#knitr::opts_chunk$set(echo = TRUE)
options(width = 120)
# knitr::opts_chunk$set(cache=F)
# knitr::opts_chunk$set(fig.width=6, fig.height=6) # for rstudio
# knitr::opts_chunk$set(fig.width=14, fig.height=14) # for html

Prérequis

Installation éventuelle des librairies R dans un environnement conda.

shell:

conda create -n idh
conda deactivate
conda activate idh
conda install r-base=4.0.2 r-reticulate r-tidyverse r-kableextra r-dt r-rmysql bioconductor-stringdb openjdk=11.0.8 r-knitr r-igraph scipy numpy openjdk

Librairies et fonctions utilitaires

library(reticulate) # to execute bash or python chunks (only in notebooks)
library(tidyverse)
## ── Attaching packages ─────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
## ✓ ggplot2 3.3.2     ✓ purrr   0.3.4
## ✓ tibble  3.0.4     ✓ dplyr   1.0.2
## ✓ tidyr   1.1.2     ✓ stringr 1.4.0
## ✓ readr   1.3.1     ✓ forcats 0.5.0
## Warning: package 'tibble' was built under R version 4.0.3
## ── Conflicts ────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()
library(magrittr)
## 
## Attaching package: 'magrittr'
## The following object is masked from 'package:purrr':
## 
##     set_names
## The following object is masked from 'package:tidyr':
## 
##     extract
library(kableExtra) # nicer tables
## 
## Attaching package: 'kableExtra'
## The following object is masked from 'package:dplyr':
## 
##     group_rows
kabex = function(o) o %>% kable(format="html", escape=F) %>% kable_styling(bootstrap_options = c("striped"))
library(DT) # other nice tables
## Warning: package 'DT' was built under R version 4.0.3
dted = function(o) o %>% datatable(rownames=F, filter="top", options=list(pageLength = 10), escape=F)

library(igraph)
## 
## Attaching package: 'igraph'
## The following objects are masked from 'package:dplyr':
## 
##     as_data_frame, groups, union
## The following objects are masked from 'package:purrr':
## 
##     compose, simplify
## The following object is masked from 'package:tidyr':
## 
##     crossing
## The following object is masked from 'package:tibble':
## 
##     as_data_frame
## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum
## The following object is masked from 'package:base':
## 
##     union
igraph.options(vertex.color=NA)
igraph.options(vertex.label.cex=.6) # font size
igraph.options(vertex.label.family='sans')
igraph.options(vertex.size=2)
igraph.options(edge.label.cex=.6)
igraph.options(edge.label.family='sans')

library(STRINGdb) # client STRING

Génome/Protéome

La première étape consiste à récupérer l’ensemble du génome/protéome qui nous intéresse.

STRINGdb Proteins

Création du répertoire pour les données de STRING (shell) :

mkdir string.data

Connexion au serveur de STRING (NCBI taxon id de Ecoli est 511145: https://string-db.org/cgi/input.pl?input_page_active_form=organism )

confidence_threshold = 700
stringdb = STRINGdb$new(version='11', species=511145, score_threshold=confidence_threshold, input_directory='string.data')

Téléchargement du génome/protéome :

proteins = stringdb$get_proteins() %>% as_tibble
proteins %>% dted
## Warning in instance$preRenderHook(instance): It seems your data is too big for client-side DataTables. You may consider
## server-side processing: https://rstudio.github.io/DT/server.html

Neo4j installation

Sites et documentations :

Récupérer la dernière version : Téléchargement linux https://neo4j.com/download-center/#releases (onglet Community server)

Création des répertoires et désarchivage (shell):

mkdir -p neo4j/download
cd neo4j/download
version=4.1.3
tar xf neo4j-community-$version-unix.tar.gz
ln -s neo4j-community-$version neo4j-community
cd neo4j-community/

Démarrage et arrêt du serveur (shell):

./bin/neo4j console

Le processus est au premier plan donc pour arrêter le serveur il faut faire Ctrl + C dans le terminal.

Utilisation depuis le navigateur (vérifier le port renseigné lors de la précédente commande) : http://localhost:7474/

A la première connexion, le mot de passe est neo4j, le système demande ensuite de changer le mot de passe. Explorez l’interface Web de Neo4j browser, notamment le côté gauche avec les paramètres, et les informations sur la base de données.

Utilisation depuis le shell :

./bin/cypher-shell

Nous allons maintenant créer un fichier CSV pour le protéome d’Ecoli pour l’importer dans Neo4j (créer les sommets correspondant aux protéines) :

proteins %>%
  mutate(taxon_id = str_extract(protein_external_id, "([0-9]+)"), protein_id= str_match(protein_external_id, "\\.(.+)$")[,2]) %>%
  select(protein_external_id, taxon_id, protein_id, name=preferred_name, length=protein_size, annotation) %>%
  write_csv("neo4j/download/neo4j-community/import/ecoli.proteins.csv")

Librairie neo4r

if (!require('neo4r')) { # client neo4j (pas dispo avec conda)
  install.packages('neo4r')
}
## Loading required package: neo4r
library(neo4r)
neodb = neo4j_api$new(
  url = "http://localhost:7474", 
  user = "neo4j", 
  password = "bioinfo"
)
cypher = function(query, neo4j=neodb, ...) call_neo4j(query=query, con=neo4j, ...)
# 'MATCH (p:Protein {name:"dnaJ"}) RETURN p.protein_id, p.annotation' %>% cypher

Import dans neo4j

# DELETE PREVIOUS ATTEMPTS ON Protein
'MATCH ()-[r:STRINGdb]-() DELETE r' %>% cypher 
'MATCH ()-[r:GO_annotation]-() DELETE r' %>% cyper
'MATCH (n:Protein) DELETE n' %>% cypher
# IMPORT
'LOAD CSV WITH HEADERS FROM "file:///ecoli.proteins.csv" AS row 
CREATE (n:Protein)
SET n = row,
 n.protein_external_id = row.protein_external_id,
 n.taxon_id = toInteger(row.taxon_id),
 n.protein_id = row.protein_id,
 n.name = row.name,
 n.length = toInteger(row.length),
 n.annotation = row.annotation
'  %>% cypher

Vérification via des requêtess cyper:

'MATCH (p:Protein {name:"dnaJ"}) RETURN p.protein_id, p.annotation'  %>% cypher(type="row") 
## $p.protein_id
## # A tibble: 1 x 1
##   value
##   <chr>
## 1 b0015
## 
## $p.annotation
## # A tibble: 1 x 1
##   value                                                                                                                 
##   <chr>                                                                                                                 
## 1 "Chaperone protein DnaJ; Interacts with DnaK and GrpE to disassemble a protein complex at the origins of replication …
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"
'MATCH (p:Protein) WHERE p.length <= 40 RETURN p'  %>% cypher %>% extract2('p') %>% dted
## Column 4 ['length'] of item 8 appears in position 3 in item 7. Set use.names=TRUE to match by column name, or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
'MATCH (p:Protein) RETURN count(p)'  %>% cypher 
## $`count(p)`
## # A tibble: 1 x 1
##   value
##   <int>
## 1  4127
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Ajout d’un index (pour accélérer la création des liens par la suite):

'CREATE INDEX ON :Protein(protein_external_id)' %>% cypher

Données d’expression

Nous allons utiliser les données d’expression déjà intégrées dans STRINGdb. Il est bien sûr possible de calculer un score de co-expression entre les paires de gènes à partir de données de microarray et/ou RNAseq.

Données d’interaction protéine-protéine

STRINGdb protein-protein interactions → neo4j

Pour le réseau d’interaction ppi, la colonne experimental contient des interactions physiques et fonctionnelles. Un autre fichier est donc nécessaire : protein.actions (binding)

actions = read_delim("string.data/511145.protein.actions.v11.0.txt.gz", delim="\t")
## Parsed with column specification:
## cols(
##   item_id_a = col_character(),
##   item_id_b = col_character(),
##   mode = col_character(),
##   action = col_character(),
##   is_directional = col_logical(),
##   a_is_acting = col_logical(),
##   score = col_double()
## )
actions
## # A tibble: 73,224 x 7
##    item_id_a    item_id_b    mode    action is_directional a_is_acting score
##    <chr>        <chr>        <chr>   <chr>  <lgl>          <lgl>       <dbl>
##  1 511145.b0002 511145.b3607 binding <NA>   FALSE          FALSE         183
##  2 511145.b0002 511145.b0031 binding <NA>   FALSE          FALSE         309
##  3 511145.b0002 511145.b0033 binding <NA>   FALSE          FALSE         211
##  4 511145.b0002 511145.b0268 binding <NA>   FALSE          FALSE         213
##  5 511145.b0002 511145.b0600 binding <NA>   FALSE          FALSE         357
##  6 511145.b0002 511145.b0674 binding <NA>   FALSE          FALSE         258
##  7 511145.b0002 511145.b1096 binding <NA>   FALSE          FALSE         243
##  8 511145.b0002 511145.b1622 binding <NA>   FALSE          FALSE         208
##  9 511145.b0002 511145.b2058 binding <NA>   FALSE          FALSE         183
## 10 511145.b0002 511145.b2290 binding <NA>   FALSE          FALSE         357
## # … with 73,214 more rows

Seulement les binding

links.ppi = actions %>% 
  filter(mode=='binding' & item_id_a<item_id_b) %>% 
  dplyr::select(protein1 = item_id_a, protein2 = item_id_b, ppi = score) %>%
  filter(ppi >= confidence_threshold)

experimetal: BIND, DIP, GRID, HPRD, IntAct, MINT, and PID. (src: https://string-db.org/help/faq/#which-databases-does-string-extract-experimental-data-from)

Comme précédemment, création du fichier CSV puis import dans neo4j

links.ppi %>% write_csv("neo4j/download/neo4j-community/import/ecoli.string.ppi.csv")
'LOAD CSV WITH HEADERS FROM "file:///ecoli.string.ppi.csv" AS line
MATCH (p1:Protein)-[r:STRINGdb]-(p2:Protein)
WHERE p1.protein_external_id=line.protein1 AND p2.protein_external_id=line.protein2
WITH p1,p2, toInteger(line.ppi) AS value
MERGE (p1)-[r:STRINGdb]-(p2)
SET r.ppi=value
'  %>% cypher
'MATCH p = (p1:Protein {name:"dnaJ"})-[r]-(p2:Protein {name:"dnaK"}) return p' %>% cypher
## New names:
## * annotation -> annotation...1
## * protein_id -> protein_id...2
## * length -> length...3
## * name -> name...4
## * taxon_id -> taxon_id...5
## * ...
## $p
## # A tibble: 1 x 15
##   annotation...1 protein_id...2 length...3 name...4 taxon_id...5 protein_externa…   ppi neighborhood coexpression
##   <chr>          <chr>               <int> <chr>           <int> <chr>            <int>        <int>        <int>
## 1 "Chaperone pr… b0015                 376 dnaJ           511145 511145.b0015       873          710          862
## # … with 6 more variables: annotation...10 <chr>, protein_id...11 <chr>, length...12 <int>, name...13 <chr>,
## #   taxon_id...14 <int>, protein_external_id...15 <chr>
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Graphe de coexpression & ppi

Extraction du graphe et visualisation

g.ppi.coexpr = 'MATCH p = ()-[r:STRINGdb]-() WHERE r.coexpression>=700 AND r.ppi>=700 RETURN p'  %>% cypher(type="graph")
g.ppi.coexpr$nodes = g.ppi.coexpr$nodes %>% unnest_nodes(what="properties")
g.ppi.coexpr$relationships = g.ppi.coexpr$relationships %>% 
  unnest_relationships %>% 
  select(startNode, endNode, type, everything()) %>% 
  mutate(coexpression = unlist(coexpression), ppi = unlist(ppi))
g.ppi.coexpr = graph_from_data_frame(d=g.ppi.coexpr$relationships, directed=F, vertices = g.ppi.coexpr$nodes)
g.ppi.coexpr
## IGRAPH 2316509 UN-- 378 1498 -- 
## + attr: name (v/c), label (v/x), annotation (v/c), protein_id (v/c), length (v/n), taxon_id (v/n),
## | protein_external_id (v/c), type (e/c), id (e/c), ppi (e/n), neighborhood (e/n), coexpression (e/n)
## + edges from 2316509 (vertex names):
##  [1] dnaK--dnaJ dnaK--grpE dnaK--groL rpsT--rpmG rpsT--rpsI rpsT--rplY rpsT--rpsO rpsT--rpmA rpsT--rpmF rpsT--rplM
## [11] rpsT--rpmB rpsT--rpsU rpsT--rpmE rpsT--rpmH carA--carB carB--pyrB leuD--leuC ftsA--ftsZ aceE--aceF aceF--lpd 
## [21] fecD--fhuC rpsB--rpsC rpmA--rpsB rpsI--rpsB rpsB--rpsK rpsB--rplP rpsB--rpsE rpsB--rplB rpsB--rpsH rpsB--rplS
## [31] rpsB--rplE rpsO--rpsB rpsB--rplN rpmF--rpsB rpmB--rpsB rpsB--rpsF rpsB--rplR rpsB--rpmD rplM--rpsB rpsB--rpsN
## [41] rpsB--rplC rpsB--rpsL rpsB--rpsG rpsB--rpsA rpsB--rpsP rpsB--rpsQ rpsB--rplI rpsB--rplQ rpsB--rpsJ rplY--rpsB
## [51] rpsB--rplV rpsB--rplU rpsB--rplW rpsB--rplK rpsB--rplL rpsB--rplD rpsB--rplX rpsB--rplF rpsB--rpsR rpsB--rpsS
## [61] rpsB--rpsM rpsB--rplJ rpsB--rpmJ rpsB--rplO rpsB--rpsD rpsB--rpmC rpsB--rplA rpmG--rpsB metQ--metI metI--metN
## + ... omitted several edges
plot(g.ppi.coexpr, vertex.label=NA, main='coexpr & ppi')

Les contraintes de coexpression > 0.7 et de ppi > 0.7 semblent un peu trop restrictives. Nous allons prendre un OR à la place pour avoir un graphe plus dense :

g.ppi.coexpr = 'MATCH p = ()-[r:STRINGdb]-() WHERE r.coexpression>=700 OR r.ppi>=700 RETURN p'  %>% cypher(type="graph")
g.ppi.coexpr$nodes = g.ppi.coexpr$nodes %>% unnest_nodes(what="properties")
g.ppi.coexpr$relationships = g.ppi.coexpr$relationships %>% 
  unnest_relationships %>% 
  select(startNode, endNode, type, everything()) %>% 
  mutate(coexpression = unlist(coexpression), ppi = unlist(ppi))
g.ppi.coexpr = graph_from_data_frame(d=g.ppi.coexpr$relationships, directed=F, vertices = g.ppi.coexpr$nodes)
g.ppi.coexpr
## IGRAPH a5bb856 UN-- 1510 5601 -- 
## + attr: name (v/c), label (v/x), annotation (v/c), protein_id (v/c), length (v/n), taxon_id (v/n),
## | protein_external_id (v/c), type (e/c), id (e/c), neighborhood (e/n), coexpression (e/n), ppi (e/n)
## + edges from a5bb856 (vertex names):
##  [1] thrA --thrB  thrA --lysC  thrA --thrC  thrA --metL  thrB --thrC  thrC --usg   thrC --metL  thrC --asd  
##  [9] gltA --yaaJ  yaaJ --prpC  mobB --mog   dnaK --clpB  dnaK --hslR  dnaK --hslV  dnaK --cbpA  dnaK --dnaJ 
## [17] dnaK --hslU  dnaK --groS  dnaK --rpoH  dnaK --grpE  dnaK --groL  dnaK --htpG  dnaJ --hslU  hslR --dnaJ 
## [25] hslV --dnaJ  dnaJ --grpE  dnaJ --prmA  dnaJ --lon   clpB --dnaJ  dnaJ --hslO  dnaJ --htpG  b0021--insB2
## [33] b0021--b1893 b0021--b0264 b0021--insB4 b1894--b0022 b0022--b0265 b0022--insA1 rpsT --rplV  rpsT --rplI 
## [41] rpsT --rpmG  rpsT --rplB  rpsT --rplF  rpsT --rpsJ  rpsT --rplS  rpsT --rpsQ  rpsT --rpsI  rpsT --rplY 
## [49] rpsT --rpsA  rpsT --rplR  rpsT --rpmJ  rpsT --dusB  rpsT --rplU  rpsT --fis   rpsT --rpsM  rpsT --rpmI 
## + ... omitted several edges
plot(g.ppi.coexpr, vertex.label=NA, vertex.size=1, main="coexpr | ppi")

Données phylogénomiques

Dans STRINGdb, ces données sont disponibles pour les bactéries. Elles résultent de l’analyse de la conservation des gènes otrhologues dans le voisinage sur les chromosomes d’autres organismes.

