOL', to='ENTREZID'){
  hs <- org.Hs.eg.db::org.Hs.eg.db
  
  gene_symbols <- names(y)
  if(from == 'SYMBOL'){
    gene_symbols <- purrr::map_chr(gene_symbols, toupper)
    names(y) <- gene_symbols
  }
  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)
=======
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)
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
}

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_'))
Fitting logistic susie...
    Experiment = SNMF_Topic2
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic3
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic4
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic5
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic6
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic7
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic8
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic9
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic10
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic11
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic12
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic13
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic14
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic15
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic16
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic17
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic18
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic19
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic20
    Database = gobp_nr
    thresh = 1e-04
negative.fits <- map_dfr(
  params.genesets,
  ~do_logistic_susie_cached(snmf.data, .x, params.thresh, c(-1), 'negative_'))
Fitting logistic susie...
    Experiment = SNMF_Topic2
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic3
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic4
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic5
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic6
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic7
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic8
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic9
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic10
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic11
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic12
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic13
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic14
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic15
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic16
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic17
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic18
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic19
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic20
    Database = gobp_nr
    thresh = 1e-04
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
<<<<<<< HEAD
ix  <- order(nmf$fl$pve[-1], decreasing = T) + 1  # exclude first topic
Y <- purrr::map(ix, ~get_y(nmf$fl$L.lfsr[,.x], 1e-5))
names(Y) = paste0('topic_', ix)

nmf.gobp <- xfun::cache_rds({
  susie.args <- list(L=10, maxit=200, verbose=T)
  purrr::map(Y, ~do_logistic_susie(.x, 'gobp', susie.args = susie.args))},
  dir = 'cache/deng_example/', file='nmf.gobp')

nmf.gomf <- xfun::cache_rds({
  susie.args <- list(L=10, maxit=200, verbose=T)
  purrr::map(Y, ~do_logistic_susie(.x, 'gomf', susie.args = susie.args))},
  dir = 'cache/deng_example/', file='nmf.gomf')

nmf.kegg <- xfun::cache_rds({
  susie.args <- list(L=10, maxit=200, verbose=T)
  purrr::map(Y, ~do_logistic_susie(.x, 'kegg', susie.args = susie.args))},
  dir = 'cache/deng_example/', file='nmf.kegg')

nmf.fits <- mget(ls(pattern='^nmf.+'))
names(nmf.fits) <- purrr::map_chr(names(nmf.fits), ~str_split(.x, '\\.')[[1]][2])

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

Threshold sensitivity
thresh <- map_dbl(1:20, ~10**-.x)
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

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

<<<<<<< HEAD
for(i in 1:length(y.mean.thresh)){
  lines(3:10, y.mean.thresh[[i]]/y.mean.thresh[[i]][1])
}
library(htmltools)
=======
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






a102c2d


karltayeb


2022-04-13




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)
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13








NMF_Topic7










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13








NMF_Topic16










Version


Author


Date






a102c2d


karltayeb


2022-04-13








NMF_Topic17










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13








NMF_Topic20










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







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










Version


Author


Date






a102c2d


karltayeb


2022-04-13






<<<<<<< HEAD

topic_5

gobp
=======

gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





=======


>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L1




<<<<<<< HEAD
GO:0044403


symbiont process


0.618


0.103


0.0182


6.29e-09


216


643


2.21
=======
GO:0070972


protein localization to endoplasmic reticulum


0.996


1.08


0.183


2.12e-41


2.12e-41


84


131


14




L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0044419


interspecies interaction between organisms


0.235


0.0999


0.0182


2.79e-08


217


657


2.16
=======
GO:0022613


ribonucleoprotein complex biogenesis


1


0.881


0.106


1.96e-24


2.03e-24


130


391


3.94




L3
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0016032


viral process


0.144


0.0983


0.0182


1.65e-08


202


600


2.21




L2
=======
GO:0006414


translational elongation


1


1.52


0.183


3.07e-14


3.07e-14


50


121


5.35




L4
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0006952


defense response


0.993


-0.113


0.019


1


193


1010


0.985




L3
=======
GO:0009141


nucleoside triphosphate metabolic process


0.999


0.979


0.133


4.81e-09


6.22e-09


67


244


2.88




L5
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0016192


vesicle-mediated transport
=======
GO:0006413


translational initiation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.144


0.0176


7.09e-15


495


1550


2.17




L4
=======
1.12


0.157


3.87e-40


3.87e-40


98


177


9.76




L6
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0009060


aerobic respiration


0.888


0.115


0.0185


1.96e-10


40


66


6.52




GO:0045333


cellular respiration


0.103


0.109


0.0187


1.12e-10


70


145


3.98




L5
=======
GO:0006605


protein targeting


1


0.865


0.11


6.81e-34


6.81e-34


140


364


5
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1







SNMF_Topic9







<<<<<<< HEAD

=======

>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD



GO:0010469


regulation of signaling receptor activity


1


-0.129


0.0207


1


40


330


0.571




L6

Version


Author


Date




GO:0006996


organelle organization


1


0.155


0.0164


4.63e-20


897


2980


2.19
=======

a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1







gobp_nr

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




<<<<<<< HEAD
GO:0004888


transmembrane signaling receptor activity
=======
GO:0006401


RNA catabolic process
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.999

-0.24


0.0215


1
=======

0.694


0.114


2.96e-09


4.51e-09
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


47


<<<<<<< HEAD
527


0.399




L2
=======
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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0045296


cadherin binding
=======
GO:0070972


protein localization to endoplasmic reticulum
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.962


<<<<<<< HEAD
0.16


0.0183


7.12e-20


137


282


4.1




L3
=======
1.14


0.174


7.35e-10


1.26e-09


55


131


3.91
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0022836


gated channel activity


0.584


-0.109


0.0209


1


25


244


0.473
=======
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
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0022839


ion gated channel activity


0.221


-0.105


0.0209


1


25


237


0.488
=======
GO:0048013


ephrin receptor signaling pathway


0.998


1.26


0.229


2.21e-09


2.21e-09


37


75


5.23




L3
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0005216


ion channel activity


0.0451


-0.0961


0.0205


1


37


295


0.594
=======
GO:0038127


ERBB signaling pathway


0.971


0.893


0.181


1.02e-07


1.32e-07


48


122


3.49
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0022843


voltage-gated cation channel activity


0.0388


-0.0965


0.0207


1


6


100


0.265
=======
GO:0070671


response to interleukin-12


0.00272


1.04


0.305


1.28e-05


1.28e-05


21


44


4.88
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0022803


passive transmembrane transporter activity


0.0282


-0.0934


0.0203


1


43


324


0.634
=======
GO:1990823


response to leukemia inhibitory factor


0.00161


0.737


0.221


1.53e-05


1.71e-05


34


89


3.31
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0015267


channel activity


0.0256


-0.0929


0.0203


1


43


323


0.636
=======
GO:0034109


homotypic cell-cell adhesion


0.00152


0.836


0.255


1.96e-05


2.08e-05


27


65


3.8
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0005261


cation channel activity


0.0214


-0.0931


0.0206


1


27


231


0.549




L4
=======
GO:0007015


actin filament organization


0.00131


0.404


0.117


6.55e-09


1.05e-08


105


329


2.56
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0048018


receptor ligand activity


0.984


-0.18


0.0217


1


22


258


0.385




L5
=======
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
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0051020


GTPase binding


0.941


0.117


0.0183


2.3e-09


191


548


2.33
=======
GO:0008544


epidermis development


0.000718


0.433


0.133


1.6e-05


2.3e-05


76


256


2.28
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0031267


small GTPase binding


0.0365


0.108


0.0184


7.84e-08


162


469


2.28
=======
GO:0072337


modified amino acid transport


0.000602


1.16


0.412


0.000954


0.000954


11


22


5.32







SNMF_Topic11










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic12










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1





<<<<<<< HEAD

kegg
=======


gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




<<<<<<< HEAD
hsa04144


Endocytosis
=======
GO:0006413


translational initiation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.186


0.0267


6.52e-11


95


210


3.48




=======
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




>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L3




<<<<<<< HEAD
hsa04080


Neuroactive ligand-receptor interaction


1


-0.279


0.0337


1


9


163


0.228




=======
GO:0006403


RNA localization


0.998


1.15


0.146


5.16e-12


5.16e-12


49


211


3.95




>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L4




<<<<<<< HEAD
hsa04060


Cytokine-cytokine receptor interaction
=======
GO:0071824


protein-DNA complex subunit organization
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.24


0.0324
=======

1.2


0.158
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1.92e-09


<<<<<<< HEAD
13


173


0.318




L5
=======
1.92e-09


40


180


3.7







SNMF_Topic13










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa05010


Alzheimer disease


0.91


0.146


0.0269


4.27e-08


65


142


3.49




hsa05012


Parkinson disease


0.0461


0.132


0.0272


5.13e-07


50


106


3.67




L6
=======
GO:0070972


protein localization to endoplasmic reticulum


1


4.29


0.18


7.55e-52


7.55e-52


40


131


75.8







SNMF_Topic14










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1








SNMF_Topic15







<<<<<<< HEAD



hsa01200


Carbon metabolism


0.984


0.141


0.0268


2.09e-07


48


98


3.94
=======

Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic16










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic17










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1







gobp_nr

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





L7
=======

L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa04530


Tight junction
=======
GO:0034976


response to endoplasmic reticulum stress
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.994