Ajout des liens conserved genomic neighborhood

Génération des fichiers CSV pour l’import comment pour coexpression

Ajout des lien dans neo4j

'LOAD CSV WITH HEADERS FROM "file:///ecoli.string.neighborhood.csv" AS line
MATCH (p1:Protein)-[r:STRINGdb]-(p2:Protein)
WHERE p1.protein_external_id=line.protein1 AND p2.protein_external_id=line.protein2
WITH p1,p2, toInteger(line.neighborhood) AS value
MERGE (p1)-[r:STRINGdb]-(p2)
SET r.neighborhood=value
'  %>% cypher

Extraction du graphe et visualisation

g.string = 'MATCH p = ()-[r:STRINGdb]-() WHERE r.coexpression>=700 OR r.ppi>=700 OR r.neighborhood>=700 RETURN p'  %>% cypher(type="graph")
g.string$nodes = g.string$nodes %>% unnest_nodes(what="properties")
g.string$relationships = g.string$relationships %>% 
  unnest_relationships %>% 
  select(startNode, endNode, type, everything()) %>% 
  mutate(coexpression = unlist(coexpression), ppi = unlist(ppi), neighborhood = unlist(neighborhood))
g.string = graph_from_data_frame(d=g.string$relationships, directed=F, vertices = g.string$nodes)
g.string
## IGRAPH 1f1ada6 UN-- 2602 7338 -- 
## + attr: name (v/c), label (v/x), annotation (v/c), protein_id (v/c), length (v/n), taxon_id (v/n),
## | protein_external_id (v/c), type (e/c), id (e/c), neighborhood (e/n), coexpression (e/n), ppi (e/n)
## + edges from 1f1ada6 (vertex names):
##  [1] thrA --thrB  thrA --lysC  thrA --thrC  thrA --metL  thrB --thrC  thrC --usg   thrC --metL  thrC --asd  
##  [9] gltA --yaaJ  yaaJ --prpC  mobB --mog   yaaW --yaaI  dnaK --clpB  dnaK --hslR  dnaK --hslV  dnaK --cbpA 
## [17] dnaK --dnaJ  dnaK --hslU  dnaK --groS  dnaK --rpoH  dnaK --grpE  dnaK --groL  dnaK --htpG  dnaJ --hslU 
## [25] hslR --dnaJ  hslV --dnaJ  dnaJ --grpE  dnaJ --prmA  dnaJ --lon   clpB --dnaJ  dnaJ --hslO  dnaJ --htpG 
## [33] nhaA --nhaR  b0021--insB2 b0021--b1893 b0021--b0022 b0021--b0264 b0021--insB4 b0022--b1894 b0022--b0265
## [41] b0022--insA1 rpsT --rplV  rpsT --rplI  rpsT --rpmG  rpsT --rplB  rpsT --rplF  rpsT --rpsJ  rpsT --rplS 
## [49] rpsT --rpsQ  rpsT --rpsI  rpsT --rplY  rpsT --rpsA  rpsT --rplR  rpsT --rpmJ  rpsT --dusB  rpsT --rplU 
## + ... omitted several edges
plot(g.string, vertex.label=NA, vertex.size=1, main='coexpr | pppi | neighborhood')

Tailles des composantes connexes

clusters(g.string)$csize
##   [1] 1147    5    2    2   12    4    4    2    2    2    2    2    3    2    3    2    2    3    5    2    7    2    3
##  [24]    2    2    2    2    2    4    2    5    2    2    2    2    4    4    6    2   11    2    2    6   12    4    2
##  [47]    7    2    2    3   13    5    2    2    3    6    2    2    2    4    2    2    3    2    4    2    4    3    2
##  [70]    4    5    2    6    2    8    3    2    4    4    6    2    2    4    2    2    4    3    5    5    3    5    3
##  [93]    2    2    3    4   11    2    2   11    3    4    2    5    5    3    2    2    6    2    2    2    4    2    4
## [116]    2    2    2    2    2    3   60    2    2    6    3    4    2    3    2    2    4    2    2    5    2    2    2
## [139]    2    2    5    3    7    4    2    3    2    2    2    2    4    2    2    2    3    2    5    2    5    7    6
## [162]    2    2    7    2    3    2    3    2    3    2    2    2    2    2    2    2    7    3    2    3    3    2    2
## [185]    2   13    5    5    2    6    4    2    3    2    3    3    2    2    2    3    2    2    2    4    2    2    2
## [208]    2    2    3    3    2    2   21    2    2    3   25    3    2    4    2    2    4    2    2    2    2    2    3
## [231]    4    2    2    2    2    2    4    2    2    2    7    6    2    3    6    2    2    3    3    2    2    2    5
## [254]    2    3    2    2    2    7    2    2    2    2    2    2    2    2    2    2    2    2    4    2    3    2    3
## [277]    2    3    4    2    2    3    2    2    2    5    2    4    7    3    2    3    2    2    2    2    3    2    4
## [300]    4    2    2    2    2    3    2    2    3    2    4    4    4    2    5    3    2    2    2    2    2    2    2
## [323]    2    2    2    2    2    2    3    2    2    2    4    3    5    2    2    2    3    2    4    2    3    6    3
## [346]    2   14    3    2    2    2    2    2    2    4    2    4    3    2    3    2    2    6    5    2    3    2    2
## [369]    4    3    5    2    2    2    3    2    2    2    2    3    2    3    2    8    2    3    3    3    2    2    2
## [392]    3    5    2    2    2    2    2    3    2    2    3    2    4    4    5    2    2    2    2    2    6    2    3
## [415]    2    2    2    2    3    5   11    2    3    2    2    2    2    2    4    2    2    2    4    2    2    2    3
## [438]    2    3    4    3    2    2    2    2    3    2    2    2    2    3    4    4

Extraction des sous-graphes correspondant aux CC de taille minimum 10

CCs.num = which(clusters(g.string)$csize >=10)
CCs.size = clusters(g.string)$csize[CCs.num]
V.ids = V(g.string)[ clusters(g.string)$membership %in% CCs.num ]
g = induced_subgraph(g.string, V.ids)
plot(g, vertex.label=NA)

Calcul du score combiné avant détection de communautés (source: http://version11.string-db.org/help/faq/#how-are-the-scores-computed)

prior=0.041
no_prior = function(x, prior = 0.041) (ifelse(is.na(x), 0, x) / 1000 - prior) / (1-prior)
s_coexp_nop = no_prior(E(g)$coexpression)
s_ppi_nop = no_prior(E(g)$ppi)
s_neighborhood_nop = no_prior(E(g)$neighborhood)
s_tot_nop = 1 - (1 - s_coexp_nop) * (1 - s_ppi_nop) * (1 - s_neighborhood_nop)
E(g)$combined_score = round(1000 * (s_tot_nop + prior *(1 - s_tot_nop)))

Détection de communautés prenant en compte le score combiné

g.communities = cluster_louvain(g, weights=E(g)$combined_score)
plot(g.communities, g, vertex.label=NA)

Nombre de communautés

length(g.communities)
## [1] 43

Tailles des communautés

sizes(g.communities)
## Community sizes
##   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 
##  12  12  13  29  13  82  71  31  84   8 111  11   9   6  47  65   6  55  46  28  31   6   6  98  13  71   9  11  19   2 
##  31  32  33  34  35  36  37  38  39  40  41  42  43 
##  95  18  14   5  21  26  51  13  11  54  11  25  12

Modularité

modularity(g, g.communities$membership, weights=E(g)$combined)
## [1] 0.7930186

Génération des fichiers par clusters/communautés pour la recherche d’enrichissement en termes GO

tibble(protein_id = V(g)$protein_id, name=V(g)$name, cluster = g.communities$membership) %>% dted
groups(g.communities) %>% head(2)
## $`1`
##  [1] "b0021"  "insB2"  "b1893"  "b0022"  "b0264"  "insB4"  "b1894"  "b0265"  "insA1"  "JW0020" "b0275"  "insA2" 
## 
## $`2`
##  [1] "b1403"  "b0360"  "b0361"  "b1402"  "b2860"  "b1996"  "b1997"  "JW5919" "JW0352" "b2861"  "b3044"  "b3045"

Remplacement des noms par les identifiants “stringdb”

g.clusters = lapply(groups(g.communities), function(x) V(g)[ name %in% x]$protein_id)
head(g.clusters, 2)
## $`1`
##  [1] "b0021" "b0274" "b1893" "b0022" "b0264" "b0988" "b1894" "b0265" "b3444" "b3445" "b0275" "b4516"
## 
## $`2`
##  [1] "b1403" "b0360" "b0361" "b1402" "b2860" "b1996" "b1997" "b4272" "b4273" "b2861" "b3044" "b3045"

Génération du fichier

lines = sapply(g.clusters, function(x) paste(x, collapse = '\t')) %>% simplify2array 
write_lines(lines, "enrichment.coli/g.communities.txt")

Split by lines (shell)

split -l 1 --numeric-suffix=1 --additional-suffix=.txt enrichment.coli/g.communities.txt g.com.
mv g.com.*.txt enrichment.coli/

Données d’annotation

Gene Ontology → neo4j

Restauration de la base fournie par GO

Librairie MariaDb/MySQL

library(RMySQL) # client MariaDb
## Loading required package: DBI
dbh=dbConnect(MySQL(), user="guest", password="bioinfo", dbname="go_idh_2020", host="127.0.0.1")
dbget = function(query) as_tibble(dbGetQuery(dbh, query))

Variables d’environnement (shell) qui facilitent les changements de nom de DB etc. (shell)

dbname=go_idh_2020
mysql="mysql -uguest -pbioinfo -h 127.0.0.1 $dbname"
mysql -uguest -pbioinfo -e "CREATE DATABASE $dbname"

Restauration de GO db (shell)

mkdir go.data
cd go.data
wget http://archive.geneontology.org/latest-termdb/go_daily-termdb-data.gz
gunzip go_daily-termdb-data.gz
$mysql < go_daily-termdb-data

Extraction de go.terms.csv pour import dans neo4j

"SELECT id, acc, term_type, name FROM term 
WHERE acc LIKE 'GO:%' AND is_obsolete=0 
LIMIT 10;
" %>% dbget %>% head %>% kabex
id acc term_type name
23 GO:0000001 biological_process mitochondrion inheritance
25 GO:0000002 biological_process mitochondrial genome maintenance
26 GO:0000003 biological_process reproduction
33 GO:0000006 molecular_function high-affinity zinc transmembrane transporter activity
35 GO:0000007 molecular_function low-affinity zinc ion transmembrane transporter activity
39 GO:0000009 molecular_function alpha-1,6-mannosyltransferase activity

Export dans un shell

$mysql -e "SELECT id, acc, term_type, name FROM term WHERE acc LIKE 'GO:%' AND is_obsolete=0;" > neo4j/download/neo4j-community/import/go.terms.tsv

Ajout des GOTerm dans Neo4j

  • put data into neo4j subdir “import” qui correspond dans neoj browser à file://
  • import des termes GO dans Neo4j
"MATCH ()-[r:is_a]->() DELETE r" %>% cypher
"MATCH ()-[r:part_of]->() DELETE r" %>% cypher
"MATCH (n:GOTerm) DELETE n" %>% cypher
"
LOAD CSV WITH HEADERS FROM 'file:///go.terms.tsv' AS row FIELDTERMINATOR '\t'
CREATE (n:GOTerm)
SET n = row,
  n.id = toInteger(row.id),
  n.acc = row.acc,
  n.term_type = row.term_type,
  n.name = row.name  
" %>% cypher
"MATCH (n:GOTerm) RETURN count(n)" %>% cypher
## $`count(n)`
## # A tibble: 1 x 1
##   value
##   <int>
## 1 45051
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Création des index pour accélérer la suite

'CREATE INDEX ON :GOTerm(id)' %>% cypher

'CREATE INDEX ON :GOTerm(acc)' %>% cypher

Exploration

"MATCH (n:GOTerm { name: 'reproduction'} ) RETURN n" %>% cypher
## $n
## # A tibble: 1 x 4
##   acc        name            id term_type         
##   <chr>      <chr>        <int> <chr>             
## 1 GO:0000003 reproduction    26 biological_process
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Ajout des relations entre GOTerms

Il faut identifier les types is_a (1) et part_of (20) dans la table term

"SELECT * FROM term WHERE name = 'is_a' OR name = 'part_of';" %>% dbget %>% kabex
id name term_type acc is_obsolete is_root is_relation
1 is_a relationship is_a 0 0 1
20 part_of external part_of 0 0 1 
is_a=1
part_of=20
$mysql -B -e "SELECT term1_id, term2_id FROM term2term WHERE relationship_type_id = $is_a;" > neo4j/download/neo4j-community/import/go.rel.is_a.dump.tsv
"MATCH ()-[r:is_a]->() DELETE r" %>% cypher
"
LOAD CSV WITH HEADERS FROM 'file:///go.rel.is_a.dump.tsv' AS line FIELDTERMINATOR '\t' 
MATCH (t1:GOTerm),(t2:GOTerm) 
WHERE t1.id=toInteger(line.term1_id) AND t2.id=toInteger(line.term2_id) 
WITH t1,t2 
MERGE (t2)-[:is_a]->(t1)
" %>% cypher
"MATCH ()-[r:is_a]->() RETURN count(r)" %>% cypher
## $`count(r)`
## # A tibble: 1 x 1
##   value
##   <int>
## 1 77251
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"
$mysql -B -e "SELECT term1_id, term2_id FROM term2term WHERE relationship_type_id = $part_of;" > neo4j/download/neo4j-community/import/go.rel.part_of.dump.tsv
"MATCH ()-[r:part_of]->() DELETE r" %>% cypher
"
LOAD CSV WITH HEADERS FROM 'file:///go.rel.part_of.dump.tsv' AS line FIELDTERMINATOR '\t'
MATCH (t1:GOTerm),(t2:GOTerm)
WHERE t1.id=toInteger(line.term1_id) AND t2.id=toInteger(line.term2_id)
WITH t1,t2
MERGE (t2)-[:part_of]->(t1)
" %>% cypher
"MATCH ()-[r:part_of]->() RETURN count(r)" %>% cypher
## $`count(r)`
## # A tibble: 1 x 1
##   value
##   <int>
## 1  6860
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Ajout de l’annotation d’un génome/protéome

GO Annotations hébergées à l’EBI

Fichier GOA de l’EBI : ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/

Celui d’Ecoli

mkdir go.data
curl ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/18.E_coli_MG1655.goa -o go.data/18.E_coli_MG1655.goa
head go.data/18.E_coli_MG1655.goa
## !gaf-version: 2.1
## !GO-version: http://purl.obolibrary.org/obo/go/releases/2020-09-30/extensions/go-plus.owl
## UniProtKB    A0A385XJ53  insA9       GO:0006310  GO_REF:0000043  IEA UniProtKB-KW:KW-0233    P   Insertion element IS1 9 protein InsA    insA9|b4709 protein 83333   20201003    UniProt     
## UniProtKB    A0A385XJ53  insA9       GO:0006313  GO_REF:0000002  IEA InterPro:IPR003220  P   Insertion element IS1 9 protein InsA    insA9|b4709 protein 83333   20200919    InterPro        
## UniProtKB    A0A385XJ53  insA9       GO:0006313  PMID:21873635   IBA PANTHER:PTN002936609|UniProtKB:P0CF07|UniProtKB:P0CF08  P   Insertion element IS1 9 protein InsA    insA9|b4709 protein 83333   20180328    GO_Central      
## UniProtKB    A0A385XJ53  insA9       GO:0032196  GO_REF:0000043  IEA UniProtKB-KW:KW-0815    P   Insertion element IS1 9 protein InsA    insA9|b4709 protein 83333   20201003    UniProt     
## UniProtKB    A0A385XJE6  insH21      GO:0003677  GO_REF:0000002  IEA InterPro:IPR002559  F   Transposase InsH for insertion sequence element IS5U    insH21|b4711    protein 83333   20200919    InterPro        
## UniProtKB    A0A385XJE6  insH21      GO:0003677  GO_REF:0000043  IEA UniProtKB-KW:KW-0238    F   Transposase InsH for insertion sequence element IS5U    insH21|b4711    protein 83333   20201003    UniProt     
## UniProtKB    A0A385XJE6  insH21      GO:0004803  GO_REF:0000002  IEA InterPro:IPR002559  F   Transposase InsH for insertion sequence element IS5U    insH21|b4711    protein 83333   20200919    InterPro        
## UniProtKB    A0A385XJE6  insH21      GO:0006310  GO_REF:0000043  IEA UniProtKB-KW:KW-0233    P   Transposase InsH for insertion sequence element IS5U    insH21|b4711    protein 83333   20201003    UniProt

Le fichier est au format GAF2.1

Chargement (noms des colonnes de http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/)

gaf.cnames = c('DB', 'DB Object ID','DB Object Symbol', 'Qualifier', 'GO ID', 'DB:Reference', 'Evidence Code', 'With (or) From', 'Aspect', 'DB Object Name', 'DB Object Synonym', 'DB Object Type', 'Taxon', 'Date', 'Assigned By', 'Annotation Extension', 'Gene Product Form ID')

go.ecoli = read_tsv('go.data/18.E_coli_MG1655.goa', skip = 2, col_names = gaf.cnames)
## Parsed with column specification:
## cols(
##   DB = col_character(),
##   `DB Object ID` = col_character(),
##   `DB Object Symbol` = col_character(),
##   Qualifier = col_character(),
##   `GO ID` = col_character(),
##   `DB:Reference` = col_character(),
##   `Evidence Code` = col_character(),
##   `With (or) From` = col_character(),
##   Aspect = col_character(),
##   `DB Object Name` = col_character(),
##   `DB Object Synonym` = col_character(),
##   `DB Object Type` = col_character(),
##   Taxon = col_double(),
##   Date = col_double(),
##   `Assigned By` = col_character(),
##   `Annotation Extension` = col_logical(),
##   `Gene Product Form ID` = col_logical()
## )
## Warning: 433 parsing failures.
##  row                  col           expected                                      actual                           file
## 1178 Annotation Extension 1/0/T/F/TRUE/FALSE occurs_in(GO:0005737)                       'go.data/18.E_coli_MG1655.goa'
## 1397 Annotation Extension 1/0/T/F/TRUE/FALSE occurs_in(GO:0005737)                       'go.data/18.E_coli_MG1655.goa'
## 1400 Annotation Extension 1/0/T/F/TRUE/FALSE occurs_in(GO:0005737)                       'go.data/18.E_coli_MG1655.goa'
## 1411 Annotation Extension 1/0/T/F/TRUE/FALSE has_input(UniProtKB:P0A6M8)                 'go.data/18.E_coli_MG1655.goa'
## 1435 Annotation Extension 1/0/T/F/TRUE/FALSE occurs_in(GO:0043234)|occurs_in(GO:0005886) 'go.data/18.E_coli_MG1655.goa'
## .... .................... .................. ........................................... ..............................
## See problems(...) for more details.
go.ecoli %>% head %>% kabex
DB DB Object ID DB Object Symbol Qualifier GO ID DB:Reference Evidence Code With (or) From Aspect DB Object Name DB Object Synonym DB Object Type Taxon Date Assigned By Annotation Extension Gene Product Form ID
UniProtKB A0A385XJ53 insA9 NA GO:0006310 GO_REF:0000043 IEA UniProtKB-KW:KW-0233 P Insertion element IS1 9 protein InsA insA9|b4709 protein 83333 20201003 UniProt NA NA
UniProtKB A0A385XJ53 insA9 NA GO:0006313 GO_REF:0000002 IEA InterPro:IPR003220 P Insertion element IS1 9 protein InsA insA9|b4709 protein 83333 20200919 InterPro NA NA
UniProtKB A0A385XJ53 insA9 NA GO:0006313 PMID:21873635 IBA PANTHER:PTN002936609|UniProtKB:P0CF07|UniProtKB:P0CF08 P Insertion element IS1 9 protein InsA insA9|b4709 protein 83333 20180328 GO_Central NA NA
UniProtKB A0A385XJ53 insA9 NA GO:0032196 GO_REF:0000043 IEA UniProtKB-KW:KW-0815 P Insertion element IS1 9 protein InsA insA9|b4709 protein 83333 20201003 UniProt NA NA
UniProtKB A0A385XJE6 insH21 NA GO:0003677 GO_REF:0000002 IEA InterPro:IPR002559 F Transposase InsH for insertion sequence element IS5U insH21|b4711 protein 83333 20200919 InterPro NA NA
UniProtKB A0A385XJE6 insH21 NA GO:0003677 GO_REF:0000043 IEA UniProtKB-KW:KW-0238 F Transposase InsH for insertion sequence element IS5U insH21|b4711 protein 83333 20201003 UniProt NA NA

Les identifiants utilisés dans le graphe de STRING sont sur la colonne DB Object Synonym. mais nécessitent d’être parsés :

go.ecoli %>% select(toparse=`DB Object Synonym`) %>% mutate(bnumber=str_extract(toparse, 'b\\d+'))
## # A tibble: 59,628 x 2
##    toparse      bnumber
##    <chr>        <chr>  
##  1 insA9|b4709  b4709  
##  2 insA9|b4709  b4709  
##  3 insA9|b4709  b4709  
##  4 insA9|b4709  b4709  
##  5 insH21|b4711 b4711  
##  6 insH21|b4711 b4711  
##  7 insH21|b4711 b4711  
##  8 insH21|b4711 b4711  
##  9 insH21|b4711 b4711  
## 10 insH21|b4711 b4711  
## # … with 59,618 more rows

Ok, on garde seulement les colonnes qui nous intéressent

go.ecoli = go.ecoli %>% 
  mutate(bnumber=str_extract(`DB Object Synonym`, 'b\\d+')) %>%
  mutate(protein_external_id=paste0('511145.',bnumber)) %>%
  select(GOTerm=`GO ID`, evidence_code=`Evidence Code`,protein_external_id)
go.ecoli
## # A tibble: 59,628 x 3
##    GOTerm     evidence_code protein_external_id
##    <chr>      <chr>         <chr>              
##  1 GO:0006310 IEA           511145.b4709       
##  2 GO:0006313 IEA           511145.b4709       
##  3 GO:0006313 IBA           511145.b4709       
##  4 GO:0032196 IEA           511145.b4709       
##  5 GO:0003677 IEA           511145.b4711       
##  6 GO:0003677 IEA           511145.b4711       
##  7 GO:0004803 IEA           511145.b4711       
##  8 GO:0006310 IEA           511145.b4711       
##  9 GO:0006313 IEA           511145.b4711       
## 10 GO:0032196 IEA           511145.b4711       
## # … with 59,618 more rows

Génération du fichier pour l’import dans neo4j

go.ecoli %>% write_csv("neo4j/download/neo4j-community/import/ecoli.goannotation.csv")

Ajout des lien dans neo4j

'MATCH ()-[r:GO_annotation]-() DELETE r' %>% cypher
'
LOAD CSV WITH HEADERS FROM "file:///ecoli.goannotation.csv" AS line
MATCH (p:Protein),(t:GOTerm)
WHERE p.protein_external_id=line.protein_external_id AND t.acc=line.GOTerm
WITH p,t,line
MERGE (p)-[r:GO_annotation]-(t)
SET r.evidence_code=line.evidence_code
'  %>% cypher
'MATCH ()-[r:GO_annotation]-() RETURN count(r)' %>% cypher
## $`count(r)`
## # A tibble: 1 x 1
##   value
##   <int>
## 1 66014
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Exploration

Annotations directes

"
MATCH (:Protein {name:'dnaJ'})-[:GO_annotation]-(t:GOTerm) RETURN t ORDER BY t.name
" %>% cypher
## $t
## # A tibble: 23 x 4
##    acc        name                                                           id term_type         
##    <chr>      <chr>                                                       <int> <chr>             
##  1 GO:0005524 ATP binding                                                  4506 molecular_function
##  2 GO:0006260 DNA replication                                                92 biological_process
##  3 GO:0051087 chaperone binding                                            2931 molecular_function
##  4 GO:0051085 chaperone cofactor-dependent protein refolding              27968 biological_process
##  5 GO:0005737 cytoplasm                                                    4620 cellular_component
##  6 GO:0005829 cytosol                                                      3765 cellular_component
##  7 GO:0031072 heat shock protein binding                                  11349 molecular_function
##  8 GO:0016020 membrane                                                     2965 cellular_component
##  9 GO:0046872 metal ion binding                                            4491 molecular_function
## 10 GO:1903507 negative regulation of nucleic acid-templated transcription 42727 biological_process
## # … with 13 more rows
## 
## attr(,"class")
## [1] "neo"  "neo"  "list"

Annotations implicites

"
MATCH (:Protein {name:'dnaJ'})-[:GO_annotation]-(:GOTerm)-[*]->(t:GOTerm) 
RETURN DISTINCT t 
ORDER BY t.name
" %>% cypher  %>% 
  extract2('t') %>% 
  select(-id) %>%
  dted

Annotations directes et implicites

terms = "
MATCH (:Protein {name:'dnaJ'})-[:GO_annotation]-(t_direct:GOTerm)-[*]->(t_implicit:GOTerm) 
RETURN t_direct, t_implicit 
" %>% cypher
terms$t_direct %>% unique %>% arrange(name) %>% select(-id) %>% kabex
acc name term_type
GO:0005524 ATP binding molecular_function
GO:0051087 chaperone binding molecular_function
GO:0051085 chaperone cofactor-dependent protein refolding biological_process
GO:0005737 cytoplasm cellular_component
GO:0005829 cytosol cellular_component
GO:0006260 DNA replication biological_process
GO:0031072 heat shock protein binding molecular_function
GO:0016020 membrane cellular_component
GO:0046872 metal ion binding molecular_function
GO:1903507 negative regulation of nucleic acid-templated transcription biological_process
GO:0055114 oxidation-reduction process biological_process
GO:0005515 protein binding molecular_function
GO:0003756 protein disulfide isomerase activity molecular_function
GO:0015035 protein disulfide oxidoreductase activity molecular_function
GO:0006457 protein folding biological_process
GO:0042026 protein refolding biological_process
GO:0032991 protein-containing complex cellular_component
GO:0065003 protein-containing complex assembly biological_process
GO:0009408 response to heat biological_process
GO:0016989 sigma factor antagonist activity molecular_function
GO:0051082 unfolded protein binding molecular_function
GO:0016032 viral process biological_process
GO:0008270 zinc ion binding molecular_function 
terms$t_implicit %>% unique %>% arrange(name) %>% select(-id) %>% dted

Protéines annotées directement par un terme

"
MATCH (p:Protein)-[:GO_annotation]-(:GOTerm {name: 'chaperone binding'}) 
RETURN DISTINCT p 
" %>% cypher %>% extract2('p') %>% select(-annotation) %>% kabex
protein_id length name taxon_id protein_external_id
b0014 638 dnaK 511145 511145.b0014
b0015 376 dnaJ 511145 511145.b0015
b0055 271 djlA 511145 511145.b0055
b0473 624 htpG 511145 511145.b0473
b0881 106 clpS 511145 511145.b0881
b1823 69 cspC 511145 511145.b1823
b2527 171 hscB 511145 511145.b2527
b2614 197 grpE 511145 511145.b2614
b3510 110 hdeA 511145 511145.b3510
b4142 97 groS 511145 511145.b4142

Terme chaperone binding trop spécifique, prenons-en un plus générique

"
MATCH (p:Protein)-[:GO_annotation]-(:GOTerm)-[:is_a|part_of*]->(:GOTerm {name: 'protein folding'}) 
RETURN DISTINCT p
ORDER BY p.name
" %>% cypher %>% extract2('p') %>% select(-annotation) %>% dted

Protéines annotées directement ou implicitement

"
MATCH (p:Protein)-[:GO_annotation|is_a|part_of*]->(:GOTerm {name: 'protein folding'}) 
RETURN DISTINCT p
ORDER BY p.name
" %>% cypher %>% extract2('p') %>% select(-annotation) %>% dted

Génération des fichiers pour la recherche de termes GO sur-représentés

Fonction pour récupérer les termes directs

get_GeneProducts = function(goterm, all=F) {
  query = paste0("MATCH (p:Protein)-[:GO_annotation]-(:GOTerm {acc: '", goterm, "'}) RETURN DISTINCT p.protein_id ORDER BY p.protein_id")
  if (all) {
  query = paste0("MATCH (p:Protein)-[:GO_annotation|is_a|part_of*]->(:GOTerm {acc: '", goterm,"'}) RETURN DISTINCT p.protein_id ORDER BY p.protein_id")
  }
  res = query %>% cypher 
  if (length(res) > 0) {
    res = res %>% extract2(1) %>% unlist
  }
  else {
    res = c()
  }
  res
}
get_GeneProducts("GO:0006457", all=F)
##  value1  value2  value3  value4  value5  value6  value7  value8  value9 value10 value11 value12 value13 value14 value15 
## "b0014" "b0015" "b0053" "b0161" "b0178" "b0436" "b0438" "b0473" "b0525" "b0717" "b0920" "b0998" "b1000" "b1185" "b1926" 
## value16 value17 value18 value19 value20 value21 value22 value23 value24 value25 value26 
## "b2526" "b2527" "b2614" "b3347" "b3363" "b3401" "b3609" "b3705" "b4142" "b4143" "b4207"
get_GeneProducts("GO:0006457", all=T)
##  value1  value2  value3  value4  value5  value6  value7  value8  value9 value10 value11 value12 value13 value14 value15 
## "b0014" "b0015" "b0028" "b0053" "b0098" "b0140" "b0161" "b0178" "b0220" "b0424" "b0436" "b0438" "b0441" "b0473" "b0492" 
## value16 value17 value18 value19 value20 value21 value22 value23 value24 value25 value26 value27 value28 value29 value30 
## "b0525" "b0531" "b0604" "b0717" "b0920" "b0939" "b0944" "b0998" "b1000" "b1185" "b1243" "b1591" "b1743" "b1926" "b2110" 
## value31 value32 value33 value34 value35 value36 value37 value38 value39 value40 value41 value42 value43 value44 value45 
## "b2336" "b2494" "b2526" "b2527" "b2592" "b2614" "b2893" "b3047" "b3143" "b3347" "b3349" "b3363" "b3401" "b3544" "b3609" 
## value46 value47 value48 value49 value50 value51 value52 value53 
## "b3705" "b3706" "b4142" "b4143" "b4207" "b4316" "b4376" "b4484"

Identification des termes GO concernant Ecoli

#go.ecoli %>% select(GOTerm) %>% unique %>% arrange(GOTerm)
ecoli.terms = "
MATCH (:Protein {taxon_id:511145})-[:GO_annotation|is_a|part_of*]->(t:GOTerm) 
RETURN DISTINCT t.acc
" %>% cypher %>% unlist

Direct GeneProducts

go.sets.direct = lapply(ecoli.terms, get_GeneProducts)
names(go.sets.direct)=ecoli.terms
go.sets.direct[['GO:0006457']]

Fichiers sets

header = paste0("# format: sets
# version: 1.3
# strain: Escherichia coli K-12 MG1655
# date: ", format(Sys.time(), '%d %B, %Y'), "
# comment: Gene Ontology terms")
sets = lapply(ecoli.terms, function(x) paste(go.sets.direct[[x]], collapse = '|')) %>% unlist
tb = tibble(GOTerm=ecoli.terms, GeneProducts = sets)
go.terms = read_tsv("neo4j/download/neo4j-community/import/go.terms.tsv")
lines = tb %>% inner_join(go.terms, by=c('GOTerm'='acc')) %>% mutate(desc=paste0(term_type,': ', name)) %>% mutate(txt=paste(GOTerm, desc, GeneProducts, sep='\t')) %>% filter(str_detect(GeneProducts,"\\|"))
write_lines(header,"enrichment.coli/ecoli.go.direct.sets")
write_lines(lines$txt,"enrichment.coli/ecoli.go.direct.sets", append=T)

Direct and implicit GeneProducts

go.sets.implicit = lapply(ecoli.terms, function(x) get_GeneProducts(x, all=T))
names(go.sets.implicit)=ecoli.terms
go.sets.implicit[['GO:0006457']]

Fichiers sets

header = paste0("# format: sets
# version: 1.3
# strain: Escherichia coli K-12 MG1655
# date: ", format(Sys.time(), '%d %B, %Y'), "
# comment: Gene Ontology terms")
sets = lapply(ecoli.terms, function(x) paste(go.sets.implicit[[x]], collapse = '|')) %>% unlist
tb = tibble(GOTerm=ecoli.terms, GeneProducts = sets)
lines = tb %>% inner_join(go.terms, by=c('GOTerm'='acc')) %>% mutate(desc=paste0(term_type,': ', name)) %>% mutate(txt=paste(GOTerm, desc, GeneProducts, sep='\t')) %>% filter(str_detect(GeneProducts,"\\|"))
write_lines(header,"enrichment.coli/ecoli.go.implicit.sets")
write_lines(lines$txt,"enrichment.coli/ecoli.go.implicit.sets", append=T)