<<<<<<< HEAD
0.133


0.0267


2.11e-07


64


144


3.31







topic_10

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1
=======
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
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0006996


organelle organization


1


0.116


0.0168


7.73e-11


739


2980


1.86




L10
=======
GO:0036230


granulocyte activation


0.0405


1.11


0.116


5.47e-10


5.47e-10


49


384


3.19
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1







SNMF_Topic18







<<<<<<< HEAD

=======

>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD



GO:0022613


ribonucleoprotein complex biogenesis


0.99


0.104


0.0184


6.02e-22


163


391


3.64




L2

Version


Author


Date




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.751


0.199


0.0197


2e-32


72


92


17.9
=======

a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1








SNMF_Topic19







<<<<<<< HEAD

=======



GO:0006613


cotranslational protein targeting to membrane


0.242


0.196


0.0197


2.13e-31


73


96


15.8




L3

Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic20







>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




Version


Author


Date




GO:0043269


regulation of ion transport


0.964


-0.115


0.0204


1


59


481


0.669




L4
=======

a102c2d


karltayeb


2022-04-13









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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr

<<<<<<< HEAD

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0010467


gene expression
=======
GO:0022613


ribonucleoprotein complex biogenesis
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

0.195


0.0159


2.52e-27


1020


3830


2.29




L6
=======

-1.15


0.117


1


7.26e-20


48


391


0.432




L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0070646


protein modification by small protein removal
=======
GO:0140053


mitochondrial gene expression
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.739