Gene Set Enrichment Analysis

git clone git@gitlab.com:rbarriot/enrichment.git
for i in $(seq 1 9); do 
  ./enrichment/blastset.py -q enrichment.coli/g.com.0$i.txt -t enrichment.coli/ecoli.go.direct.sets -c > enrichment.coli/g.com.0$i.enriched.tsv
done
for i in $(seq 10 42); do 
  ./enrichment/blastset.py -q enrichment.coli/g.com.$i.txt -t enrichment.coli/ecoli.go.direct.sets -c > enrichment.coli/g.com.$i.enriched.tsv
done

Résultats

read_tsv("enrichment.coli/g.com.01.enriched.tsv") %>% kabex
## Parsed with column specification:
## cols(
##   `GO:0006313` = col_character(),
##   `1.478e-23` = col_double(),
##   `12/48` = col_character(),
##   `biological_process: transposition, DNA-mediated` = col_character(),
##   `b3445, b0275, b1893, b0988, b0022, b1894, b3444, b0265, b4516, b0264, b0274, b0021` = col_character()
## )
GO:0006313 1.478e-23 12/48 biological_process: transposition, DNA-mediated b3445, b0275, b1893, b0988, b0022, b1894, b3444, b0265, b4516, b0264, b0274, b0021
GO:0032196 0 12/57 biological_process: transposition b3445, b0275, b1893, b0988, b0022, b1894, b3444, b0265, b4516, b0264, b0274, b0021
GO:0006310 0 12/107 biological_process: DNA recombination b3445, b0275, b1893, b0988, b0022, b1894, b3444, b0265, b4516, b0264, b0274, b0021
GO:0004803 0 6/39 molecular_function: transposase activity b3445, b1893, b0988, b0264, b0274, b0021 
cat(sapply(2:9, function(i) kabex(read_tsv(paste0("enrichment.coli/g.com.0",i,".enriched.tsv")))))
GO:0032196 1.162e-22 12/57 biological_process: transposition b3045, b1403, b1996, b3044, b4272, b4273, b1402, b2860, b2861, b0361, b1997, b0360
GO:0006310 0e+00 12/107 biological_process: DNA recombination b3045, b1403, b1996, b3044, b4272, b4273, b1402, b2860, b2861, b0361, b1997, b0360
GO:0003677 0e+00 12/496 molecular_function: DNA binding b3045, b1403, b1996, b3044, b4272, b4273, b1402, b2860, b2861, b0361, b1997, b0360
GO:0015074 0e+00 6/31 biological_process: DNA integration b3045, b1996, b4273, b1402, b2860, b0361
GO:0004803 0e+00 6/39 molecular_function: transposase activity b1403, b3044, b4272, b2861, b1997, b0360
GO:0006313 0e+00 6/48 biological_process: transposition, DNA-mediated b1403, b3044, b4272, b2861, b1997, b0360
GO:0003676 1e-07 6/89 molecular_function: nucleic acid binding b3045, b1996, b4273, b1402, b2860, b0361
GO:0009231 2.132e-08 4/9 biological_process: riboflavin biosynthetic process b0414, b1277, b3041, b0415
GO:0008962 1.00e-07 3/3 molecular_function: phosphatidylglycerophosphatase activity b0418, b1278, b2560
GO:0009395 1.00e-07 3/3 biological_process: phospholipid catabolic process b0418, b1278, b2560
GO:0006655 3.00e-07 3/4 biological_process: phosphatidylglycerol biosynthetic process b0418, b1278, b2560
GO:0046474 6.00e-07 3/5 biological_process: glycerophospholipid biosynthetic process b0418, b1278, b2560
GO:0016042 6.60e-06 3/11 biological_process: lipid catabolic process b0418, b1278, b2560
GO:0046872 7.15e-05 9/692 molecular_function: metal ion binding b3041, b4162, b2560, b1277, b0418, b0414, b0413, b0417, b4161
GO:0006629 8.62e-05 4/74 biological_process: lipid metabolic process b4160, b0418, b1278, b2560
GO:0051301 9.409e-19 15/73 biological_process: cell division b0094, b0093, b0085, b0091, b0090, b0083, b0890, b0086, b0634, b0084, b0089, b0088, b0087, b0095, b3933
GO:0007049 0.0000000 14/67 biological_process: cell cycle b0094, b0093, b0085, b0091, b0090, b0083, b0890, b0086, b0084, b0089, b0088, b0087, b0095, b3933
GO:0009252 0.0000000 12/47 biological_process: peptidoglycan biosynthetic process b0092, b0635, b0091, b0090, b0634, b0086, b0084, b0089, b0088, b0087, b0085, b0149
GO:0008360 0.0000000 12/49 biological_process: regulation of cell shape b0092, b0635, b0091, b0090, b0634, b0086, b0084, b0089, b0088, b0087, b0085, b0149
GO:0071555 0.0000000 13/78 biological_process: cell wall organization b0092, b0635, b0091, b0090, b0634, b0086, b0633, b0084, b0089, b0088, b0087, b0085, b0149
GO:0032153 0.0000000 8/32 cellular_component: cell division site b0094, b0093, b0083, b0634, b0084, b0089, b0095, b3933
GO:0043093 0.0000000 7/29 biological_process: FtsZ-dependent cytokinesis b0094, b0093, b0083, b0084, b0089, b0095, b3933
GO:0008955 0.0000003 4/7 molecular_function: peptidoglycan glycosyltransferase activity b0634, b0089, b0084, b0149
GO:0000917 0.0000039 4/14 biological_process: division septum assembly b0095, b0084, b0093, b3933
GO:0005515 0.0000259 19/1066 molecular_function: protein binding b0094, b0635, b0890, b0636, b3034, b0149, b0090, b3019, b0091, b0083, b0095, b0084, b0089, b3030, b3933, b0637, b0085, b0088, b0093
GO:0009002 0.0000616 3/10 molecular_function: serine-type D-Ala-D-Ala carboxypeptidase activity b0084, b0635, b0149
GO:0090529 0.0000815 3/11 biological_process: cell septum assembly b0095, b0093, b3933
GO:0008658 0.0000815 3/11 molecular_function: penicillin binding b0084, b0635, b0149
GO:0030541 0.0001094 2/2 biological_process: plasmid partitioning b3019, b3030
GO:0007059 0.0001656 3/14 biological_process: chromosome segregation b0890, b3019, b3030
GO:0004180 0.0002026 3/15 molecular_function: carboxypeptidase activity b0084, b0635, b0149
GO:0015836 0.0002450 2/3 biological_process: lipid-linked peptidoglycan transport b0634, b0089
GO:0015648 0.0002450 2/3 molecular_function: lipid-linked peptidoglycan transporter activity b0634, b0089
GO:0007062 0.0004335 2/4 biological_process: sister chromatid cohesion b3019, b3030
GO:0003918 0.0004335 2/4 molecular_function: DNA topoisomerase type II (ATP-hydrolyzing) activity b3019, b3030
GO:0009058 0.0004538 4/48 biological_process: biosynthetic process b0086, b0088, b0085, b0091
GO:0055072 1.072e-27 22/28 biological_process: iron ion homeostasis b4287, b0151, b0585, b4289, b0589, b4293, b4290, b0592, b0153, b0590, b2155, b3409, b0150, b0805, b4292, b3408, b1102, b4288, b0152, b0584, b0588, b4291
GO:0006811 0.0000000 27/113 biological_process: ion transport b4287, b0585, b0151, b4289, b0589, b0697, b4293, b4036, b4290, b0696, b0592, b0153, b0590, b2155, b3409, b0150, b3966, b0805, b4292, b3408, b4288, b1102, b0698, b0152, b0584, b0588, b4291
GO:0043190 0.0000000 22/90 cellular_component: ATP-binding cassette (ABC) transporter complex b1125, b0151, b0887, b0857, b1124, b3450, b3749, b4035, b0153, b0855, b0886, b1709, b1711, b4032, b0590, b1126, b0856, b0914, b4033, b3750, b4034, b0588
GO:0033214 0.0000000 10/11 biological_process: iron assimilation by chelation and transport b4367, b4290, b0590, b0151, b0585, b4288, b4289, b0589, b0584, b0153
GO:0009239 0.0000000 8/8 biological_process: enterobactin biosynthetic process b0595, b0593, b0583, b4511, b0596, b0594, b0586, b0597
GO:0055085 0.0000000 29/357 biological_process: transmembrane transport b4287, b1125, b4289, b0589, b3452, b0887, b0857, b1124, b3006, b0153, b0199, b0855, b0886, b1709, b4032, b1711, b1252, b0590, b3451, b1126, b0856, b0914, b4033, b0198, b3750, b3005, b4034, b4288, b3453
GO:0044718 0.0000000 7/8 biological_process: siderophore transmembrane transport b0150, b0805, b2155, b1102, b0584, b1252, b4291
GO:0015847 0.0000000 8/15 biological_process: putrescine transport b1123, b1125, b1126, b0856, b0857, b1124, b0855, b0854
GO:0055052 0.0000000 9/23 cellular_component: ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing b4035, b4034, b3451, b0197, b0589, b3452, b0199, b3450, b0198
GO:0015889 0.0000000 6/6 biological_process: cobalamin transport b3966, b1710, b0158, b1709, b1711, b1252
GO:0015344 0.0000000 6/7 molecular_function: siderophore uptake transmembrane transporter activity b0150, b0805, b2155, b1102, b0584, b4291
GO:0015891 0.0000001 6/9 biological_process: siderophore transport b0150, b0805, b1102, b0584, b1252, b4291
GO:0042956 0.0000001 5/5 biological_process: maltodextrin transport b4036, b4035, b4034, b4032, b4033
GO:0038023 0.0000003 5/6 molecular_function: signaling receptor activity b0150, b0805, b1102, b0584, b4291
GO:0015685 0.0000003 5/6 biological_process: ferric-enterobactin transport b0590, b0592, b0589, b0584, b0588
GO:0015768 0.0000003 5/6 biological_process: maltose transport b4036, b4035, b4034, b4032, b4033
GO:0016020 0.0000004 52/1299 cellular_component: membrane b4287, b1125, b0695, b0151, b0197, b4289, b0589, b3452, b0887, b0857, b0697, b1124, b3450, b3749, b4036, b4035, b0583, b0696, b3006, b0153, b0199, b0855, b0886, b1709, b4032, b1711, b1252, b4367, b0590, b2155, b3451, b3409, b1126, b0856, b3751, b0914, b0594, b4033, b0198, b0150, b3750, b3966, b0805, b3005, b4288, b1102, b0698, b0584, b0588, b3661, b4291, b0915
GO:0016887 0.0000016 13/114 molecular_function: ATPase activity b4287, b3749, b4035, b0151, b1126, b0886, b0887, b0199, b0855, b1709, b0588, b0914, b3450
GO:0001407 0.0000023 4/4 biological_process: glycerophosphodiester transmembrane transport b3451, b3452, b3450, b3453
GO:0015620 0.0000056 4/5 molecular_function: ferric-enterobactin transmembrane transporter activity b0590, b0589, b0584, b0588
GO:0015846 0.0000056 4/5 biological_process: polyamine transport b1123, b0854, b1126, b0855
GO:0015794 0.0000056 4/5 biological_process: glycerol-3-phosphate transmembrane transport b3451, b3452, b3450, b3453
GO:0042626 0.0000066 6/20 molecular_function: ATPase activity, coupled to transmembrane movement of substances b4287, b0887, b0199, b0914, b0886, b1709
GO:0048473 0.0000467 3/3 biological_process: D-methionine transport b0197, b0199, b0198
GO:0047527 0.0000467 3/3 molecular_function: 2,3-dihydroxybenzoate-serine ligase activity b0586, b0595, b0594
GO:0015595 0.0000467 3/3 molecular_function: spermidine-importing ATPase activity b1125, b1124, b1126
GO:0031992 0.0000467 3/3 molecular_function: energy transducer activity b3006, b1252, b3005
GO:0015420 0.0000467 3/3 molecular_function: cobalamin-transporting ATPase activity b1709, b1711, b3966
GO:0015752 0.0000467 3/3 biological_process: D-ribose transmembrane transport b3750, b3749, b3751
GO:1904981 0.0000467 3/3 biological_process: maltose transmembrane transport b4033, b4035, b4032
GO:0015423 0.0000467 3/3 molecular_function: maltose-transporting ATPase activity b4033, b4035, b4032
GO:1990060 0.0000467 3/3 cellular_component: maltose transport complex b4033, b4035, b4032
GO:0043213 0.0000552 4/9 biological_process: bacteriocin transport b3006, b2155, b1252, b3005
GO:0005886 0.0000620 43/1139 cellular_component: plasma membrane b4287, b1125, b0695, b0151, b0197, b4289, b0589, b3452, b0887, b0857, b0697, b1124, b3450, b3749, b4035, b0696, b3006, b0153, b0199, b0855, b0886, b1709, b4032, b1711, b1252, b4367, b0590, b3451, b0595, b3409, b1126, b0856, b0914, b4033, b0198, b3750, b3005, b4288, b0698, b0588, b0586, b3661, b0915
GO:0031230 0.0000828 4/10 cellular_component: intrinsic component of cell outer membrane b2155, b0584, b4036, b3966
GO:0019290 0.0001088 3/4 biological_process: siderophore biosynthetic process b0596, b0594, b4511
GO:0008556 0.0001088 3/4 molecular_function: potassium-transporting ATPase activity b0697, b0696, b0698
GO:0031004 0.0001088 3/4 cellular_component: potassium ion-transporting ATPase complex b0697, b0696, b0698
GO:0015169 0.0001088 3/4 molecular_function: glycerol-3-phosphate transmembrane transporter activity b3451, b3452, b3450
GO:0008643 0.0001162 10/104 biological_process: carbohydrate transport b3750, b3749, b4036, b4035, b4034, b4037, b3751, b4032, b4033, b3450
GO:0019904 0.0001191 4/11 molecular_function: protein domain specific binding b0150, b0584, b1252, b3966
GO:1903711 0.0002092 3/5 biological_process: spermidine transmembrane transport b1125, b1124, b1126
GO:0005887 0.0002892 25/546 cellular_component: integral component of plasma membrane b1125, b0695, b4289, b0589, b3452, b0887, b0697, b1124, b0696, b3006, b0153, b0886, b4032, b1711, b0590, b3451, b3409, b0856, b0914, b4033, b0198, b3750, b3005, b4288, b0698
GO:0098797 0.0003556 3/6 cellular_component: plasma membrane protein complex b3006, b1252, b3005
GO:0030288 0.0003830 13/194 cellular_component: outer membrane-bounded periplasmic space b4290, b4034, b1123, b1452, b0158, b3453, b0592, b0197, b4037, b3751, b0152, b0854, b1252
GO:0005524 0.0006126 21/441 molecular_function: ATP binding b4287, b0151, b0695, b0887, b0697, b3450, b3749, b4035, b0696, b0199, b0855, b0886, b1709, b1126, b0914, b0594, b3752, b3418, b0588, b0586, b0915
GO:0042597 0.0008289 12/184 cellular_component: periplasmic space b4290, b4034, b1123, b4292, b1710, b0158, b3453, b0592, b4037, b0152, b3751, b0854
GO:0090482 0.0009655 2/2 molecular_function: vitamin transmembrane transporter activity b1711, b3966
GO:0035461 0.0009655 2/2 biological_process: vitamin transmembrane transport b1711, b3966
GO:0015343 0.0009655 2/2 molecular_function: siderophore transmembrane transporter activity b2155, b1252
GO:0015603 0.0009655 2/2 molecular_function: iron chelate transmembrane transporter activity b4288, b4289
GO:0015191 0.0009655 2/2 molecular_function: L-methionine transmembrane transporter activity b0199, b0198
GO:0009366 0.0009655 2/2 cellular_component: enterobactin synthetase complex b0586, b0583
GO:0042914 0.0009655 2/2 biological_process: colicin transport b0584, b1252
GO:0019810 0.0009655 2/2 molecular_function: putrescine binding b1123, b0854
GO:0015417 0.0009655 2/2 molecular_function: polyamine-transporting ATPase activity b1126, b0855
GO:0001406 0.0009655 2/2 molecular_function: glycerophosphodiester transmembrane transporter activity b3452, b3450
GO:0019303 0.0009655 2/2 biological_process: D-ribose catabolic process b3748, b3752
GO:0015591 0.0009655 2/2 molecular_function: D-ribose transmembrane transporter activity b3750, b3749
GO:0006826 0.0011440 3/9 biological_process: iron ion transport b0585, b3409, b4291
GO:0016021 0.0011530 35/966 cellular_component: integral component of membrane b1125, b0695, b4289, b0589, b3452, b0887, b0857, b0697, b1124, b4036, b0696, b3006, b0153, b0886, b4032, b1711, b1252, b0590, b2155, b3451, b3409, b0856, b0914, b4033, b0198, b0150, b3750, b3966, b0805, b3005, b4288, b1102, b0698, b0584, b4291
GO:0009389 6.730e-15 6/6 molecular_function: dimethyl sulfoxide reductase activity b0895, b1587, b1588, b0894, b1590, b0896
GO:0009061 0.0000000 8/49 biological_process: anaerobic respiration b0997, b0895, b1587, b1588, b0996, b0894, b1590, b0896
GO:0009390 0.0000000 4/4 cellular_component: dimethyl sulfoxide reductase complex b0895, b0896, b0894, b1590
GO:0043546 0.0000000 5/18 molecular_function: molybdopterin cofactor binding b0997, b1587, b1588, b0998, b0894
GO:0019645 0.0000001 4/15 biological_process: anaerobic electron transport chain b0896, b1590, b0997, b0996
GO:0030151 0.0000001 4/16 molecular_function: molybdenum ion binding b1588, b0894, b1587, b0997
GO:0055114 0.0000002 9/448 biological_process: oxidation-reduction process b0997, b0895, b1587, b1588, b0996, b0894, b1590, b1589, b0896
GO:0009055 0.0000020 5/83 molecular_function: electron transfer activity b0997, b1587, b1588, b0996, b0894
GO:0051539 0.0000105 5/117 molecular_function: 4 iron, 4 sulfur cluster binding b0895, b1587, b1588, b1589, b0894
GO:0033797 0.0000149 2/2 molecular_function: selenate reductase activity b1587, b1588
GO:0051536 0.0000305 5/146 molecular_function: iron-sulfur cluster binding b0895, b1587, b1588, b1589, b0894
GO:0030288 0.0001183 5/194 cellular_component: outer membrane-bounded periplasmic space b0997, b1587, b1588, b0996, b0894
GO:0031237 0.0001812 2/7 cellular_component: intrinsic component of periplasmic side of plasma membrane b0895, b0894
GO:0016491 0.0001956 6/356 molecular_function: oxidoreductase activity b0997, b1587, b1588, b0894, b1590, b0896
GO:0006212 9.813e-13 7/9 biological_process: uracil catabolic process b1009, b1006, b1010, b1007, b1012, b1011, b1008
GO:0070814 0.0000000 6/6 biological_process: hydrogen sulfide biosynthetic process b2762, b2764, b2750, b2752, b2763, b2751
GO:0000103 0.0000000 6/7 biological_process: sulfate assimilation b4214, b2764, b2750, b2752, b2763, b2751
GO:0019740 0.0000000 6/8 biological_process: nitrogen utilization b1009, b1010, b1007, b1012, b1011, b1008
GO:0006208 0.0000000 6/9 biological_process: pyrimidine nucleobase catabolic process b1009, b1010, b1007, b1012, b1011, b1008
GO:0015419 0.0000000 5/5 molecular_function: ATPase-coupled sulfate transmembrane transporter activity b2423, b2424, b3917, b2425, b2422
GO:0006790 0.0000000 6/14 biological_process: sulfur compound metabolic process b2762, b4214, b2752, b3917, b2751, b2425
GO:0008272 0.0000000 5/7 biological_process: sulfate transport b2423, b2424, b3917, b2425, b2422
GO:1902358 0.0000000 5/7 biological_process: sulfate transmembrane transport b2423, b2424, b3917, b2425, b2422
GO:0019344 0.0000000 5/8 biological_process: cysteine biosynthetic process b2764, b2763, b2421, b2414, b3607
GO:0006535 0.0000050 3/4 biological_process: cysteine biosynthetic process from serine b2414, b2421, b3607
GO:0043190 0.0000742 6/90 cellular_component: ATP-binding cassette (ABC) transporter complex b2423, b0832, b0831, b2424, b0830, b2422
GO:1901681 0.0001252 2/2 molecular_function: sulfur compound binding b2425, b3917
GO:0004124 0.0001252 2/2 molecular_function: cysteine synthase activity b2414, b2421
GO:0009333 0.0001252 2/2 cellular_component: cysteine synthase complex b2414, b3607
GO:0015709 0.0001252 2/2 biological_process: thiosulfate transport b2425, b2422
GO:0043199 0.0001252 2/2 molecular_function: sulfate binding b2425, b3917
GO:0004781 0.0001252 2/2 molecular_function: sulfate adenylyltransferase (ATP) activity b2751, b2752
GO:0009337 0.0001252 2/2 cellular_component: sulfite reductase complex (NADPH) b2763, b2764
GO:0004783 0.0001252 2/2 molecular_function: sulfite reductase (NADPH) activity b2763, b2764
GO:0042602 0.0002803 2/3 molecular_function: riboflavin reductase (NADPH) activity b1007, b2764
GO:0071973 5.242e-41 27/33 biological_process: bacterial-type flagellum-dependent cell motility b1939, b1941, b1944, b1890, b1194, b1938, b1073, b1082, b1923, b1942, b1945, b1079, b1946, b1076, b1937, b1925, b1078, b1077, b1072, b1926, b1080, b1074, b1943, b1924, b1081, b1083, b1940
GO:0009288 0.0000000 25/25 cellular_component: bacterial-type flagellum b1939, b1194, b1938, b1949, b1878, b1073, b1082, b1923, b1942, b1945, b1079, b1946, b1076, b1937, b1078, b1077, b1080, b1074, b1924, b1083, b1948, b1940, b1947, b1950, b1881
GO:0009425 0.0000000 18/18 cellular_component: bacterial-type flagellum basal body b1076, b1939, b1074, b1937, b1073, b1944, b1948, b1078, b1077, b1194, b1938, b1947, b1949, b1950, b1945, b1079, b1946, b1080
GO:0006935 0.0000000 19/24 biological_process: chemotaxis b1939, b1944, b1890, b1887, b1885, b1421, b1889, b1942, b1945, b1883, b1946, b3072, b1882, b1886, b4355, b1888, b1884, b1947, b1881
GO:0044781 0.0000000 16/18 biological_process: bacterial-type flagellum organization b1070, b1943, b1941, b1081, b1879, b1940, b1925, b1071, b1948, b1072, b1947, b1075, b1880, b1926, b1942, b1878
GO:0097588 0.0000000 12/12 biological_process: archaeal or bacterial-type flagellum-dependent cell motility b1939, b1937, b1882, b1944, b1890, b1947, b1889, b1881, b1945, b1079, b1946, b1080
GO:0044780 0.0000000 12/17 biological_process: bacterial-type flagellum assembly b1070, b1939, b1943, b1941, b1081, b1879, b1082, b1925, b1072, b1949, b1950, b1880
GO:0009424 0.0000000 10/10 cellular_component: bacterial-type flagellum hook b1076, b1074, b1943, b1924, b1073, b1083, b1082, b1078, b1077, b1075
GO:0003774 0.0000000 8/8 molecular_function: motor activity b1939, b1937, b1940, b1938, b1942, b1945, b1079, b1946
GO:0071978 0.0000000 9/15 biological_process: bacterial-type flagellum-dependent swarming motility b1076, b1074, b1073, b1944, b1890, b1078, b1077, b1075, b1881
GO:0098561 0.0000000 7/7 cellular_component: methyl accepting chemotaxis protein complex b1421, b1886, b4355, b1887, b1884, b1881, b1888
GO:0007165 0.0000000 9/36 biological_process: signal transduction b3072, b1421, b1886, b1887, b4355, b1885, b1888, b1883, b3210
GO:0004888 0.0000000 5/5 molecular_function: transmembrane signaling receptor activity b3072, b1421, b1886, b4355, b1885
GO:1902021 0.0000000 5/6 biological_process: regulation of bacterial-type flagellum-dependent cell motility b1882, b1921, b4355, b3525, b1888
GO:0050920 0.0000004 4/4 biological_process: regulation of chemotaxis b1888, b4355, b1886, b1881
GO:0005198 0.0000019 5/14 molecular_function: structural molecule activity b1937, b1083, b1082, b1923, b1080
GO:1901875 0.0000122 3/3 biological_process: positive regulation of post-translational protein modification b1888, b1887, b1886
GO:0009306 0.0000392 4/13 biological_process: protein secretion b1948, b1880, b1879, b1949
GO:0005576 0.0000392 4/13 cellular_component: extracellular region b1083, b1923, b1082, b1924
GO:0023014 0.0001147 5/33 biological_process: signal transduction by protein phosphorylation b1882, b1887, b1888, b1883, b3210
GO:0015031 0.0003959 6/67 biological_process: protein transport b1941, b1879, b1940, b1948, b1880, b1942
GO:0030694 0.0003965 2/2 cellular_component: bacterial-type flagellum basal body, rod b1074, b1073
GO:0009454 0.0003965 2/2 biological_process: aerotaxis b1887, b1882
GO:0007172 0.0003965 2/2 biological_process: signal complex assembly b1886, b4355
GO:0051286 0.0003965 2/2 cellular_component: cell tip b1886, b1887 
cat(sapply(10:42, function(i) kabex(read_tsv(paste0("enrichment.coli/g.com.",i,".enriched.tsv")))))
GO:0006096 4.889e-16 13/19 biological_process: glycolytic process b3612, b4025, b1779, b1676, b2779, b4395, b0755, b3919, b3916, b2926, b2925, b1723, b1854
GO:0006094 0.0000000 7/14 biological_process: gluconeogenesis b3403, b4025, b0755, b3919, b2926, b2925, b4232
GO:0008152 0.0000003 14/119 biological_process: metabolic process b3403, b3428, b3430, b3080, b1676, b3956, b0403, b3916, b3417, b1767, b1854, b4232, b3431, b4167
GO:0005737 0.0000007 39/848 cellular_component: cytoplasm b4173, b3813, b3416, b1780, b2779, b4395, b0143, b0755, b3919, b3064, b1084, b4025, b1779, b3164, b1676, b2927, b1807, b0687, b3432, b4168, b2926, b3780, b4232, b0779, b4058, b4166, b3916, b1493, b2518, b1913, b1767, b1854, b3612, b3403, b3428, b0403, b3417, b1914, b0688
GO:0005980 0.0000021 4/4 biological_process: glycogen catabolic process b3416, b3428, b3417, b3431
GO:0005977 0.0000021 4/4 biological_process: glycogen metabolic process b3428, b3430, b3431, b3432
GO:0003824 0.0000039 23/375 molecular_function: catalytic activity b3430, b1780, b4395, b0755, b3919, b1676, b3432, b4232, b3517, b3916, b1493, b3614, b2925, b1767, b1854, b4167, b3612, b3403, b3428, b3956, b0403, b3417, b3431
GO:0005975 0.0000063 14/154 biological_process: carbohydrate metabolic process b3428, b3430, b3416, b3080, b1780, b0403, b3432, b3614, b3417, b2925, b1723, b0688, b4232, b3431
GO:0006289 0.0000105 4/6 biological_process: nucleotide-excision repair b1913, b3813, b0779, b4058
GO:0005829 0.0000154 41/1032 cellular_component: cytosol b4173, b3813, b3416, b1780, b2779, b0143, b0755, b3919, b1867, b3064, b1723, b4025, b1779, b4172, b3164, b1676, b2927, b4174, b3407, b1807, b0687, b3432, b3429, b2926, b3780, b4232, b4058, b3517, b3916, b1493, b2518, b2925, b1767, b1854, b3612, b3403, b0144, b3956, b2733, b3417, b0688
GO:0042802 0.0000349 23/429 molecular_function: identical protein binding b3430, b2779, b3510, b3919, b3064, b1723, b1084, b4025, b3164, b1676, b1807, b0687, b4168, b4232, b0779, b4058, b3916, b2925, b1767, b1854, b3506, b2733, b4170
GO:0004619 0.0000435 3/3 molecular_function: phosphoglycerate mutase activity b3612, b0755, b4395
GO:0009381 0.0000435 3/3 molecular_function: excinuclease ABC activity b1913, b0779, b4058
GO:0005978 0.0000435 3/3 biological_process: glycogen biosynthetic process b3430, b3429, b3432
GO:0000287 0.0000452 14/184 molecular_function: magnesium ion binding b3403, b3430, b3164, b1676, b3956, b2779, b3916, b0142, b3064, b1723, b1854, b0688, b1084, b4232
GO:0005524 0.0000538 23/441 molecular_function: ATP binding b4173, b3813, b3430, b2786, b0143, b0755, b0142, b1723, b1676, b4168, b2926, b3780, b0779, b4058, b3916, b4171, b2518, b1854, b4167, b3403, b0144, b2733, b4170
GO:0006298 0.0000755 4/10 biological_process: mismatch repair b2733, b3813, b4170, b1960
GO:0000166 0.0000801 25/517 molecular_function: nucleotide binding b4173, b3813, b3430, b2786, b0143, b0142, b1723, b1779, b1676, b4168, b2628, b2926, b3780, b4232, b0779, b4058, b3916, b4171, b2518, b1854, b4167, b3403, b0144, b2733, b4170
GO:0009380 0.0001015 3/4 cellular_component: excinuclease repair complex b1913, b0779, b4058
GO:0002949 0.0001015 3/4 biological_process: tRNA threonylcarbamoyladenosine modification b3064, b1807, b4168
GO:0051454 0.0001951 3/5 biological_process: intracellular pH elevation b3517, b1492, b1493
GO:0006974 0.0002994 15/248 biological_process: cellular response to DNA damage stimulus b3813, b3080, b1780, b2733, b3431, b1960, b4170, b3429, b3432, b3516, b4058, b1913, b1723, b3515, b0779
GO:0009268 0.0003319 3/6 biological_process: response to pH b0486, b3509, b3511
GO:0016868 0.0003319 3/6 molecular_function: intramolecular transferase activity, phosphotransferases b0688, b0755, b4395
GO:0016226 1.225e-13 7/19 biological_process: iron-sulfur cluster assembly b2524, b2529, b2526, b2530, b3807, b2528, b2525
GO:0051537 0.0000001 5/33 molecular_function: 2 iron, 2 sulfur cluster binding b2531, b2529, b2530, b2528, b2525
GO:0019285 0.0000003 3/4 biological_process: glycine betaine biosynthetic process from choline b0312, b0311, b0313
GO:0005506 0.0000007 5/55 molecular_function: iron ion binding b2524, b2531, b2529, b3807, b2528
GO:0008198 0.0000010 4/24 molecular_function: ferrous iron binding b3807, b2528, b2524, b2529
GO:0097428 0.0000011 3/6 biological_process: protein maturation by iron-sulfur cluster transfer b2528, b2527, b2526
GO:0008802 0.0000211 2/2 molecular_function: betaine-aldehyde dehydrogenase activity b0312, b0311
GO:1990230 0.0000211 2/2 cellular_component: iron-sulfur cluster transfer complex b2527, b2526
GO:0044571 0.0000211 2/2 biological_process: [2Fe-2S] cluster assembly b2527, b2530
GO:0005829 0.0000237 11/1032 cellular_component: cytosol b0312, b2527, b2524, b3895, b2531, b2530, b2529, b2526, b3807, b2528, b2525
GO:0006970 0.0000285 3/18 biological_process: response to osmotic stress b0312, b0311, b0313
GO:0051536 0.0000796 5/146 molecular_function: iron-sulfur cluster binding b2531, b2529, b2530, b2528, b2525
GO:0097163 0.0002564 2/7 molecular_function: sulfur carrier activity b3895, b2530
GO:0005975 5.280e-06 5/154 biological_process: carbohydrate metabolic process b1313, b1317, b1316, b1315, b1314
GO:0055114 1.732e-31 64/448 biological_process: oxidation-reduction process b0722, b2276, b0733, b2286, b2481, b2486, b2770, b1387, b1479, b2278, b1378, b2485, b2482, b0724, b1136, b0429, b0307, b3152, b2488, b2288, b2287, b4515, b1698, b2483, b2489, b2285, b1800, b2490, b0431, b4154, b1109, b2484, b0042, b2487, b0978, b3003, b2463, b2283, b2769, b2277, b2279, b0726, b1415, b3962, b0721, b1697, b3236, b1656, b0979, b3908, b2281, b4211, b0306, b0073, b2282, b0430, b0041, b0723, b2210, b2284, b0432, b0734, b4153, b2280
GO:0009060 0.0000000 17/24 biological_process: aerobic respiration b0722, b2276, b2287, b2277, b2281, b2282, b0721, b0429, b0724, b0431, b0430, b1109, b0723, b2284, b0432, b2488, b2283