0.124


0.0184


7.25e-12


98


249


3.23
=======

-1.66


0.206


1


2.62e-12


10


139


0.241




L3
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0016579


protein deubiquitination


0.255


0.121


0.0184


2.59e-11


92


233


3.25




L7
=======
GO:0009123


nucleoside monophosphate metabolic process


0.906


-0.781


0.136


1


1.27e-07


44


255


0.651
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0045165


cell fate commitment


0.999


-0.121


0.021
=======
GO:0009141


nucleoside triphosphate metabolic process


0.0892


-0.734


0.138
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
22


201


0.591




L9




GO:0006119


oxidative phosphorylation


0.94


0.102


0.0183


4.07e-08


41


88


4.28




GO:0042773


ATP synthesis coupled electron transport


0.0287


0.0893


0.0183


2.17e-06


31


67


4.21






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.165


0.0185


6.67e-26


91


152


7.39




L3




GO:0003676


nucleic acid binding


1


0.239


0.0167


2.38e-33


813


2790


2.46






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.329


0.0274


1.2e-29


85


129


10.1




L3




hsa03050


Proteasome


1


0.182


0.0273


5.25e-10


28


44


8.75




L5




hsa05016


Huntington disease


0.974


0.18


0.0269


2.4e-09


61


146


3.65







topic_11

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0048584


positive regulation of response to stimulus


0.998


-0.148


0.0213


0.999


103


1710


0.806




L3




GO:0051234


establishment of localization


0.724


0.21


0.0178


3.46e-10


389


3910


1.75




GO:0006810


transport


0.276


0.21


0.0178


5.7e-10


381


3830


1.74




L5




GO:0034976


response to endoplasmic reticulum stress


1


0.159


0.0197


1.72e-11


51


239


3.65




L6




GO:0006487


protein N-linked glycosylation


0.988


0.115


0.019


4.9e-09


22


69


6.17




L7




GO:0006665


sphingolipid metabolic process


0.93


0.138


0.0193


9.57e-10


30


112


4.85




GO:0006643


membrane lipid metabolic process


0.0698


0.136


0.02


3.18e-09


36


159


3.9






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0004576


oligosaccharyl transferase activity


0.946


0.228


0.0303


6.42e-12


10


10


Inf




GO:0004579


dolichyl-diphosphooligosaccharide-protein glycotransferase activity


0.0542


0.216


0.0304


8.49e-11


9


9


Inf




L4




GO:0003756


protein disulfide isomerase activity


0.491


0.0956


0.0185


2.22e-06


8


14


17.6




GO:0016864


intramolecular oxidoreductase activity, transposing S-S bonds


0.491


0.0956


0.0185


2.22e-06


8


14


17.6




L5




GO:0022857


transmembrane transporter activity


0.993


0.172


0.0201


1.75e-09


106


779


2.21






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




hsa04141


Protein processing in endoplasmic reticulum


1


0.246


0.0281


1.13e-14


46


149


5.39




L3




hsa04912


GnRH signaling pathway


1


-0.242


0.0395


1


1


83


0.134




L4




hsa04142


Lysosome


1


0.25


0.0276


1.7e-12


37


116


5.57




L5




hsa00510


N-Glycan biosynthesis


1


0.176


0.0275


5.7e-11


21


46


9.73




L6




hsa00564


Glycerophospholipid metabolism


1


0.167


0.0287


5.88e-05


19


80


3.57







topic_8

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.965


0.252


0.0194


3.07e-50


67


92


31.7




L4




GO:0022613


ribonucleoprotein complex biogenesis


1


0.161


0.0197


1.03e-21


98


391


3.99




L5




GO:0044271


cellular nitrogen compound biosynthetic process


1


0.232


0.0178


1.16e-24


461


3470


2.26




L7




GO:0042743


hydrogen peroxide metabolic process


0.951


0.1


0.0187


7.66e-06


13


36


6.34




L8




GO:1990823


response to leukemia inhibitory factor


0.5


0.12


0.019


8.65e-09


27


89


4.94




GO:1990830


cellular response to leukemia inhibitory factor


0.5


0.12


0.019


8.65e-09


27


89


4.94






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.239


0.0185


9.03e-46


82


152


13.9




L4




GO:0003723


RNA binding


1


0.214


0.0193


3.98e-28


244


1370


2.82




L6




GO:0001054


RNA polymerase I activity


0.975


0.101


0.0195


1.51e-06


7


9


38.8




L7




GO:0016209


antioxidant activity


0.988


0.113


0.0188


1.51e-06


18


57


5.16






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.417


0.0272


1.25e-44


78


129


16.6




L3




hsa04664


Fc epsilon RI signaling pathway


1


-0.389


0.0472


1


0


58


0




L4




hsa03013


RNA transport


1


0.182


0.0282


1.77e-06


34


139


3.19







topic_14

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L3




GO:0016192


vesicle-mediated transport


1


0.202


0.02


8.07e-10


165


1550


1.95




L4




GO:0045047


protein targeting to ER


0.674


0.154


0.0192


4.98e-10


27


102


5.45




GO:0072599


establishment of protein localization to endoplasmic reticulum


0.18


0.151


0.0193


1.27e-09


27


106


5.18




GO:0070972


protein localization to endoplasmic reticulum


0.105


0.153


0.0197


1.21e-10


32


131


4.92






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0004888


transmembrane signaling receptor activity


0.984


-0.144


0.0239


1


17


527


0.488




L3




GO:0005515


protein binding


1


0.16


0.0115


1.4e-05


626


8650


1.87






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa05012


Parkinson disease


0.998


0.19


0.0283


1.49e-07


26


106


4.24




L10




hsa03060


Protein export


0.984


0.126


0.0273


1.58e-06


10


21


11.6




L2




hsa04141


Protein processing in endoplasmic reticulum


1


0.183


0.0288


4.49e-08


33


149


3.76




L3




hsa05100


Bacterial invasion of epithelial cells


1


0.165


0.0281


5.55e-06


17


63


4.75







topic_6

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0044237


cellular metabolic process


0.295


-0.102


0.0122


1


917


7710


1.13




GO:0008152


metabolic process


0.241


-0.0954


0.0115


1


981


8190


1.17




GO:0006807


nitrogen compound metabolic process


0.197


-0.107


0.0129


1


857


7250


1.1




GO:0044238


primary metabolic process


0.136


-0.102


0.0124


1


903


7580


1.13




GO:0071704


organic substance metabolic process


0.131


-0.099


0.012


1


939


7850


1.16






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0016740


transferase activity


0.999


-0.115


0.0195


1


191


1920


0.843






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L4




hsa03050


Proteasome


1


0.15


0.027


1.71e-07


20


44


6.43







topic_12

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.92


0.288


0.0185


1.58e-48


49


92


39.1




GO:0006613


cotranslational protein targeting to membrane


0.0572


0.287


0.0187


2.62e-47


49


96


35.8




L4




GO:0090304


nucleic acid metabolic process


1


0.376


0.0196


1.62e-22


212


3640


2.91






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.213


0.0189


7.82e-39


52


152


17.7




L4




GO:0003723


RNA binding


1


0.45


0.0204


2.42e-49


158


1370


5.83




L5




GO:0038023


signaling receptor activity


0.985


-0.26


0.0279


1


5


697


0.204






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.459


0.0272


3.43e-39


51


129


21







topic_13

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L3




GO:0045047


protein targeting to ER


0.84


0.222


0.0191


2.89e-18


29


102


11.4




GO:0072599


establishment of protein localization to endoplasmic reticulum


0.149


0.221


0.0192


9.23e-18


29


106


10.8




L4




GO:0009994


oocyte differentiation


0.982


0.126


0.0194


1.44e-06


10


40


9.14






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0003735


structural constituent of ribosome


1


0.218


0.0197


6.33e-15


31


152


7.29






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.316


0.0283


2.27e-16


32


129


8.53




L2




hsa04660


T cell receptor signaling pathway


1


-0.334


0.046


1


0


88


0







topic_20

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L3




GO:0071704


organic substance metabolic process


0.998


0.267


0.0142


2.13e-07


268


7850


2.12




L4




GO:0072594


establishment of protein localization to organelle


1


0.255


0.0214


5.01e-13


45


462


4.17






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0060089


molecular transducer activity


0.99


-0.299


0.0281


1


5


751


0.221




L3




GO:0003723


RNA binding


1


0.377


0.0212


4.05e-20


101


1370


3.53






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa04926


Relaxin signaling pathway


1


-0.415


0.0467


1


0


114


0







topic_18

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.907


0.259


0.0188


2.17e-58


57


92


49.3




GO:0006613


cotranslational protein targeting to membrane


0.081


0.258


0.0189


7.66e-57


57


96


44.2




L4




GO:0042773


ATP synthesis coupled electron transport


0.496


0.213


0.0189


1.28e-16


23


67


14.5




GO:0042775


mitochondrial ATP synthesis coupled electron transport


0.496


0.213


0.0189


1.28e-16


23


67


14.5




L5




GO:0006518


peptide metabolic process


1


0.308


0.0207


1.03e-44


113


666


6.91




L6




GO:0006278


RNA-dependent DNA biosynthetic process


0.84


0.154


0.0199


1.05e-07


14


65


7.46




GO:0007004


telomere maintenance via telomerase


0.117


0.148


0.0198


5.1e-07


13


63


7.05






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.264


0.0187


2.37e-55


67


152


24.4




L3




GO:0003723


RNA binding


1


0.468


0.0203


9.01e-57


179


1370


6.04




L4




GO:0003954


NADH dehydrogenase activity


0.333


0.174


0.0189


1.75e-11


14


36


17.4




GO:0008137


NADH dehydrogenase (ubiquinone) activity


0.333


0.174


0.0189


1.75e-11


14


36


17.4




GO:0050136


NADH dehydrogenase (quinone) activity


0.333


0.174


0.0189


1.75e-11


14


36


17.4




L5




GO:0015318


inorganic molecular entity transmembrane transporter activity


0.983


-0.197


0.027


0.997


12


612


0.516




L6




GO:0004298


threonine-type endopeptidase activity


0.5


0.158


0.0187


4.97e-11


11


21


29.8




GO:0070003


threonine-type peptidase activity


0.5


0.158


0.0187


4.97e-11


11


21


29.8




L7




GO:0004129


cytochrome-c oxidase activity


0.297


0.171


0.0191


7.82e-07


8


22


15.4




GO:0015002


heme-copper terminal oxidase activity


0.297


0.171


0.0191


7.82e-07


8


22


15.4




GO:0016676


oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor


0.297


0.171


0.0191


7.82e-07


8


22


15.4




GO:0016675


oxidoreductase activity, acting on a heme group of donors


0.109


0.17


0.0193


1.16e-06


8


23


14.4




L8




GO:0051082


unfolded protein binding


1


0.167


0.0203


4.16e-09


19


99


6.52




L9




GO:0016679


oxidoreductase activity, acting on diphenols and related substances as donors


0.332


0.0968


0.0187


6.43e-05


4


7


35.6




GO:0008121


ubiquinol-cytochrome-c reductase activity


0.332


0.0968


0.0187


6.43e-05


4


7


35.6




GO:0016681


oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor


0.332


0.0968


0.0187


6.43e-05


4


7


35.6






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.504


0.027


2.79e-48


65


129


22.4




L3




hsa03050


Proteasome


1


0.26


0.0274


6.37e-12


18


44


12.9




L4




hsa05016


Huntington disease


1


0.202


0.0287


2.37e-15


37


146


6.65




L5




hsa05012


Parkinson disease


1


0.206


0.028


1.07e-16


33


106


8.79







topic_9

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006955


immune response


1


0.392


0.0202


7.37e-41


158


1330


4.72




L3




GO:0008152


metabolic process


0.999


-0.223


0.0137


1


283


8190


0.775




L4




GO:0046649


lymphocyte activation


1


0.201


0.0202


1.33e-28


80


495


5.76






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L3




GO:0038023


signaling receptor activity


0.996


0.267


0.0209


9.29e-15


73


697


3.32




L4




GO:0050662


coenzyme binding


1


-0.17


0.0274


0.999


2


239


0.21






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa04640


Hematopoietic cell lineage


1


0.17


0.0289


4.58e-06


12


55


6.4




L2




hsa01100


Metabolic pathways


1


-0.292


0.0343


1


22


1020


0.431




L3




hsa04621


NOD-like receptor signaling pathway


1


0.221


0.0295


2.96e-08


22


125


5.06







topic_19

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_16

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_15

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”




SNMF
ix  <- order(snmf$fl$pve[-1], decreasing = T) + 1  # exclude first topic
Y.snmf <- purrr::map(ix, ~get_y(snmf$fl$L.lfsr[,.x], 1e-5))
names(Y.snmf) = paste0('topic_', ix)

snmf.gobp <- xfun::cache_rds({
  susie.args <- list(L=10, maxit=200, verbose=T)
  purrr::map(Y.snmf, ~do_logistic_susie(.x, 'gobp', susie.args = susie.args))},
  dir = 'cache/deng_example/', file='snmf.gobp', rerun=T)

snmf.gomf <- xfun::cache_rds({
  susie.args <- list(L=10, maxit=200, verbose=T)
  purrr::map(Y.snmf, ~do_logistic_susie(.x, 'gomf', susie.args = susie.args))},
  dir = 'cache/deng_example/', file='snmf.gomf')

snmf.kegg <- xfun::cache_rds({
  susie.args <- list(L=10, maxit=200, verbose=T)
  purrr::map(Y.snmf, ~do_logistic_susie(.x, 'kegg', susie.args = susie.args))},
  dir = 'cache/deng_example/', file='snmf.kegg')

snmf.fits <- mget(ls(pattern='^snmf.+'))
names(snmf.fits) <- purrr::map_chr(names(snmf.fits), ~str_split(.x, '\\.')[[1]][2])
for(topic in names(Y.snmf)){
  cat("\n") 
  cat("###", topic, "\n") # Create second level headings with the names.
  
  for(db in names(genesets)){
    cat("####", db, "\n") # Create second level headings with the names.
    possibly_make_susie_html_table(snmf.fits, db, topic) %>% print()
    cat("\n")
  }
}

topic_2

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.5


0.181


0.0203


1.52e-19


79


92


15.3




GO:0045047


protein targeting to ER


0.247


0.178


0.0202


3.53e-19


85


102


12.6




GO:0006613


cotranslational protein targeting to membrane


0.164


0.178


0.0203


5.19e-19


81


96


13.6




GO:0072599


establishment of protein localization to endoplasmic reticulum


0.0877


0.175


0.0201


9.61e-19


87


106


11.6




L3




GO:0042773


ATP synthesis coupled electron transport


0.43


0.0915


0.0186


7.01e-07


47


67


5.88




GO:0042775


mitochondrial ATP synthesis coupled electron transport


0.43


0.0915


0.0186


7.01e-07


47


67


5.88




GO:0006119


oxidative phosphorylation


0.0721


0.0841


0.0185


2.89e-06


57


88


4.6




GO:0022904


respiratory electron transport chain


0.0115


0.0763


0.0185


3.12e-05


52


83


4.2




GO:0045333


cellular respiration


0.0102


0.0751


0.0183


2.57e-05


83


145


3.36






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.2


0.0196


3.39e-23


121


152


9.88






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.315


0.0296


1.03e-23


108


129


13.1




L2




hsa05012


Parkinson disease


0.936


0.165


0.0274


5.98e-09


73


106


5.51




hsa05016


Huntington disease


0.0373


0.148


0.0271


1.55e-07


91


146


4.14




L4




hsa03050


Proteasome


0.998


0.144


0.0283


1.14e-06


34


44


8.36







topic_3

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006613


cotranslational protein targeting to membrane


0.794


0.206


0.0196


9.16e-39


74


96


20.7




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.206


0.204


0.0196


1.53e-38


72


92


22.2




L3




GO:0042773


ATP synthesis coupled electron transport


0.499


0.196


0.0191


3.66e-23


48


67


15.4




GO:0042775


mitochondrial ATP synthesis coupled electron transport


0.499


0.196


0.0191


3.66e-23


48


67


15.4




L5




GO:0070646


protein modification by small protein removal


0.838


0.127


0.0186


7.39e-13


88


249


3.35




GO:0016579


protein deubiquitination


0.162


0.123


0.0186


5.82e-12


82


233


3.33




L6




GO:0006412


translation


0.903


0.171


0.0188


2.82e-30


195


527


3.77




GO:0043043


peptide biosynthetic process


0.0812


0.166


0.0188


1.47e-28


196


545


3.6




L8




GO:0051276


chromosome organization


1


0.142


0.0186


8.88e-12


233


924


2.14






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.214


0.0188


1.65e-41


100


152


11.9




L10




GO:0004298


threonine-type endopeptidase activity


0.495


0.0958


0.0187


5.38e-07


14


21


11.9




GO:0070003


threonine-type peptidase activity


0.495


0.0958


0.0187


5.38e-07


14


21


11.9




L2




GO:0004888


transmembrane signaling receptor activity


1


-0.194


0.0222


1


34


527


0.397




L3




GO:0003954


NADH dehydrogenase activity


0.333


0.18


0.0203


4.05e-18


30


36


30




GO:0008137


NADH dehydrogenase (ubiquinone) activity


0.333


0.18


0.0203


4.05e-18


30


36


30




GO:0050136


NADH dehydrogenase (quinone) activity


0.333


0.18


0.0203


4.05e-18


30


36


30




L5




GO:0003723


RNA binding


1


0.179


0.0182


2.85e-31


392


1370


2.72




L6




GO:0031625


ubiquitin protein ligase binding


0.779


0.0988


0.0188


1.26e-07


77


257


2.59




GO:0044389


ubiquitin-like protein ligase binding


0.206


0.094


0.0189


6.36e-07


78


271


2.44




L8




GO:0016679


oxidoreductase activity, acting on diphenols and related substances as donors


0.333


0.152


0.0281


3.95e-06


7


7


Inf




GO:0008121


ubiquinol-cytochrome-c reductase activity


0.333


0.152


0.0281


3.95e-06


7


7


Inf




GO:0016681


oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor


0.333


0.152


0.0281


3.95e-06


7


7


Inf




L9




GO:0045296


cadherin binding


0.978


0.104


0.0187


7.64e-10


89


282


2.81






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.397


0.0279


5.06e-39


92


129


14.2




L2




hsa05012


Parkinson disease


1


0.331


0.0277


1.67e-28


72


106


11.9




L3




hsa04110


Cell cycle


0.997


0.149


0.0271


1.5e-05


42


118


2.98




L4




hsa03050


Proteasome


1


0.191


0.0273


6.79e-10


27


44


8.52







topic_9

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L4




GO:0006996


organelle organization


1


0.171


0.0166


2.85e-12


799


2980


1.94




L5




GO:0030154


cell differentiation


0.912


-0.105


0.017


1


587


3040


1.1




GO:0048869


cellular developmental process


0.0703


-0.097


0.0169


1


633


3180


1.15




L6




GO:0099537


trans-synaptic signaling


0.297


-0.125


0.0202


1


69


521


0.678




GO:0099536


synaptic signaling


0.248


-0.124


0.0202


1


70


526


0.682




GO:0007268


chemical synaptic transmission


0.228


-0.124


0.0202


1


68


514


0.677




GO:0098916


anterograde trans-synaptic signaling


0.228


-0.124


0.0202


1


68


514


0.677




L7




GO:0044281


small molecule metabolic process


1


0.156


0.0178


3.03e-12


449


1540


2.04




L8




GO:0006401


RNA catabolic process


0.737


0.111


0.0184


1.44e-08


110


304


2.62




GO:0006402


mRNA catabolic process


0.17


0.106


0.0184


5.48e-08


101


279


2.62




GO:0000184


nuclear-transcribed mRNA catabolic process, nonsense-mediated decay


0.0536


0.102


0.0185


3.35e-08


52


115


3.77




L9




GO:1990823


response to leukemia inhibitory factor


0.481


0.0885


0.0182


5.04e-07


41


89


3.89




GO:1990830


cellular response to leukemia inhibitory factor


0.481


0.0885


0.0182


5.04e-07


41


89


3.89






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0004888


transmembrane signaling receptor activity


0.675


-0.118


0.0202


1


66


527


0.633




GO:0038023


signaling receptor activity


0.313


-0.113


0.0198


1


97


697


0.715




L2




GO:0022836


gated channel activity


0.437


-0.115


0.0211


1


23


244


0.462




GO:0022839


ion gated channel activity


0.396


-0.115


0.0211


1


22


237


0.455




GO:0005216


ion channel activity


0.0914


-0.107


0.0207


1


32


295


0.54




GO:0022838


substrate-specific channel activity


0.0302


-0.103


0.0207


1


35


304


0.578




L4




GO:0003723


RNA binding


0.985


0.104


0.0178


1e-08


388


1370


1.92






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L4




hsa04080


Neuroactive ligand-receptor interaction


1


-0.231


0.0323


1


12


163


0.321







topic_10

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0043299


leukocyte degranulation


0.187


0.101


0.0188


4.82e-08


110


406


2.3




GO:0002446


neutrophil mediated immunity


0.175


0.101


0.0188


7.84e-08


105


386


2.31




GO:0002444


myeloid leukocyte mediated immunity


0.162


0.101


0.0188


7.17e-08


113


423


2.26




GO:0042119


neutrophil activation


0.11


0.0996


0.0188


1.46e-07


103


381


2.29




GO:0043312


neutrophil degranulation


0.0916


0.099


0.0188


2.04e-07


101


374


2.29




GO:0002275


myeloid cell activation involved in immune response


0.0789


0.0985


0.0188


1.45e-07


110


414


2.24




GO:0036230


granulocyte activation


0.0779


0.0984


0.0188


2.21e-07


103


384


2.27




GO:0002283


neutrophil activation involved in immune response


0.0739


0.0982


0.0188


2.69e-07


101


376


2.27




L3




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.569


0.152


0.0184


3.34e-12


44


92


5.61




GO:0006613


cotranslational protein targeting to membrane


0.356


0.152


0.0185


4.59e-12


45


96


5.4




GO:0045047


protein targeting to ER


0.0686


0.149


0.0186


1.44e-11


46


102


5.03




L4




GO:0030029


actin filament-based process


0.987


0.161


0.0185


2.43e-17


183


609


2.74




L5




GO:0048013


ephrin receptor signaling pathway


0.978


0.0947


0.0184


2.73e-10


36


75


5.63




L6




GO:0006396


RNA processing


0.998


-0.133


0.0207


1


80


757


0.697






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0038023


signaling receptor activity


0.853


-0.125


0.0206


1


73


697


0.689




GO:0060089


molecular transducer activity


0.0922


-0.117


0.0205


1


84


751


0.744




GO:0004888


transmembrane signaling receptor activity


0.0545


-0.117


0.0208


1


52


527


0.647




L2




GO:0045296


cadherin binding


1


0.175


0.0184


3.57e-19


109


282


3.94




L3




GO:0140098


catalytic activity, acting on RNA


0.998


-0.121


0.0217


1


21


265


0.51






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa04080


Neuroactive ligand-receptor interaction


1


-0.316


0.0359


1


5


163


0.165




L2




hsa04530


Tight junction


1


0.165


0.027


9.63e-10


58


144


3.76




L3




hsa03010


Ribosome


0.998


0.137


0.027


3.37e-06


46


129


3.05




L4




hsa05100


Bacterial invasion of epithelial cells


0.981


0.128


0.0269


1.53e-07


30


63


4.97







topic_8

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.915


0.301


0.0206


4.41e-56


78


92


46.2




GO:0006613


cotranslational protein targeting to membrane


0.0843


0.298


0.0206


9.03e-55


79


96


38.6




L4




GO:0006414


translational elongation


0.909


0.148


0.0187


5.9e-14


48


121


5.32




GO:0070125


mitochondrial translational elongation


0.0517


0.14


0.0186


2.46e-12


37


86


6.07




L5




GO:0022613


ribonucleoprotein complex biogenesis


1


0.169


0.0192


9.1e-25


126


391


4




L6




GO:0022900


electron transport chain


1


0.145


0.0187


5.98e-11


49


147


4.04




L7




GO:2000145


regulation of cell motility


0.597


-0.126


0.0216


1


47


686


0.565




GO:0030334


regulation of cell migration


0.344


-0.124


0.0217


1


44


644


0.564




GO:0051270


regulation of cellular component movement


0.0298


-0.113


0.0215


1


58


749


0.647




L9




GO:0072655


establishment of protein localization to mitochondrion


0.453


0.117


0.0189


3.83e-08


37


115


3.8




GO:0070585


protein localization to mitochondrion


0.277


0.115


0.0189


6.36e-08


37


117


3.71




GO:0006626


protein targeting to mitochondrion


0.268


0.114


0.0188


2.5e-08


31


86


4.51






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.274


0.019


2.09e-60


106


152


19.5




L2




GO:0004888


transmembrane signaling receptor activity


1


-0.219


0.0235


1


22


527


0.333




L5




GO:0003723


RNA binding