GO:0003954 0.0000000 15/18 molecular_function: NADH dehydrogenase activity b2287, b2276, b2279, b2277, b2281, b2286, b2285, b2282, b2278, b2484, b2284, b2488, b2283, b2280, b2288
GO:0030964 0.0000000 14/14 cellular_component: NADH dehydrogenase complex b2287, b2276, b2277, b2279, b2281, b2286, b2285, b2282, b2278, b1109, b2284, b2283, b2280, b2288
GO:0006099 0.0000000 17/29 biological_process: tricarboxylic acid cycle b0722, b0320, b0728, b0518, b0726, b1612, b4122, b1611, b0721, b1136, b0724, b0727, b3236, b0723, b2210, b4153, b0729
GO:0048038 0.0000000 15/20 molecular_function: quinone binding b2287, b2276, b2284, b2277, b2286, b2279, b2281, b2489, b2285, b2282, b2278, b2487, b2283, b2280, b2288
GO:0045272 0.0000000 14/16 cellular_component: plasma membrane respiratory chain complex I b2287, b2276, b2277, b2279, b2281, b2286, b2285, b2282, b2278, b2284, b2488, b2283, b2280, b2288
GO:0008137 0.0000000 14/17 molecular_function: NADH dehydrogenase (ubiquinone) activity b2287, b2276, b2284, b2277, b2279, b2286, b2489, b2278, b2482, b1109, b2487, b2283, b2280, b2288
GO:0009055 0.0000000 21/83 molecular_function: electron transfer activity b0722, b0733, b2770, b0429, b0724, b1698, b0431, b4154, b0042, b0978, b2283, b2769, b0721, b1697, b0979, b0430, b0041, b0723, b0432, b0734, b4153
GO:0015990 0.0000000 9/9 biological_process: electron transport coupled proton transport b2287, b2276, b2277, b2278, b0429, b0430, b0431, b2484, b0432
GO:0019646 0.0000000 9/9 biological_process: aerobic electron transport chain b0979, b0733, b0429, b0430, b0431, b1109, b0978, b0432, b0734
GO:0016491 0.0000000 35/356 molecular_function: oxidoreductase activity b2481, b2486, b1387, b1479, b2485, b1378, b0724, b2482, b1136, b0429, b2483, b2489, b2285, b1800, b2490, b4154, b1109, b2484, b3003, b2487, b2463, b2283, b0726, b1415, b3962, b3236, b1656, b3908, b4211, b0073, b0430, b0723, b2210, b0432, b4153
GO:0016651 0.0000000 8/11 molecular_function: oxidoreductase activity, acting on NAD(P)H b2284, b2279, b2286, b2281, b2487, b2488, b2283, b2288
GO:0022900 0.0000000 14/63 biological_process: electron transport chain b0722, b2769, b1698, b2770, b0721, b1378, b1136, b1697, b4154, b0041, b0723, b0042, b0432, b4153
GO:0042773 0.0000000 7/8 biological_process: ATP synthesis coupled electron transport b2276, b2277, b2279, b2278, b2482, b0432, b2283
GO:0044569 0.0000000 8/13 cellular_component: [Ni-Fe] hydrogenase complex b2483, b2481, b2486, b2485, b2482, b2484, b2487, b2488
GO:0000104 0.0000000 6/6 molecular_function: succinate dehydrogenase activity b0722, b0721, b4152, b4151, b0723, b4154
GO:0050136 0.0000000 6/6 molecular_function: NADH dehydrogenase (quinone) activity b2287, b2276, b2279, b2286, b2281, b2288
GO:0016682 0.0000001 6/8 molecular_function: oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor b0979, b0733, b0431, b0978, b0432, b0734
GO:0006119 0.0000004 5/5 biological_process: oxidative phosphorylation b0979, b0733, b4515, b0978, b0734
GO:0015078 0.0000009 6/11 molecular_function: proton transmembrane transporter activity b0432, b0430, b0429, b0431, b3737, b3738
GO:0006108 0.0000010 5/6 biological_process: malate metabolic process b1800, b1479, b3236, b2463, b1611
GO:0051539 0.0000014 15/117 molecular_function: 4 iron, 4 sulfur cluster binding b2287, b2284, b2481, b2281, b2489, b4122, b1612, b1378, b0724, b2487, b0307, b2488, b0072, b2283, b4153
GO:0051287 0.0000039 9/42 molecular_function: NAD binding b2284, b2286, b0073, b1800, b1479, b1136, b2487, b3152, b2463
GO:0006113 0.0000040 5/8 biological_process: fermentation b4152, b4151, b3236, b4154, b4153
GO:0051536 0.0000045 16/146 molecular_function: iron-sulfur cluster binding b2287, b2284, b2481, b2281, b2489, b2285, b4122, b1612, b1378, b0724, b2487, b0307, b2488, b0072, b2283, b4153
GO:0004775 0.0000063 4/4 molecular_function: succinate-CoA ligase (ADP-forming) activity b0320, b0518, b0729, b0728
GO:0009361 0.0000063 4/4 cellular_component: succinate-CoA ligase complex (ADP-forming) b0320, b0518, b0729, b0728
GO:0015453 0.0000063 4/4 molecular_function: oxidoreduction-driven active transmembrane transporter activity b0429, b0430, b0432, b0431
GO:0009486 0.0000063 4/4 molecular_function: cytochrome bo3 ubiquinol oxidase activity b0429, b0430, b0432, b0431
GO:0009319 0.0000063 4/4 cellular_component: cytochrome o ubiquinol oxidase complex b0429, b0430, b0432, b0431
GO:0070069 0.0000063 4/4 cellular_component: cytochrome complex b0979, b0733, b0978, b0734
GO:0102040 0.0000063 4/4 molecular_function: fumarate reductase (menaquinone) b4152, b4151, b4154, b4153
GO:0045284 0.0000063 4/4 cellular_component: plasma membrane fumarate reductase complex b4152, b4151, b4154, b4153
GO:0009098 0.0000916 4/8 biological_process: leucine biosynthetic process b0074, b0073, b0071, b0072
GO:0004776 0.0000970 3/3 molecular_function: succinate-CoA ligase (GDP-forming) activity b0320, b0518, b0729
GO:0008827 0.0000970 3/3 molecular_function: cytochrome o ubiquinol oxidase activity b0429, b0430, b0432
GO:0004129 0.0000970 3/3 molecular_function: cytochrome-c oxidase activity b0430, b0431, b0432
GO:0008177 0.0000970 3/3 molecular_function: succinate dehydrogenase (ubiquinone) activity b0724, b0723, b0721
GO:0006754 0.0001436 4/9 biological_process: ATP biosynthetic process b3738, b3733, b3731, b3737
GO:0046933 0.0001436 4/9 molecular_function: proton-transporting ATP synthase activity, rotational mechanism b3738, b3733, b3731, b3737
GO:0015986 0.0001436 4/9 biological_process: ATP synthesis coupled proton transport b3738, b3733, b3731, b3737
GO:0016627 0.0002141 4/10 molecular_function: oxidoreductase activity, acting on the CH-CH group of donors b0722, b4154, b0723, b0721
GO:0016655 0.0002253 3/4 molecular_function: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor b4211, b2282, b2286
GO:0015765 0.0002253 3/4 biological_process: methylgalactoside transport b2148, b2149, b2150
GO:0045263 0.0002253 3/4 cellular_component: proton-transporting ATP synthase complex, coupling factor F(o) b3738, b3739, b3737
GO:0005886 0.0003455 50/1139 cellular_component: plasma membrane b0722, b2276, b0733, b2286, b0518, b2486, b2278, b2485, b4152, b2482, b0724, b0429, b2288, b2287, b4515, b2483, b2148, b2285, b0428, b3731, b0869, b0431, b3733, b4154, b2484, b1109, b0978, b0321, b2283, b2277, b2279, b3739, b0721, b3737, b2149, b3738, b0979, b4123, b1496, b2281, b2282, b3528, b0430, b4151, b0723, b2284, b0432, b0734, b4153, b2280
GO:0050660 0.0003985 8/61 molecular_function: flavin adenine dinucleotide binding b2769, b1698, b3962, b4154, b1109, b0723, b0042, b2210
GO:0048039 0.0004309 3/5 molecular_function: ubiquinone binding b0431, b2277, b0721
GO:0004333 0.0004309 3/5 molecular_function: fumarate hydratase activity b4122, b1612, b1611
GO:0009061 0.0005620 7/49 biological_process: anaerobic respiration b4152, b4151, b3236, b4154, b1109, b0723, b4153
GO:0020037 0.0009619 6/39 molecular_function: heme binding b0722, b0733, b0721, b0431, b0978, b0734
GO:0015757 0.0011340 3/7 biological_process: galactose transmembrane transport b2148, b2149, b2150
GO:0009432 3.596e-09 5/30 biological_process: SOS response b2616, b2698, b1848, b0958, b2699
GO:0006740 9.80e-06 2/2 biological_process: NADPH regeneration b1602, b1603
GO:0008750 9.80e-06 2/2 molecular_function: NAD(P)+ transhydrogenase (AB-specific) activity b1602, b1603
GO:0006281 2.19e-05 4/80 biological_process: DNA repair b2699, b1848, b2616, b2698
GO:0008746 2.20e-05 2/3 molecular_function: NAD(P)+ transhydrogenase activity b1602, b1603
GO:0016226 1.479e-14 6/19 biological_process: iron-sulfur cluster assembly b1680, b1682, b1679, b1683, b1681, b1684
GO:1990229 0.00e+00 3/3 cellular_component: iron-sulfur cluster assembly complex b1682, b1683, b1681
GO:0031162 4.10e-06 2/2 biological_process: sulfur incorporation into metallo-sulfur cluster b1680, b1679
GO:0006979 4.56e-05 3/51 biological_process: response to oxidative stress b1679, b1681, b1684
GO:0006526 3.521e-14 9/12 biological_process: arginine biosynthetic process b3359, b3960, b3959, b3957, b3172, b0273, b4254, b2818, b3958
GO:0042908 0.0000000 10/20 biological_process: xenobiotic transport b3514, b2075, b3265, b3513, b3266, b2470, b2074, b2076, b0463, b0462
GO:0015721 0.0000000 8/12 biological_process: bile acid and bile salt transport b3514, b2075, b0463, b3035, b3513, b2074, b2076, b2470
GO:0015125 0.0000000 7/8 molecular_function: bile acid transmembrane transporter activity b3514, b2075, b3035, b3513, b2074, b2076, b2470
GO:0015562 0.0000000 8/17 molecular_function: efflux transmembrane transporter activity b3514, b3035, b0462, b3266, b2074, b2470, b0879, b0878
GO:0022857 0.0000000 16/213 molecular_function: transmembrane transporter activity b2074, b3514, b2075, b3265, b1117, b3513, b0462, b0862, b2077, b3266, b2470, b0861, b2076, b0463, b0879, b0878
GO:1990281 0.0000000 5/5 cellular_component: efflux pump complex b3035, b2074, b0463, b0462, b0878
GO:0044874 0.0000000 5/5 biological_process: lipoprotein localization to outer membrane b1209, b1118, b1116, b1117, b0891
GO:0042450 0.0000001 5/8 biological_process: arginine biosynthetic process via ornithine b3359, b3960, b3959, b0273, b4254
GO:0097638 0.0000002 4/4 biological_process: L-arginine import across plasma membrane b0862, b0861, b0864, b0860
GO:0042953 0.0000002 4/4 biological_process: lipoprotein transport b1118, b0891, b1116, b1117
GO:0042910 0.0000002 6/21 molecular_function: xenobiotic transmembrane transporter activity b3514, b3265, b3513, b2074, b0463, b0462
GO:0055085 0.0000028 16/357 biological_process: transmembrane transport b2074, b3514, b2075, b3265, b3035, b1117, b3513, b0862, b2077, b3266, b2470, b0861, b2076, b0463, b0462, b0878
GO:0008652 0.0000031 9/100 biological_process: cellular amino acid biosynthetic process b3359, b3960, b3959, b3957, b3172, b0273, b4254, b2818, b3958
GO:0046677 0.0000034 9/101 biological_process: response to antibiotic b3514, b3265, b3035, b3513, b2470, b0463, b3191, b0879, b0878
GO:1990196 0.0000076 3/3 cellular_component: MacAB-TolC complex b0878, b0879, b3035
GO:0030288 0.0000177 11/194 cellular_component: outer membrane-bounded periplasmic space b1209, b3192, b3193, b1116, b3035, b0860, b0891, b0863, b1743, b0463, b0462
GO:0015914 0.0000178 3/4 biological_process: phospholipid transport b3194, b3192, b3193
GO:0098797 0.0000590 3/6 cellular_component: plasma membrane protein complex b1118, b1116, b1117
GO:0071705 0.0000591 4/17 biological_process: nitrogen compound transport b0862, b0863, b0861, b0860
GO:0009636 0.0000906 4/19 biological_process: response to toxic substance b3514, b2470, b3035, b3513
GO:0016020 0.0002728 28/1299 cellular_component: membrane b1118, b1116, b1846, b0862, b3194, b0863, b0861, b1209, b2075, b3265, b2076, b0463, b3193, b3035, b0860, b1117, b3513, b3266, b2074, b0864, b0879, b0462, b2078, b3514, b2077, b2470, b3195, b0878
GO:0014070 0.0002894 2/2 biological_process: response to organic cyclic compound b1743, b3035
GO:0006591 0.0002894 2/2 biological_process: ornithine metabolic process b0273, b4254
GO:0005548 0.0002894 2/2 molecular_function: phospholipid transporter activity b3194, b3193
GO:0031226 0.0005649 3/13 cellular_component: intrinsic component of plasma membrane b3265, b0463, b3513
GO:0006189 2.158e-16 11/12 biological_process: ‘de novo’ IMP biosynthetic process b1131, b4005, b2476, b1849, b2557, b2312, b2499, b0522, b2500, b4006, b0523
GO:0006164 0.0000000 12/18 biological_process: purine nucleotide biosynthetic process b1131, b4005, b2476, b0529, b1849, b2557, b2312, b2499, b0522, b2500, b4006, b0523
GO:0006221 0.0000000 9/11 biological_process: pyrimidine nucleotide biosynthetic process b4246, b0945, b1281, b0033, b3642, b1062, b4244, b0032, b4245
GO:0044205 0.0000000 7/7 biological_process: ‘de novo’ UMP biosynthetic process b0945, b1281, b0033, b3642, b1062, b0032, b4245
GO:0006207 0.0000000 7/9 biological_process: ‘de novo’ pyrimidine nucleobase biosynthetic process b0945, b1281, b3642, b1062, b4244, b0032, b4245
GO:0005829 0.0000000 41/1032 cellular_component: cytosol b2154, b1849, b0522, b0355, b4006, b3951, b4245, b0033, b1131, b2903, b2453, b0528, b3114, b2498, b1062, b0337, b4243, b3117, b2476, b2905, b2904, b2557, b2499, b1281, b0903, b3642, b3589, b2551, b2500, b0523, b0114, b0032, b0945, b0529, b0116, b2312, b0356, b1241, b1133, b3113, b0823
GO:0004022 0.0000001 5/6 molecular_function: alcohol dehydrogenase (NAD) activity b1478, b2453, b0356, b1241, b3589
GO:0019464 0.0000008 4/4 biological_process: glycine decarboxylation via glycine cleavage system b0116, b2903, b2905, b2904
GO:0070689 0.0000069 4/7 biological_process: L-threonine catabolic process to propionate b3117, b3113, b3115, b3114
GO:0006546 0.0000202 3/3 biological_process: glycine catabolic process b2551, b2903, b2905
GO:0046294 0.0000202 3/3 biological_process: formaldehyde catabolic process b0355, b0356, b2154
GO:0006567 0.0000276 4/10 biological_process: threonine catabolic process b3117, b0903, b3115, b3114
GO:0019856 0.0000472 3/4 biological_process: pyrimidine nucleobase biosynthetic process b1062, b4246, b0033
GO:0003824 0.0001271 17/375 molecular_function: catalytic activity b1131, b3117, b0945, b3952, b0529, b2903, b0824, b3114, b1281, b2498, b4006, b0903, b2551, b1241, b0823, b3951, b0114
GO:0005737 0.0001305 28/848 cellular_component: cytoplasm b3952, b0824, b1132, b4245, b0033, b3114, b0512, b1062, b4244, b4243, b2904, b2873, b2557, b2499, b1281, b0903, b3642, b2551, b2500, b0032, b0115, b3953, b0945, b0116, b2312, b0356, b1133, b0357