1


0.189


0.0187


1.27e-32


322


1370


2.83




L7




GO:0003954


NADH dehydrogenase activity


0.325


0.106


0.0184


6.24e-08


18


36


7.96




GO:0008137


NADH dehydrogenase (ubiquinone) activity


0.325


0.106


0.0184


6.24e-08


18


36


7.96




GO:0050136


NADH dehydrogenase (quinone) activity


0.325


0.106


0.0184


6.24e-08


18


36


7.96






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.467


0.0284


3.24e-55


98


129


23.5




L4




hsa00190


Oxidative phosphorylation


0.992


0.208


0.0271


9.62e-11


41


97


5.01




L5




hsa04060


Cytokine-cytokine receptor interaction


1


-0.309


0.037


1


4


173


0.151




L6




hsa03013


RNA transport


0.998


0.14


0.0276


0.000144


38


139


2.54




L7




hsa03050


Proteasome


0.985


0.126


0.0271


0.000128


17


44


4.2







topic_7

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0042254


ribosome biogenesis


1


0.216


0.0188


1.92e-56


152


247


10




L10




GO:0070647


protein modification by small protein conjugation or removal


1


0.17


0.0187


5.21e-15


238


876


2.34




L2




GO:0048731


system development


0.954


-0.181


0.0178


1


462


3550


0.836




L3




GO:0006397


mRNA processing


0.998


0.2


0.0184


8.57e-44


193


425


5.28




L4




GO:0006413


translational initiation


1


0.183


0.0189


1.43e-41


110


177


10.1




L5




GO:0006996


organelle organization


1


0.216


0.0173


4.76e-18


665


2980


2.02




L6




GO:0003008


system process


0.968


-0.134


0.0206


1


120


1240


0.606




L7




GO:0034641


cellular nitrogen compound metabolic process


1


0.336


0.0154


2.87e-84


1190


4670


3.48




L8




GO:0035270


endocrine system development


1


-0.23


0.0265


1


2


113


0.104




L9




GO:0006360


transcription by RNA polymerase I


0.999


0.121


0.0195


2.25e-18


38


53


15.1






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003723


RNA binding


1


0.408


0.0176


4.87e-115


570


1370


5.33




L2




GO:0038023


signaling receptor activity


0.998


-0.277


0.0229


1


35


697


0.291




L5




GO:0003954


NADH dehydrogenase activity


0.333


0.122


0.0186


5.56e-09


22


36


9.11




GO:0008137


NADH dehydrogenase (ubiquinone) activity


0.333


0.122


0.0186


5.56e-09


22


36


9.11




GO:0050136


NADH dehydrogenase (quinone) activity


0.333


0.122


0.0186


5.56e-09


22


36


9.11




L6




GO:0003735


structural constituent of ribosome


1


0.123


0.0185


1.61e-29


88


152


8.21




L7




GO:0042393


histone binding


1


0.12


0.0186


2.65e-11


64


163


3.8




L8




GO:0005509


calcium ion binding


1


-0.185


0.0224


1


31


491


0.377




L9




GO:0003677


DNA binding


1


0.138


0.0182


5.15e-14


383


1580


2.04






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome


1


0.35


0.0273


1.19e-28


82


129


9.65




L10




hsa03020


RNA polymerase


0.799


0.124


0.0277


1.09e-07


18


27


10.4




hsa00240


Pyrimidine metabolism


0.165


0.117


0.0285


3.15e-05


33


86


3.27




L3




hsa03040


Spliceosome


1


0.257


0.0271


9.96e-17


64


121


6.09




L4




hsa03013


RNA transport


1


0.213


0.0273


8.44e-15


67


139


5.05




L5




hsa05016


Huntington disease


1


0.244


0.0272


1.16e-14


69


146


4.86




L6




hsa03050


Proteasome


1


0.195


0.0273


1.05e-09


27


44


8.36




L7




hsa03008


Ribosome biogenesis in eukaryotes


1


0.193


0.0274


3.89e-12


39


68


7.15




L8




hsa04110


Cell cycle


1


0.183


0.0271


1.87e-07


47


118


3.52




L9




hsa04080


Neuroactive ligand-receptor interaction


1


-0.536


0.042


1


1


163


0.0308







topic_4

gobp




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




GO:0006614


SRP-dependent cotranslational protein targeting to membrane


0.577


0.151


0.0184


7.93e-16


50


92


7




GO:0045047


protein targeting to ER


0.323


0.15


0.0185


1.38e-15


53


102


6.37




GO:0006613


cotranslational protein targeting to membrane


0.0604


0.146


0.0184


7.78e-15


50


96


6.39






gomf

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2
=======
6.37e-07


43


244


0.668




L5
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0003735


structural constituent of ribosome
=======
GO:0002446


neutrophil mediated immunity
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.803

0.117


0.0183


3.6e-12


63


152


4.12




L4
=======

-0.57


0.108


1


3.48e-06


82


386


0.844
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0003676


nucleic acid binding


1


0.128


0.0171


3.36e-11


608


2790


1.83






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




hsa03010


Ribosome
=======
GO:0036230


granulocyte activation


0.192


-0.541


0.109
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


0.228


<<<<<<< HEAD
0.0269


8.76e-15


60


129


5.28




L4




hsa05016


Huntington disease


0.999


0.162


0.0271


1.79e-07


51


146


3.21
=======
1.27e-05


84


384


0.876







SNMF_Topic3










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






<<<<<<< HEAD

topic_5

gobp
=======

gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


<<<<<<< HEAD
pValueHypergeometric
=======
pHypergeometric


pFishersExact
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


overlap


geneSetSize


oddsRatio





=======


>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L1




<<<<<<< HEAD
GO:0006613


cotranslational protein targeting to membrane


0.853


0.235


0.0191


4.32e-36
=======
GO:0006413


translational initiation


1


2.14


0.158


4.42e-57
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


4.42e-57


<<<<<<< HEAD
96


17.7
=======
90


177


16.6




L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0000184


nuclear-transcribed mRNA catabolic process, nonsense-mediated decay


0.106


0.236


0.0195


1.32e-35


76


115


13.5




L2
=======
GO:0010257


NADH dehydrogenase complex assembly


0.998


2.63


0.306


1.9e-25


1.9e-25


31


46


30.6




L3
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0034622


cellular protein-containing complex assembly


0.998


0.137


0.0191


1.02e-07


178


823


1.93




L5
=======
GO:0070972


protein localization to endoplasmic reticulum


1


1.96


0.184


2.42e-51


2.42e-51


74


131


20.3




L4
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0006996


organelle organization
=======
GO:0006091


generation of precursor metabolites and energy
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.122


0.0179


0.998


401


2980


1.05
=======

1.43


0.115


2.58e-27


2.58e-27


91


371


5.11
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






gomf

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio





L1
=======

L5
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0003735


structural constituent of ribosome
=======
GO:0006414


translational elongation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.227


0.0184


8.29e-32


85


152


8.82




=======
2.08


0.19


5.8e-15


5.8e-15


37


121


6.53




>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L6




<<<<<<< HEAD
GO:0036402


proteasome-activating ATPase activity


0.955


0.129


0.0261


1.15e-05


6


6


Inf
=======
GO:0070671


response to interleukin-12


1


2.43


0.307


2.64e-11


2.64e-11


19


44


11.1




L7
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






kegg

<<<<<<< HEAD

<<<<<<< HEAD



geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1
=======

GO:0002446


neutrophil mediated immunity


0.75


0.987


0.117


1.36e-09


1.53e-09


61


386


2.81
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa03010


Ribosome


1


0.349


0.0274


2.72e-34


83


129


11.7




L4
=======
GO:0036230


granulocyte activation


0.25


0.975


0.117


2.91e-09


3.11e-09


60


384


2.77




L8
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa03050


Proteasome
=======
GO:0070585


protein localization to mitochondrion
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.166


0.027


1.22e-08


24


44


7.28




L5
=======
1.62


0.198


1.38e-09


1.38e-09


29


117


4.83




L9
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa04973


Carbohydrate digestion and absorption
=======
GO:0043687


post-translational protein modification
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.258


0.0431


1


0


32


0
=======

1.05


0.13


2.38e-06


2.66e-06


45


310


2.5







SNMF_Topic4










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






<<<<<<< HEAD

topic_12

gobp
=======

gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





L3




GO:0034641


cellular nitrogen compound metabolic process


1


0.277


0.0173


2.29e-22


421


4670


2.33




L5
=======

L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0070125


mitochondrial translational elongation


0.863


0.141


0.0187


2.46e-15


30


86


8.81




GO:0070126


mitochondrial translational termination


0.119


0.137


0.0188


2e-14


29


86


8.36




L6
=======
GO:0016072


rRNA metabolic process


1


0.929


0.141


1.58e-11


2.05e-11


71


210


3.43




L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0034622


cellular protein-containing complex assembly


1


0.208


0.0203


9.39e-17


115


823


2.87




L7




GO:0006405


RNA export from nucleus


0.537


0.136


0.0194


1.46e-13


34


125


6.16




GO:0071426


ribonucleoprotein complex export from nucleus


0.276


0.134


0.0193


6.51e-13
=======
GO:0006413


translational initiation


0.998


0.872


0.154


1.54e-09


2.31e-09
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


59


<<<<<<< HEAD
117


6.19
=======
177


3.34
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1







SNMF_Topic5







<<<<<<< HEAD

=======

>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD



GO:0071166


ribonucleoprotein complex localization


0.183


0.133


0.0193


8.41e-13


32


118


6.12




L8

Version


Author


Date




GO:0032501


multicellular organismal process


1


-0.307


0.0182


1


219


5120


0.584




L9
=======

a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0044265


cellular macromolecule catabolic process
=======
GO:0006413


translational initiation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.987


<<<<<<< HEAD
0.191


0.0204
=======
1.38


0.154


1.18e-32


1.18e-32


82


177


8.25




L2




GO:0070972


protein localization to endoplasmic reticulum
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