GO:0006541 0.0001310 4/15 biological_process: glutamine metabolic process b0033, b2557, b2312, b0032
GO:0016597 0.0001310 4/15 molecular_function: amino acid binding b0033, b3117, b2551, b4245
GO:0046336 0.0001674 4/16 biological_process: ethanolamine catabolic process b2454, b2456, b2453, b2455
GO:0042802 0.0002037 18/429 molecular_function: identical protein binding b0904, b3117, b2154, b2873, b4245, b2903, b0116, b2312, b2498, b0356, b2551, b1241, b2456, b3113, b0523, b0337, b0114, b4243
GO:0006829 1.807e-07 3/8 biological_process: zinc ion transport b1857, b1859, b1858
GO:0034224 4.10e-06 2/2 biological_process: cellular response to zinc ion starvation b0296, b1973
GO:0010043 2.54e-05 2/5 biological_process: response to zinc ion b1859, b1858
GO:0008652 2.239e-29 26/100 biological_process: cellular amino acid biosynthetic process b3212, b2020, b2025, b0674, b2019, b3769, b1262, b3771, b2022, b0078, b0077, b1260, b3772, b1263, b3770, b4054, b2024, b3671, b2026, b1261, b3670, b3213, b1264, b2023, b3744, b2021
GO:0000105 0.0000000 8/9 biological_process: histidine biosynthetic process b2025, b2024, b2020, b2019, b2023, b2026, b2022, b2021
GO:0009099 0.0000000 8/11 biological_process: valine biosynthetic process b3770, b3670, b0078, b3671, b3769, b3572, b3771, b0077
GO:0009097 0.0000000 8/12 biological_process: isoleucine biosynthetic process b3772, b3770, b3670, b0078, b3671, b3769, b3771, b0077
GO:0000162 0.0000000 7/8 biological_process: tryptophan biosynthetic process b1260, b1263, b1261, b1264, b2024, b3360, b1262
GO:0009082 0.0000000 8/18 biological_process: branched-chain amino acid biosynthetic process b3772, b3770, b3670, b0078, b3671, b3769, b3771, b0077
GO:0003824 0.0000000 20/375 molecular_function: catalytic activity b3212, b2025, b0928, b1262, b3771, b3572, b2022, b0077, b1260, b3772, b1263, b3770, b2024, b3671, b2147, b2021, b2026, b1264, b4054, b2290
GO:0003984 0.0000000 5/5 molecular_function: acetolactate synthase activity b3670, b0078, b3671, b3769, b0077
GO:0009073 0.0000001 6/18 biological_process: aromatic amino acid family biosynthetic process b1260, b1263, b1261, b1264, b4054, b1262
GO:0008483 0.0000003 6/22 molecular_function: transaminase activity b3770, b0928, b2290, b4054, b3572, b2021
GO:0006537 0.0000009 4/6 biological_process: glutamate biosynthetic process b1761, b2878, b3213, b3212
GO:0006541 0.0000011 5/15 biological_process: glutamine metabolic process b1263, b3212, b0674, b2023, b3360
GO:0009058 0.0000017 7/48 biological_process: biosynthetic process b1812, b1264, b0928, b2021, b4054, b3572, b2290
GO:0030170 0.0000052 7/57 molecular_function: pyridoxal phosphate binding b3772, b1261, b0928, b2021, b4054, b3572, b2290
GO:0005948 0.0000167 3/4 cellular_component: acetolactate synthase complex b3670, b3671, b0077
GO:0006568 0.0000167 3/4 biological_process: tryptophan metabolic process b1260, b1261, b1262
GO:0006520 0.0000222 5/28 biological_process: cellular amino acid metabolic process b3772, b0928, b1761, b4054, b2957
GO:0016829 0.0000261 10/169 molecular_function: lyase activity b1260, b3772, b1263, b1261, b1264, b2025, b2023, b1262, b3771, b2022
GO:0051536 0.0000514 9/146 molecular_function: iron-sulfur cluster binding b2146, b2887, b3213, b3212, b2468, b2878, b2147, b3771, b2881
GO:1990610 0.0002772 2/2 molecular_function: acetolactate synthase regulator activity b3670, b0078
GO:0004071 0.0002772 2/2 molecular_function: aspartate-ammonia ligase activity b3744, b0674
GO:0070981 0.0002772 2/2 biological_process: L-asparagine biosynthetic process b3744, b0674
GO:0006529 0.0002772 2/2 biological_process: asparagine biosynthetic process b3744, b0674
GO:0033585 0.0002772 2/2 biological_process: L-phenylalanine biosynthetic process from chorismate via phenylpyruvate b4054, b0928
GO:0004838 0.0002772 2/2 molecular_function: L-tyrosine:2-oxoglutarate aminotransferase activity b4054, b0928
GO:0004834 0.0002772 2/2 molecular_function: tryptophan synthase activity b1260, b1261
GO:0004049 0.0002772 2/2 molecular_function: anthranilate synthase activity b1263, b1264
GO:0046820 0.0002772 2/2 molecular_function: 4-amino-4-deoxychorismate synthase activity b3360, b1812
GO:0000107 0.0002772 2/2 molecular_function: imidazoleglycerol-phosphate synthase activity b2023, b2025
GO:0009382 0.0002772 2/2 cellular_component: imidazoleglycerol-phosphate synthase complex b2023, b2025
GO:0004159 0.0002772 2/2 molecular_function: dihydrouracil dehydrogenase (NAD+) activity b2146, b2147
GO:0015930 0.0002772 2/2 molecular_function: glutamate synthase activity b2878, b3212
GO:0004355 0.0002772 2/2 molecular_function: glutamate synthase (NADPH) activity b3213, b3212
GO:0097054 0.0002772 2/2 biological_process: L-glutamate biosynthetic process b3213, b3212
GO:0006532 0.0002772 2/2 biological_process: aspartate biosynthetic process b4054, b3770
GO:0005737 0.0003371 21/848 cellular_component: cytoplasm b0852, b2025, b0928, b2020, b0674, b2946, b1761, b2019, b3572, b2022, b1260, b1812, b4054, b2024, b2147, b2947, b2026, b1261, b2023, b3744, b2290
GO:0019676 0.0006190 2/3 biological_process: ammonia assimilation cycle b2878, b3212
GO:0046872 0.0006419 18/692 molecular_function: metal ion binding b0852, b2887, b3213, b3212, b2879, b1264, b2020, b3671, b2468, b2881, b2878, b2147, b2019, b1813, b2947, b3771, b2022, b0077
GO:0016740 0.0007211 16/576 molecular_function: transferase activity b1263, b3770, b3670, b0078, b1812, b0928, b2946, b3671, b2290, b2019, b3769, b2021, b4054, b3360, b3572, b0077
GO:0043952 1.346e-11 6/7 biological_process: protein transport by the Sec complex b3609, b0409, b3175, b0098, b3981, b0408
GO:0006605 0.0000000 6/8 biological_process: protein targeting b3609, b3464, b0409, b0098, b3981, b0408
GO:0006886 0.0000000 5/6 biological_process: intracellular protein transport b0409, b3175, b0098, b3981, b0408
GO:0006072 0.0000000 5/6 biological_process: glycerol-3-phosphate metabolic process b3426, b2242, b3926, b3608, b2241
GO:0065002 0.0000000 5/9 biological_process: intracellular protein transmembrane transport b0409, b3175, b0098, b3981, b0408
GO:0019563 0.0000000 5/9 biological_process: glycerol catabolic process b3426, b2243, b2242, b3926, b2241
GO:0015031 0.0000000 8/67 biological_process: protein transport b3609, b3705, b0409, b0407, b3175, b0098, b3981, b0408
GO:0015450 0.0000000 4/4 molecular_function: P-P-bond-hydrolysis-driven protein transmembrane transporter activity b3175, b3981, b0408, b0409
GO:0046168 0.0000000 4/4 biological_process: glycerol-3-phosphate catabolic process b2242, b2241, b3426, b3608
GO:0009331 0.0000000 4/4 cellular_component: glycerol-3-phosphate dehydrogenase complex b2242, b2241, b3426, b3608
GO:0031522 0.0000001 4/5 cellular_component: cell envelope Sec protein transport complex b3175, b0098, b3981, b3705
GO:0052591 0.0000015 3/3 molecular_function: sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity b2242, b2241, b3426
GO:0052590 0.0000015 3/3 molecular_function: sn-glycerol-3-phosphate:ubiquinone oxidoreductase activity b2242, b2241, b3426
GO:0004368 0.0000015 3/3 molecular_function: glycerol-3-phosphate dehydrogenase (quinone) activity b2242, b2241, b3426
GO:0006071 0.0000025 4/13 biological_process: glycerol metabolic process b3926, b2240, b3426, b2239
GO:0002099 0.0001019 2/2 biological_process: tRNA wobble guanine modification b0405, b0406
GO:0015793 0.0001019 2/2 biological_process: glycerol transport b3927, b2240
GO:0006614 0.0001019 2/2 biological_process: SRP-dependent cotranslational protein targeting to membrane b2610, b3464
GO:0006612 0.0001019 2/2 biological_process: protein targeting to membrane b2610, b3464
GO:0032977 0.0001019 2/2 molecular_function: membrane insertase activity b4557, b3705
GO:0070678 0.0002282 2/3 molecular_function: preprotein binding b3609, b0098
GO:0006616 0.0002282 2/3 biological_process: SRP-dependent cotranslational protein targeting to membrane, translocation b3175, b3981
GO:0032978 0.0004039 2/4 biological_process: protein insertion into membrane from inner side b3175, b3981
GO:0010124 1.689e-21 12/15 biological_process: phenylacetate catabolic process b1388, b1395, b1397, b1393, b1392, b1391, b1390, b1398, b1394, b1389, b3845, b1396
GO:0006635 0.0000000 8/15 biological_process: fatty acid beta-oxidation b0221, b1397, b1393, b2341, b1394, b3845, b2342, b3846
GO:0004300 0.0000000 5/7 molecular_function: enoyl-CoA hydratase activity b1393, b2341, b1394, b2342, b3846
GO:0006631 0.0000000 7/32 biological_process: fatty acid metabolic process b1395, b0221, b1393, b2341, b3845, b2342, b3846
GO:0003857 0.0000000 4/4 molecular_function: 3-hydroxyacyl-CoA dehydrogenase activity b2341, b2342, b3846, b1395
GO:0016042 0.0000020 4/11 biological_process: lipid catabolic process b2341, b3845, b2342, b3846
GO:0047780 0.0000021 3/3 molecular_function: citrate dehydratase activity b1276, b0334, b0118
GO:0006099 0.0000036 5/29 biological_process: tricarboxylic acid cycle b0334, b0118, b0720, b1276, b0333
GO:0003994 0.0000050 3/4 molecular_function: aconitate hydratase activity b1276, b0334, b0118
GO:0003988 0.0000097 3/5 molecular_function: acetyl-CoA C-acyltransferase activity b1397, b3845, b2342
GO:0071705 0.0000110 4/17 biological_process: nitrogen compound transport b2308, b2307, b2310, b2309
GO:0006629 0.0000251 6/74 biological_process: lipid metabolic process b0221, b1393, b2341, b3845, b2342, b3846
GO:0004108 0.0001252 2/2 molecular_function: citrate (Si)-synthase activity b0720, b0333
GO:0050218 0.0001252 2/2 molecular_function: propionate-CoA ligase activity b0335, b4069
GO:0005291 0.0001252 2/2 molecular_function: high-affinity L-histidine transmembrane transporter activity b2308, b2306
GO:1903810 0.0001252 2/2 biological_process: L-histidine import across plasma membrane b2308, b2306
GO:0089709 0.0001252 2/2 biological_process: L-histidine transmembrane transport b2308, b2306
GO:0016509 0.0001252 2/2 molecular_function: long-chain-3-hydroxyacyl-CoA dehydrogenase activity b2341, b3846
GO:0008692 0.0001252 2/2 molecular_function: 3-hydroxybutyryl-CoA epimerase activity b2341, b3846
GO:0046912 0.0002803 2/3 molecular_function: transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer b0720, b0333
GO:0003730 0.0002803 2/3 molecular_function: mRNA 3’-UTR binding b1276, b0118
GO:0019679 0.0002803 2/3 biological_process: propionate metabolic process, methylcitrate cycle b0334, b0333
GO:0016829 0.0003327 7/169 molecular_function: lyase activity b0334, b0118, b1393, b1276, b2341, b1394, b3846
GO:0019629 0.0004958 2/4 biological_process: propionate catabolic process, 2-methylcitrate cycle b0335, b0118
GO:0046336 5.274e-15 6/16 biological_process: ethanolamine catabolic process b2458, b2457, b2460, b2461, b2459, b2462
GO:0031471 1.63e-05 2/4 cellular_component: ethanolamine degradation polyhedral organelle b2457, b2462
GO:0043165 3.622e-14 11/13 biological_process: Gram-negative-bacterium-type cell outer membrane assembly b0177, b2512, b0054, b0641, b0053, b2595, b3200, b2477, b2617, b3199, b0178
GO:0004812 0.0000000 12/25 molecular_function: aminoacyl-tRNA ligase activity b4129, b1713, b2514, b0026, b0526, b2400, b2890, b1714, b1876, b0642, b2697, b1719
GO:1990351 0.0000000 7/7 cellular_component: transporter complex b4261, b3201, b0054, b0641, b3200, b3199, b4262
GO:0016874 0.0000000 16/94 molecular_function: ligase activity b4129, b2780, b1713, b2514, b0026, b0526, b3421, b2400, b2890, b1714, b1876, b2507, b4475, b0642, b2697, b1719
GO:0015920 0.0000000 7/9 biological_process: lipopolysaccharide transport b4261, b3201, b0054, b0641, b3200, b3199, b4262
GO:0006418 0.0000000 8/18 biological_process: tRNA aminoacylation for protein translation b4129, b0026, b0526, b2400, b2890, b1876, b0642, b1719
GO:0000049 0.0000000 11/46 molecular_function: tRNA binding b4129, b1713, b3166, b0026, b2400, b2890, b1714, b2474, b3282, b2697, b1719
GO:0006412 0.0000001 15/107 biological_process: translation b4129, b1713, b2514, b0026, b3288, b0526, b2400, b2891, b2890, b1714, b3287, b1876, b0642, b2697, b1719
GO:1990063 0.0000002 5/5 cellular_component: Bam protein complex b0177, b2512, b2595, b2477, b2617
GO:0051205 0.0000010 5/7 biological_process: protein insertion into membrane b0177, b2512, b2595, b2477, b2617
GO:0005829 0.0000044 46/1032 cellular_component: cytosol b0174, b1712, b0051, b3166, b3179, b0469, b3288, b2891, b2508, b3287, b2507, b2697, b3198, b0125, b0912, b4129, b0179, b3281, b0026, b0526, b2959, b1714, b3289, b0178, b2594, b0121, b2593, b1713, b2514, b2400, b2478, b0120, b1876, b1778, b3282, b3180, b0642, b1719, b0238, b3290, b2780, b3167, b0104, b2890, b3203, b0844
GO:0043039 0.0000297 4/7 biological_process: tRNA aminoacylation b2400, b1714, b2697, b1719
GO:0006364 0.0000532 7/39 biological_process: rRNA processing b3167, b0051, b3179, b3289, b1835, b2594, b3282
GO:0002161 0.0000782 4/9 molecular_function: aminoacyl-tRNA editing activity b1719, b0642, b2697, b0026
GO:0106074 0.0000782 4/9 biological_process: aminoacyl-tRNA metabolism involved in translational fidelity b1719, b0642, b2697, b0026
GO:0044877 0.0001417 3/4 molecular_function: protein-containing complex binding b2782, b2513, b2783
GO:0001530 0.0001417 3/4 molecular_function: lipopolysaccharide binding b0178, b3200, b0641
GO:0015437 0.0001417 3/4 molecular_function: lipopolysaccharide-transporting ATPase activity b3201, b4262, b4261
GO:0000166 0.0002194 26/517 molecular_function: nucleotide binding b2781, b3421, b2508, b2507, b2697, b0125, b4129, b3281, b0026, b0526, b1714, b1713, b3201, b2514, b2400, b0639, b1804, b1876, b3282, b4475, b0642, b1719, b2780, b2890, b2474, b0025