9.27e-15


1.33


<<<<<<< HEAD
124


977


2.57
=======
0.178


3.96e-30


3.96e-30


67


131


9.9







SNMF_Topic6










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1





<<<<<<< HEAD

gomf
=======


gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD

<<<<<<< HEAD

=======
GO:0002250



geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





L1




GO:0003723


RNA binding


1


0.356


0.0194


1.99e-42


218


1370


3.86




L2
=======

L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0043167


ion binding
=======
GO:0002521


leukocyte differentiation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.145


0.0187


1


218


4420


0.75




L3




GO:0038023


signaling receptor activity


0.999


-0.331


0.0266


1


9


697


0.198




L4
=======

1.19


0.115


8.42e-22


8.42e-22


64


390


5.32




L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0003735


structural constituent of ribosome


0.992


0.0992


0.019


5.8e-16


41


152


6.15




L5




GO:0004298


threonine-type endopeptidase activity


0.5


0.117


0.0185


1.14e-08


11


21


17.7



adaptive immune response


1


1.19


0.137


5.43e-20


5.43e-20


50


263


6.2







SNMF_Topic7







>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




Version


Author


Date




GO:0070003


threonine-type peptidase activity


0.5


0.117


0.0185


1.14e-08


11


21


17.7




L7
=======

a102c2d


karltayeb


2022-04-13








SNMF_Topic8










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0051082


unfolded protein binding
=======
GO:0070972


protein localization to endoplasmic reticulum
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.137


0.0194


1.38e-09


25


99


5.51






kegg




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2




hsa03013


RNA transport


1


0.301


0.0278


3.42e-17


44


139


6.68




L3
=======
1.8


0.183


1.74e-45


1.74e-45


83


131


15.8




L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa03010


Ribosome
=======
GO:0006414


translational elongation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.267


0.0281


5.26e-11


34


129


5.02




L4
=======
1.65


0.185


3.5e-16


3.5e-16


49


121


6.05




L3
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa05130


Pathogenic Escherichia coli infection
=======
GO:0022613


ribonucleoprotein complex biogenesis
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.166


0.028


2.45e-05


13


46


5.3




L5
=======
0.866


0.109


6.33e-24


6.33e-24


118


391


4




L4
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa03050


Proteasome


1


0.215


0.0273


8.71e-10


18


44


9.44




L6
=======
GO:0010257


NADH dehydrogenase complex assembly


0.983


1.93


0.295


8.01e-09


8.01e-09


21


46


7.32
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa03040


Spliceosome


1


0.189


0.0289


2.43e-07


27


121


3.96
=======
GO:0033108


mitochondrial respiratory chain complex assembly


0.0174


1.54


0.259


7.55e-08


7.55e-08


24


64


5.24
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1







topic_17

gobp

<<<<<<< HEAD

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio





L2
=======

L5
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0048584


positive regulation of response to stimulus
=======
GO:0006413


translational initiation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.195


0.0234


0.995


48


1710


0.723




L3
=======

1.26


0.158


4.36e-43


4.36e-43


95


177


10.7




L6
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0006810


transport


0.97


0.322


0.0192


9.31e-13
=======
GO:0070585


protein localization to mitochondrion


1


1.3


0.19


2.14e-08


2.14e-08
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


218


<<<<<<< HEAD
3830


2.12




L5
=======
117


3.9







SNMF_Topic9










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0006302


double-strand break repair


0.996


0.821


0.153


2.03e-07


2.68e-07


64


173


2.96




L2




GO:0006520


cellular amino acid metabolic process


0.994


0.697


0.128


1.89e-07


3.02e-07


86


254


2.59







SNMF_Topic10










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0007015


actin filament organization


1


0.78


0.115


3.54e-13


4.8e-13


102


329


3.05




L2




GO:0022613


ribonucleoprotein complex biogenesis


1


-1.31


0.132


1


3.1e-12


17


391


0.288




L3




GO:0048013


ephrin receptor signaling pathway


0.999


1.28


0.231


1.34e-10


1.34e-10


35


75


5.79







SNMF_Topic11










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic12










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic13










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic14










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic15










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic16










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic17










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic18










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic19










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic20










Version


Author


Date






a102c2d


karltayeb


2022-04-13









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










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0006413


translational initiation


1


1.62


0.163


1.49e-58


1.49e-58


110


177


15.3




L10




GO:0006520


cellular amino acid metabolic process


1


0.979


0.136


8.19e-06


1.09e-05


54


254


2.36




L2




GO:0022613


ribonucleoprotein complex biogenesis


1


1.61


0.108


1.24e-53


1.24e-53


163


391


6.86




L3




GO:0006414


translational elongation


1


2.25


0.185


9.03e-27


9.03e-27


62


121


9.38




L4




GO:0010257


NADH dehydrogenase complex assembly


0.912


2.17


0.301


1.3e-17


1.3e-17


30


46


16.4




GO:0033108


mitochondrial respiratory chain complex assembly


0.0881


1.81


0.262


7.73e-17


7.73e-17


35


64


10.6




L5




GO:0070972


protein localization to endoplasmic reticulum


1


1.96


0.19


2.36e-52


2.36e-52


89


131


19.4




L6




GO:0009123


nucleoside monophosphate metabolic process


1


1.11


0.133


1.45e-18


1.45e-18


82


255


4.26




L7




GO:0036230


granulocyte activation


0.528


0.955


0.112


2.86e-09


3.56e-09


85


384


2.53




GO:0002446


neutrophil mediated immunity


0.472


0.952


0.111


3.72e-09


6.04e-09


85


386


2.51




L8




GO:0070585


protein localization to mitochondrion


0.991


1.32


0.193


2.58e-08


2.58e-08


36


117


3.87




L9




GO:0070646


protein modification by small protein removal


1


0.973


0.137


6.59e-08


7.53e-08


59


249


2.73







SNMF_Topic3










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0051321


meiotic cell cycle


0.998


0.935


0.153


5.46e-08


6.52e-08


46


190


3.09







SNMF_Topic4










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0072350


tricarboxylic acid metabolic process


1


2.35


0.338


7.25e-09


7.25e-09


13


36


11.7







SNMF_Topic5










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0006414


translational elongation


1


1.38


0.193


1.93e-08


1.93e-08


27


121


4.43







SNMF_Topic6










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic7










Version


Author


Date






a102c2d


karltayeb


2022-04-13







gobp_nr




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0022613


ribonucleoprotein complex biogenesis


1


1.58


0.106


2.03e-80


2.03e-80


232


391


9.4




L10
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0034976


response to endoplasmic reticulum stress


1


0.205


0.0206


3.13e-11


34


239


4.6






gomf

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






=======
GO:0006403


RNA localization


0.999


0.926


0.143


3.68e-28


3.68e-28


106


211


6.07




>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L2




<<<<<<< HEAD
GO:0004888


transmembrane signaling receptor activity
=======
GO:0006397


mRNA processing
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.228


0.0268
=======

1.09


0.102
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


9.02e-48


<<<<<<< HEAD
6


527


0.297




=======
9.02e-48


201


425


5.64




>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L3




<<<<<<< HEAD
GO:0004579


dolichyl-diphosphooligosaccharide-protein glycotransferase activity


0.744


0.106


0.0188


2.06e-07


6


9


54
=======
GO:0006413


translational initiation


1


1.63


0.157


6.03e-39


6.03e-39


108


177


9.45




L4
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0004576


oligosaccharyl transferase activity


0.255


0.104


0.0191


4.99e-07


6


10


40.5




L4
=======
GO:0071824


protein-DNA complex subunit organization


1


1.07


0.153


1.09e-15


1.82e-15


77


180


4.42




L5
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0003756


protein disulfide isomerase activity
=======
GO:0007059


chromosome segregation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.482


<<<<<<< HEAD
0.0985


0.0186


6.27e-06


6


14


20.2
=======
0.965


0.13


1.02e-12


1.14e-12


91


254


3.31




L6
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0016864


intramolecular oxidoreductase activity, transposing S-S bonds


0.482


0.0985


0.0186


6.27e-06


6


14


20.2






kegg

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2
=======
GO:0070646


protein modification by small protein removal


1


1.07


0.131


2.71e-13


3.07e-13


91


249


3.42




L7
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa04141


Protein processing in endoplasmic reticulum


1


0.353


0.0286


3.33e-20


40


149


8.85




L3




hsa04912


GnRH signaling pathway
=======
GO:0010257


NADH dehydrogenase complex assembly
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.927

-0.463


0.0489
=======

1.96


0.293
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


8.37e-08


<<<<<<< HEAD
0


83


0




L4
=======
8.37e-08


24


46


6.32
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa04142


Lysosome
=======
GO:0033108


mitochondrial respiratory chain complex assembly
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.0723


<<<<<<< HEAD
0.306


0.0286


2.83e-12


27


116


6.93




L5
=======
1.62


0.257


8.19e-07


8.19e-07


28


64


4.51




L8
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa05010


Alzheimer disease


1


0.237


0.0311


1.19e-05


20


142


3.61




L6
=======
GO:0098781


ncRNA transcription


0.996


1.46


0.219


5e-16


5e-16


49


88


7.36




L9
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
hsa03060


Protein export
=======
GO:0061919


process utilizing autophagic mechanism
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.153


0.0282


1.23e-08


10


21


19.6
=======
0.689


0.106


6.65e-07


9.1e-07


109


403


2.19







SNMF_Topic8










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic9










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






<<<<<<< HEAD

topic_13

gobp
=======

gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





L2
=======

L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




GO:0006413


translational initiation


<<<<<<< HEAD
0.991


0.459


0.0186


1.64e-62


39


92


186






gomf




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1




GO:0003735


structural constituent of ribosome


1


0.506


0.0192


3.94e-55


41


152


88.7
=======
1


1.73


0.163


1.36e-14


1.36e-14


36


177


6.03
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1





<<<<<<< HEAD

kegg

=======

SNMF_Topic10










geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1


>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD

=======

>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




Version


Author


Date




hsa03010


Ribosome


1


0.666


0.0277


6.07e-50


41


129


79

a102c2d


karltayeb


2022-04-13





<<<<<<< HEAD

topic_20

gobp
[1] “nothing to report…”


gomf
=======

gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


<<<<<<< HEAD
pValueHypergeometric
=======
pHypergeometric


pFishersExact
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


overlap


geneSetSize


oddsRatio





=======

>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L1




<<<<<<< HEAD
GO:0022857


transmembrane transporter activity
=======
GO:0070972


protein localization to endoplasmic reticulum
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1

-0.419


0.0315


1


1


779


0.117
=======

1.78


0.183


8.46e-37


8.46e-37


48


131


18.8
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






kegg
[1] “nothing to report…”



topic_11

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_15

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_6

gobp

<<<<<<< HEAD

=======
1.71




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio





L1
=======

L2
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0002376


immune system process
=======
GO:1990823


response to leukemia inhibitory factor
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.353


0.02


5.89e-43


198


2020


4.39




=======
2.08


0.229


1.65e-10


1.65e-10


19


89


8.12




>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
L3




<<<<<<< HEAD
GO:0046649


lymphocyte activation
=======
GO:0006413


translational initiation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


1


<<<<<<< HEAD
0.172


0.0201


3.99e-28


78


495


5.79




L4


0.161


1.51e-36


1.51e-36


54


177


14.5







SNMF_Topic11







>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




Version


Author


Date




GO:0006952


defense response
=======

a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1








SNMF_Topic12







<<<<<<< HEAD




Version


Author


Date






a102c2d

0.196


0.0205


1.72e-31
=======

karltayeb


2022-04-13







gobp_nr

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio






L1




GO:0006414


translational elongation
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


120

1010


4.5




L5




GO:0033554


cellular response to stress


0.999


-0.134


0.0233


0.826


53


1560


0.919




L6
=======

1.78


0.189


5.07e-15


5.07e-15


36


121


6.7




L2




GO:0022613


ribonucleoprotein complex biogenesis


1


1.1


0.113


2.27e-15


2.27e-15


71


391


3.62




L3
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0071840


cellular component organization or biogenesis


0.937


-0.204


0.0192


1


156


5030


0.76




GO:0016043


cellular component organization


0.0631


-0.201


0.0194


0.999


155


4880


0.794
=======
GO:0071824


protein-DNA complex subunit organization


1


1.26


0.162


5.58e-09


5.58e-09


35


180


3.79







SNMF_Topic13










Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1





<<<<<<< HEAD

gomf
=======


gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





L3
=======

L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0038023


signaling receptor activity
=======
GO:0070972


protein localization to endoplasmic reticulum
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.995


<<<<<<< HEAD
0.266


0.021


3.85e-14


70


697


3.3




L4




GO:0050662


coenzyme binding


1


-0.162


0.0273


0.999


2


239


0.218






kegg

=======
4.8




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2


0.182


3.21e-58


3.21e-58


40


131


127







SNMF_Topic14










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic15







>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




Version


Author


Date




hsa01100


Metabolic pathways


1


-0.292


0.0346


1


21


1020


0.432




L3
=======

a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1








SNMF_Topic16







<<<<<<< HEAD




Version


Author


Date





hsa04621


NOD-like receptor signaling pathway


1


0.189


0.0298


5.94e-08


21


125


5.04




L4
=======

a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1








SNMF_Topic17







<<<<<<< HEAD



hsa04062


Chemokine signaling pathway


1


0.198


0.0299


4.12e-08


23


145


4.73
=======

Version


Author


Date






a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1






<<<<<<< HEAD

topic_18

gobp
=======

gobp_nr
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD

<<<<<<< HEAD




geneSet


description


alpha


beta


beta.se


pHypergeometric


pFishersExact


overlap


geneSetSize


oddsRatio





L2
=======


L1
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD
GO:0051174


regulation of phosphorus metabolic process
=======
GO:0034976


response to endoplasmic reticulum stress
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


0.503

-0.37


0.0308


0.997


2


1360


0.241




GO:0019220


regulation of phosphate metabolic process


0.497


-0.37


0.0308


0.997


2


1360


0.241
=======

1.45


0.147


3.72e-11


3.72e-11


34


239


4.58
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1





<<<<<<< HEAD

gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_16

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_14

gobp
[1] “nothing to report…”


gomf
[1] “nothing to report…”


kegg
[1] “nothing to report…”



topic_19

gobp
[1] “nothing to report…”


gomf

=======

SNMF_Topic18










geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L1


>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




Version


Author


Date




GO:0003824


catalytic activity


1


-0.284


0.0222


1


42


4550


0.545






kegg

=======




geneSet


description


alpha


beta


beta.se


pValueHypergeometric


overlap


geneSetSize


oddsRatio






L2

a102c2d


karltayeb


2022-04-13








SNMF_Topic19










Version


Author


Date






a102c2d


karltayeb


2022-04-13








SNMF_Topic20







>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

<<<<<<< HEAD




Version


Author


Date




hsa01100


Metabolic pathways


1


-0.229


0.0374


0.993


8


1020


0.466
=======

a102c2d


karltayeb


2022-04-13
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1




<<<<<<< HEAD






sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] htmltools_0.5.2  Matrix_1.4-0     forcats_0.5.1    stringr_1.4.0   
 [5] dplyr_1.0.7      purrr_0.3.4      readr_2.1.1      tidyr_1.1.4     
 [9] tibble_3.1.6     ggplot2_3.3.5    tidyverse_1.3.1  kableExtra_1.3.4
[13] DT_0.18          susieR_0.11.92  

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2        ellipsis_0.3.2          rprojroot_2.0.2        
  [4] XVector_0.34.0          fs_1.5.2                rstudioapi_0.13        
  [7] bit64_4.0.5             AnnotationDbi_1.56.1    fansi_0.5.0            
 [10] lubridate_1.8.0         xml2_1.3.3              sparseMatrixStats_1.6.0
 [13] codetools_0.2-18        doParallel_1.0.16       cachem_1.0.6           
 [16] knitr_1.37              jsonlite_1.7.2          workflowr_1.7.0        
 [19] apcluster_1.4.8         WebGestaltR_0.4.4       broom_0.7.11           
 [22] cluster_2.1.2           dbplyr_2.1.1            png_0.1-7              
 [25] wordspace_0.2-7         BiocManager_1.30.16     compiler_4.1.0         
 [28] httr_1.4.2              backports_1.4.1         assertthat_0.2.1       
 [31] fastmap_1.1.0           cli_3.1.0               later_1.3.0            
 [34] prettyunits_1.1.1       tools_4.1.0             igraph_1.2.11          
 [37] GenomeInfoDbData_1.2.7  gtable_0.3.0            glue_1.6.0             
 [40] doRNG_1.8.2             Rcpp_1.0.7              Biobase_2.54.0         
 [43] cellranger_1.1.0        jquerylib_0.1.4         vctrs_0.3.8            
 [46] Biostrings_2.62.0       svglite_2.0.0           iterators_1.0.13       
 [49] xfun_0.29               rvest_1.0.2             lifecycle_1.0.1        
 [52] irlba_2.3.5             renv_0.15.0             rngtools_1.5.2         
 [55] org.Hs.eg.db_3.14.0     MASS_7.3-54             zlibbioc_1.40.0        
 [58] scales_1.1.1            vroom_1.5.7             MatrixGenerics_1.6.0   
 [61] hms_1.1.1               promises_1.2.0.1        parallel_4.1.0         
 [64] yaml_2.2.1              curl_4.3.2              memoise_2.0.1          
 [67] sass_0.4.0              reshape_0.8.8           stringi_1.7.6          
 [70] RSQLite_2.2.8           highr_0.9               S4Vectors_0.32.3       
 [73] foreach_1.5.1           BiocGenerics_0.40.0     GenomeInfoDb_1.30.0    
 [76] bitops_1.0-7            rlang_0.4.12            pkgconfig_2.0.3        
 [79] systemfonts_1.0.2       matrixStats_0.61.0      evaluate_0.14          
 [82] lattice_0.20-45         htmlwidgets_1.5.3       bit_4.0.4              
 [85] tidyselect_1.1.1        plyr_1.8.6              magrittr_2.0.1         
 [88] R6_2.5.1                IRanges_2.28.0          generics_0.1.1         
 [91] DBI_1.1.2               pillar_1.6.4            haven_2.4.3            
 [94] whisker_0.4             withr_2.4.3             KEGGREST_1.34.0        
 [97] RCurl_1.98-1.5          mixsqp_0.3-43           modelr_0.1.8           
[100] crayon_1.4.2            utf8_1.2.2              tzdb_0.2.0             
[103] rmarkdown_2.11          progress_1.2.2          grid_4.1.0             
[106] readxl_1.3.1            blob_1.2.2              git2r_0.29.0           
[109] sparsesvd_0.2           reprex_2.0.1            digest_0.6.29          
[112] webshot_0.5.2           httpuv_1.6.5            stats4_4.1.0           
[115] munsell_0.5.0           viridisLite_0.4.0       bslib_0.2.5.1          
[118] iotools_0.3-2          
=======
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1


knitr::knit_exit()

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
=======
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1 L1
<<<<<<< HEAD GO:0044403	symbiont process	0.618	0.103	0.0182	6.29e-09	216	643	2.21 ======= GO:0070972	protein localization to endoplasmic reticulum	0.996	1.08	0.183	2.12e-41	2.12e-41	84	131	14
L2 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0044419	interspecies interaction between organisms	0.235	0.0999	0.0182	2.79e-08	217	657	2.16 ======= GO:0022613	ribonucleoprotein complex biogenesis	1	0.881	0.106	1.96e-24	2.03e-24	130	391	3.94
L3 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0016032	viral process	0.144	0.0983	0.0182	1.65e-08	202	600	2.21
L2 ======= GO:0006414									translational elongation	1	1.52	0.183	3.07e-14	3.07e-14	50	121	5.35
L4 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0006952	defense response	0.993	-0.113	0.019	1	193	1010	0.985
L3 ======= GO:0009141									nucleoside triphosphate metabolic process	0.999	0.979	0.133	4.81e-09	6.22e-09	67	244	2.88
L5 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0016192	vesicle-mediated transport ======= GO:0006413	translational initiation >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	1	<<<<<<< HEAD 0.144	0.0176	7.09e-15	495	1550	2.17
L4 ======= 1.12									0.157	3.87e-40	3.87e-40	98	177	9.76
L6 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0009060	aerobic respiration	0.888	0.115	0.0185	1.96e-10	40	66	6.52
GO:0045333	cellular respiration	0.103	0.109	0.0187	1.12e-10	70	145	3.98
L5 ======= GO:0006605									protein targeting	1	0.865	0.11	6.81e-34	6.81e-34	140	364	5 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

Deng et al. Logistic SuSiE GSEA

karltayeb

2022-04-03

Overview

NMF

Thresholds

Threshold sensitivity

Glossary

NMF_Topic2

gobp_nr

NMF_Topic3

gobp_nr

NMF_Topic4

gobp_nr

NMF_Topic5

gobp_nr

NMF_Topic6

NMF_Topic7

gobp_nr

NMF_Topic8

gobp_nr

NMF_Topic9

gobp_nr

NMF_Topic10

gobp_nr

NMF_Topic11

gobp_nr

NMF_Topic12

gobp_nr

NMF_Topic13

gobp_nr

NMF_Topic14

gobp_nr

NMF_Topic15

NMF_Topic16

NMF_Topic17

gobp_nr

NMF_Topic18

gobp_nr

NMF_Topic19

NMF_Topic20

gobp_nr

SNMF

SNMF_Topic2

gobp_nr

SNMF_Topic3

gobp_nr

SNMF_Topic4

gobp_nr

SNMF_Topic5

gobp_nr

SNMF_Topic6

gobp_nr

SNMF_Topic7

gobp_nr

SNMF_Topic8

topic_5

gobp

gobp_nr

SNMF_Topic9

gobp_nr

SNMF_Topic10

gobp_nr

SNMF_Topic11

SNMF_Topic12

kegg

gobp_nr

SNMF_Topic13

gobp_nr

SNMF_Topic14

SNMF_Topic15

SNMF_Topic16

SNMF_Topic17

gobp_nr

topic_10

gobp

SNMF_Topic18

SNMF_Topic19

SNMF_Topic20

SNMF - Positive loadings

GO:0010469	regulation of signaling receptor activity	1	-0.129	0.0207	1	40	330	0.571
L6									Version	Author	Date
GO:0006996	organelle organization	1	0.155	0.0164	4.63e-20	897	2980	2.19 =======	a102c2d	karltayeb	2022-04-13 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
<<<<<<< HEAD GO:0004888	transmembrane signaling receptor activity ======= GO:0006401	RNA catabolic process >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	0.999	-0.24	0.0215	1 =======	0.694	0.114	2.96e-09	4.51e-09 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	47	<<<<<<< HEAD 527	0.399
L2 ======= 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

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0045296	cadherin binding ======= GO:0070972	protein localization to endoplasmic reticulum >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	0.962	<<<<<<< HEAD 0.16	0.0183	7.12e-20	137	282	4.1
L3 ======= 1.14									0.174	7.35e-10	1.26e-09	55	131	3.91 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0022836	gated channel activity	0.584	-0.109	0.0209	1	25	244	0.473 ======= 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 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0022839	ion gated channel activity	0.221	-0.105	0.0209	1	25	237	0.488 ======= GO:0048013	ephrin receptor signaling pathway	0.998	1.26	0.229	2.21e-09	2.21e-09	37	75	5.23
L3 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0005216	ion channel activity	0.0451	-0.0961	0.0205	1	37	295	0.594 ======= GO:0038127	ERBB signaling pathway	0.971	0.893	0.181	1.02e-07	1.32e-07	48	122	3.49 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0022843	voltage-gated cation channel activity	0.0388	-0.0965	0.0207	1	6	100	0.265 ======= GO:0070671	response to interleukin-12	0.00272	1.04	0.305	1.28e-05	1.28e-05	21	44	4.88 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0022803	passive transmembrane transporter activity	0.0282	-0.0934	0.0203	1	43	324	0.634 ======= GO:1990823	response to leukemia inhibitory factor	0.00161	0.737	0.221	1.53e-05	1.71e-05	34	89	3.31 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0015267	channel activity	0.0256	-0.0929	0.0203	1	43	323	0.636 ======= GO:0034109	homotypic cell-cell adhesion	0.00152	0.836	0.255	1.96e-05	2.08e-05	27	65	3.8 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0005261	cation channel activity	0.0214	-0.0931	0.0206	1	27	231	0.549
L4 ======= GO:0007015									actin filament organization	0.00131	0.404	0.117	6.55e-09	1.05e-08	105	329	2.56 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0048018	receptor ligand activity	0.984	-0.18	0.0217	1	22	258	0.385
L5 ======= 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 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0051020	GTPase binding	0.941	0.117	0.0183	2.3e-09	191	548	2.33 ======= GO:0008544	epidermis development	0.000718	0.433	0.133	1.6e-05	2.3e-05	76	256	2.28 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0031267	small GTPase binding	0.0365	0.108	0.0184	7.84e-08	162	469	2.28 ======= GO:0072337	modified amino acid transport	0.000602	1.16	0.412	0.000954	0.000954	11	22	5.32

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
<<<<<<< HEAD hsa04144	Endocytosis ======= GO:0006413	translational initiation >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	1	<<<<<<< HEAD 0.186	0.0267	6.52e-11	95	210	3.48
======= 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
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1 L3
<<<<<<< HEAD hsa04080	Neuroactive ligand-receptor interaction	1	-0.279	0.0337	1	9	163	0.228
======= GO:0006403									RNA localization	0.998	1.15	0.146	5.16e-12	5.16e-12	49	211	3.95
>>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1 L4
<<<<<<< HEAD hsa04060	Cytokine-cytokine receptor interaction ======= GO:0071824	protein-DNA complex subunit organization >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	1	-0.24	0.0324 =======	1.2	0.158 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	1.92e-09	<<<<<<< HEAD 13	173	0.318
L5 ======= 1.92e-09									40	180	3.7

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD hsa05010	Alzheimer disease	0.91	0.146	0.0269	4.27e-08	65	142	3.49
hsa05012	Parkinson disease	0.0461	0.132	0.0272	5.13e-07	50	106	3.67
L6 ======= GO:0070972									protein localization to endoplasmic reticulum	1	4.29	0.18	7.55e-52	7.55e-52	40	131	75.8

hsa01200	Carbon metabolism	0.984	0.141	0.0268	2.09e-07	48	98	3.94 =======	Version	Author	Date
a102c2d	karltayeb	2022-04-13

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L7 =======									L1 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD hsa04530	Tight junction ======= GO:0034976	response to endoplasmic reticulum stress >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1	0.994	<<<<<<< HEAD 0.133	0.0267	2.11e-07	64	144	3.31

geneSet	description	alpha	beta	beta.se	pValueHypergeometric	overlap	geneSetSize	oddsRatio
L1 ======= 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 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1
<<<<<<< HEAD GO:0006996	organelle organization	1	0.116	0.0168	7.73e-11	739	2980	1.86
L10 ======= GO:0036230									granulocyte activation	0.0405	1.11	0.116	5.47e-10	5.47e-10	49	384	3.19 >>>>>>> 689eb11fb5dbc931eb8b6b4a5c5efa65bad315c1

GO:0006613	cotranslational protein targeting to membrane	0.242	0.196	0.0197	2.13e-31	73	96	15.8
L3									Version	Author	Date
a102c2d	karltayeb	2022-04-13

Version	Author	Date
GO:0043269	regulation of ion transport	0.964	-0.115	0.0204	1	59	481	0.669
L4 =======									a102c2d	karltayeb	2022-04-13