GO:0005737 0.0002831 36/848 cellular_component: cytoplasm b0174, b1712, b0051, b3179, b0469, b2891, b2697, b0125, b0912, b4129, b0179, b0026, b0526, b1714, b3289, b0121, b0052, b1713, b3201, b2514, b2400, b2478, b1804, b0638, b1876, b1778, b3282, b3180, b4475, b0642, b1719, b2780, b3167, b2890, b1835, b2474
GO:0006417 0.0003993 5/25 biological_process: regulation of translation b0912, b1712, b3203, b2782, b1719
GO:0001510 0.0004615 3/6 biological_process: RNA methylation b3179, b3289, b1835
GO:0006260 5.281e-23 22/47 biological_process: DNA replication b3935, b3700, b1099, b0924, b0215, b3701, b0923, b0184, b2496, b2675, b0640, b2676, b3702, b0922, b3066, b4052, b2235, b4259, b4372, b2234, b3863, b0470
GO:0006633 0.0000000 14/19 biological_process: fatty acid biosynthetic process b1090, b0954, b0180, b3255, b2316, b1288, b1092, b1091, b1095, b2563, b2323, b1093, b3256, b0185
GO:0003887 0.0000000 12/14 molecular_function: DNA-directed DNA polymerase activity b0184, b1184, b4259, b1099, b0640, b4372, b0060, b0215, b1183, b3701, b3863, b0470
GO:0006629 0.0000000 17/74 biological_process: lipid metabolic process b0736, b1090, b0954, b0180, b3255, b2316, b0182, b1288, b1092, b1091, b1095, b0181, b2563, b2323, b1093, b3256, b0185
GO:0071897 0.0000000 9/11 biological_process: DNA biosynthetic process b0184, b4259, b1099, b0640, b4372, b0060, b0215, b3863, b0470
GO:0006631 0.0000000 12/32 biological_process: fatty acid metabolic process b0954, b3255, b2316, b1288, b1092, b1091, b1095, b2563, b2323, b1093, b3256, b0185
GO:0016779 0.0000000 13/47 molecular_function: nucleotidyltransferase activity b0184, b3053, b4259, b1099, b0640, b4372, b0060, b0215, b3052, b3701, b3863, b0470, b3066
GO:0006261 0.0000000 8/14 biological_process: DNA-dependent DNA replication b3935, b1099, b0640, b0060, b3699, b2231, b3863, b0470
GO:0005515 0.0000000 50/1066 molecular_function: protein binding b3935, b2580, b3700, b1099, b0924, b0215, b2567, b3701, b0214, b2674, b0923, b0184, b0736, b3255, b0741, b2496, b0948, b2553, b1183, b0737, b1288, b0471, b1097, b0949, b0738, b1184, b0640, b2316, b2676, b3639, b3702, b0922, b3256, b2566, b3066, b4052, b0182, b1100, b4259, b2235, b4372, b3699, b2231, b0739, b1095, b2234, b0470, b0742, b0185, b0740
GO:0005737 0.0000000 44/848 cellular_component: cytoplasm b2580, b3700, b0924, b2315, b0181, b2567, b3701, b0214, b4258, b0923, b2236, b0184, b1090, b3255, b0948, b0471, b1091, b2563, b2323, b2675, b0949, b0954, b0180, b2316, b2676, b4373, b1098, b2827, b3702, b0922, b3256, b2566, b0183, b3066, b0182, b2235, b2949, b3699, b3640, b2231, b3863, b4374, b0185, b2564
GO:0008408 0.0000005 6/13 molecular_function: 3’-5’ exonuclease activity b0184, b1099, b4372, b0215, b3701, b3863
GO:0008610 0.0000011 5/8 biological_process: lipid biosynthetic process b0954, b1288, b0181, b2323, b1093
GO:0009360 0.0000022 4/4 cellular_component: DNA polymerase III complex b1099, b0470, b0640, b3701
GO:0003989 0.0000022 4/4 molecular_function: acetyl-CoA carboxylase activity b3255, b2316, b3256, b0185
GO:0005971 0.0000022 4/4 cellular_component: ribonucleoside-diphosphate reductase complex b2235, b2676, b2675, b2234
GO:0007049 0.0000025 10/67 biological_process: cell cycle b2314, b0738, b0741, b0924, b0737, b0739, b0742, b0922, b0923, b0740
GO:0016740 0.0000031 30/576 molecular_function: transferase activity b3053, b1099, b0215, b3052, b0181, b3701, b0184, b1090, b0948, b1092, b1091, b2828, b2563, b2323, b0640, b2316, b0060, b4373, b1098, b2827, b3066, b0921, b0182, b4259, b4372, b1095, b3863, b0470, b0185, b2564
GO:0090305 0.0000053 10/73 biological_process: nucleic acid phosphodiester bond hydrolysis b0184, b1099, b4372, b0060, b0215, b2949, b2567, b3701, b3863, b0183
GO:0051301 0.0000053 10/73 biological_process: cell division b2314, b0738, b0741, b0924, b0737, b0739, b0742, b0922, b0923, b0740
GO:0009263 0.0000110 4/6 biological_process: deoxyribonucleotide biosynthetic process b2675, b2676, b2235, b2234
GO:0004748 0.0000110 4/6 molecular_function: ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor b2675, b2676, b2235, b2234
GO:0009314 0.0000165 8/50 biological_process: response to radiation b2565, b3700, b4259, b4372, b0472, b0471, b2827, b0949
GO:2001295 0.0000451 3/3 biological_process: malonyl-CoA biosynthetic process b2316, b3256, b0185
GO:0009317 0.0000451 3/3 cellular_component: acetyl-CoA carboxylase complex b3255, b2316, b0185
GO:0004315 0.0000451 3/3 molecular_function: 3-oxoacyl-[acyl-carrier-protein] synthase activity b2323, b1091, b1095
GO:0043213 0.0000528 4/9 biological_process: bacteriocin transport b0739, b0737, b0738, b0740
GO:0008094 0.0000528 4/9 molecular_function: DNA-dependent ATPase activity b1183, b2231, b3699, b1184
GO:0005829 0.0000559 40/1032 cellular_component: cytosol b3053, b3700, b0924, b0215, b3052, b0181, b2567, b3701, b4258, b0184, b3255, b2496, b2553, b1288, b0471, b1092, b1091, b2323, b0954, b2316, b1098, b2948, b3639, b1096, b2827, b3702, b3256, b2566, b4052, b1100, b2235, b3699, b3640, b2231, b1095, b2234, b3863, b1093, b0185, b2564
GO:0006281 0.0000738 9/80 biological_process: DNA repair b2565, b2580, b3700, b1184, b0060, b0472, b1183, b3863, b0949
GO:0032153 0.0000840 6/32 cellular_component: cell division site b2314, b0738, b0741, b0737, b0739, b0740
GO:0000166 0.0000990 25/517 molecular_function: nucleotide binding b3935, b3053, b3700, b0924, b3052, b2315, b2567, b4258, b2496, b2553, b2675, b0949, b2316, b0060, b1098, b3702, b3256, b2566, b4052, b3699, b2231, b2234, b0470, b4374, b0185
GO:0005524 0.0001900 22/441 molecular_function: ATP binding b3935, b3053, b3700, b0924, b3052, b2315, b2567, b4258, b2553, b2675, b0949, b2316, b1098, b3702, b0955, b3256, b4052, b3699, b2231, b2234, b0470, b0185
GO:0017038 0.0002021 3/5 biological_process: protein import b0739, b0737, b0740
GO:0006270 0.0002021 3/5 biological_process: DNA replication initiation b2496, b3935, b3702
GO:0030261 0.0003436 3/6 biological_process: chromosome condensation b0922, b0924, b0923
GO:0009295 0.0004687 4/16 cellular_component: nucleoid b0471, b0922, b0924, b0923
GO:1990077 0.0005371 3/7 cellular_component: primosome complex b3935, b3066, b4052
GO:0006269 0.0005371 3/7 biological_process: DNA replication, synthesis of RNA primer b3935, b3066, b4052
GO:0003676 0.0008279 8/89 molecular_function: nucleic acid binding b0184, b3863, b3935, b0060, b0948, b0215, b0214, b0183
GO:0015949 0.0008863 4/19 biological_process: nucleobase-containing small molecule interconversion b1098, b2675, b2235, b2234
GO:0008693 0.0009434 2/2 molecular_function: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity b0954, b0180
GO:0019171 0.0009434 2/2 molecular_function: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity b0954, b0180
GO:0004317 0.0009434 2/2 molecular_function: 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity b0954, b0180
GO:0008659 0.0009434 2/2 molecular_function: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity b0954, b0180
GO:0047451 0.0009434 2/2 molecular_function: 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity b0954, b0180
GO:0004523 0.0009434 2/2 molecular_function: RNA-DNA hybrid ribonuclease activity b0214, b0183
GO:0043137 0.0009434 2/2 biological_process: DNA replication, removal of RNA primer b0214, b0183
GO:0009329 0.0009434 2/2 cellular_component: acetate CoA-transferase complex b2316, b0185
GO:0042759 0.0009434 2/2 biological_process: long-chain fatty acid biosynthetic process b2316, b0185
GO:0071237 0.0009434 2/2 biological_process: cellular response to bacteriocin b0739, b0740
GO:0009355 0.0009434 2/2 cellular_component: DNA polymerase V complex b1183, b1184
GO:0034335 0.0009434 2/2 molecular_function: DNA supercoiling activity b2231, b3699
GO:0003677 0.0009708 22/496 molecular_function: DNA binding b3935, b3700, b1099, b0924, b0215, b3701, b0184, b1183, b0471, b0949, b0640, b2316, b0060, b3702, b3066, b4052, b4259, b3699, b0472, b2231, b3863, b0470
GO:0006302 0.0011060 3/9 biological_process: double-strand break repair b2565, b3935, b3700
GO:0051539 3.005e-06 5/117 molecular_function: 4 iron, 4 sulfur cluster binding b2719, b4079, b2721, b2720, b2724
GO:0008137 7.2e-06 3/17 molecular_function: NADH dehydrogenase (ubiquinone) activity b2719, b2723, b2721
GO:0055114 8.6e-06 7/448 biological_process: oxidation-reduction process b2719, b4079, b2721, b2722, b2720, b2724, b2723
GO:0051536 8.9e-06 5/146 molecular_function: iron-sulfur cluster binding b2719, b4079, b2721, b2720, b2724
GO:0051604 6.661e-15 8/16 biological_process: protein maturation b2990, b2727, b2730, b2728, b2726, b2729, b2991, b2992
GO:0033748 0.0000000 5/6 molecular_function: hydrogenase (acceptor) activity b0972, b2994, b0973, b2995, b2997
GO:0008901 0.0000000 4/4 molecular_function: ferredoxin hydrogenase activity b0972, b2997, b2994, b0973
GO:0044569 0.0000000 5/13 cellular_component: [Ni-Fe] hydrogenase complex b0972, b2995, b0973, b2997, b0974
GO:0016151 0.0000000 5/18 molecular_function: nickel cation binding b2727, b2994, b0973, b2726, b2991
GO:0006464 0.0000000 5/20 biological_process: cellular protein modification process b2993, b0975, b2726, b2729, b2991
GO:0046872 0.0000019 13/692 molecular_function: metal ion binding b2727, b2993, b0972, b0975, b2994, b2996, b2995, b0973, b2997, b0974, b2726, b2729, b2991
GO:0009061 0.0000034 5/49 biological_process: anaerobic respiration b0972, b0973, b2995, b2997, b0974
GO:0006113 0.0000086 3/8 biological_process: fermentation b0972, b0974, b0973
GO:0009375 0.0000462 2/2 cellular_component: ferredoxin hydrogenase complex b0972, b2997
GO:1902670 0.0000462 2/2 molecular_function: carbon dioxide binding b2728, b2990
GO:0031236 0.0001037 2/3 cellular_component: extrinsic component of periplasmic side of plasma membrane b2997, b2994
GO:0005506 0.0001380 4/55 molecular_function: iron ion binding b2729, b0974, b2728, b2990
GO:0016485 0.0002864 2/5 biological_process: protein processing b0975, b2993
GO:0019698 9.925e-07 3/7 biological_process: D-galacturonate catabolic process b3091, b3092, b3128
GO:0006412 2.463e-79 66/107 biological_process: translation b3980, b3637, b1716, b3168, b3304, b3313, b3170, b3185, b3590, b3230, b2609, b3294, b1718, b3319, b0170, b3984, b4200, b1717, b3591, b2606, b3303, b3296, b0169, b3310, b3321, b2185, b4506, b3312, b3340, b3307, b4202, b3342, b3703, b0884, b3301, b3231, b3983, b3315, b3186, b3936, b3302, b3317, b1089, b3065, b3314, b4147, b0023, b0911, b3636, b3339, b3309, b3320, b4203, b3297, b3986, b3311, b3298, b3305, b3165, b3318, b3308, b3341, b3316, b3299, b3306, b3985
GO:0005840 0.0000000 56/61 cellular_component: ribosome b3637, b1716, b3304, b3313, b3185, b2609, b3230, b3294, b3319, b3984, b1717, b4200, b2606, b3303, b3296, b0169, b3310, b3321, b2185, b3312, b4506, b3307, b3342, b3703, b4202, b3301, b3231, b3315, b3983, b3186, b3936, b3302, b1089, b3065, b3317, b3314, b0023, b0911, b3309, b3320, b3636, b4203, b3297, b3986, b3298, b3311, b3305, b3165, b3308, b3318, b3341, b3316, b3299, b3306, b3985, b2608
GO:0003735 0.0000000 55/58 molecular_function: structural constituent of ribosome b3637, b1716, b3304, b3313, b3185, b2609, b3230, b3294, b3319, b3984, b1717, b4200, b2606, b3303, b3296, b0169, b3310, b3321, b2185, b3312, b4506, b3307, b3342, b3703, b4202, b3301, b3231, b3315, b3983, b3186, b3936, b3302, b1089, b3065, b3317, b3314, b0023, b0911, b3309, b3320, b3636, b4203, b3297, b3986, b3298, b3311, b3305, b3165, b3308, b3318, b3341, b3316, b3299, b3306, b3985
GO:0019843 0.0000000 44/59 molecular_function: rRNA binding b3637, b1716, b3304, b3313, b3185, b3319, b2597, b3984, b4200, b2606, b3871, b3303, b3296, b3310, b2185, b3312, b3307, b3342, b0884, b4202, b3301, b3315, b3983, b3186, b3936, b3065, b3317, b3314, b0023, b3309, b3320, b4203, b3297, b3298, b3311, b3305, b3165, b3308, b3318, b3341, b3316, b3306, b3985, b2608
GO:0003723 0.0000000 54/161 molecular_function: RNA binding b3980, b3637, b1716, b3304, b3313, b3185, b3590, b3230, b1718, b3319, b2597, b4200, b3984, b3704, b2606, b3871, b3303, b3296, b3310, b3260, b3321, b2185, b3312, b4202, b3342, b0884, b3301, b3315, b3983, b3186, b3936, b3317, b3065, b3314, b0023, b0911, b3636, b3339, b3309, b3320, b4203, b3297, b3311, b3298, b3305, b3169, b3165, b3318, b3308, b3341, b3316, b3306, b3985, b2608
GO:0022625 0.0000000 32/32 cellular_component: cytosolic large ribosomal subunit b3637, b1716, b3304, b3313, b3185, b3294, b3319, b3984, b1717, b2606, b3310, b2185, b3312, b3301, b3231, b3315, b3983, b3186, b3936, b3302, b1089, b3317, b3309, b3320, b3636, b4203, b3986, b3305, b3308, b3318, b3299, b3985
GO:0022627 0.0000000 22/25 cellular_component: cytosolic small ribosomal subunit b3230, b2609, b2597, b4200, b3296, b3303, b0169, b3321, b3307, b3342, b4202, b3065, b3314, b0023, b0911, b3297, b3298, b3311, b3341, b3316, b3306, b3165
GO:0000027 0.0000000 19/28 biological_process: ribosomal large subunit assembly b3637, b1716, b3313, b3185, b3294, b3984, b2606, b2185, b3312, b3983, b3302, b1089, b3317, b3636, b3309, b3320, b3305, b3308, b3318
GO:0000028 0.0000000 17/20 biological_process: ribosomal small subunit assembly b3297, b3170, b3311, b3296, b3065, b2609, b3316, b3314, b3165, b3306, b3307, b0023, b3341, b3303, b0911, b0169, b2608
GO:0005829 0.0000000 68/1032 cellular_component: cytosol b3980, b3637, b1716, b3168, b3304, b2608, b3170, b1088, b3590, b3230, b1718, b3294, b3319, b0170, b0910, b2597, b4200, b3984, b3591, b2606, b3303, b3296, b3310, b3321, b2185, b3261, b3340, b4202, b3342, b0436, b0884, b3231, b3983, b3315, b3067, b3186, b3936, b1274, b3317, b1089, b3065, b2171, b3295, b3314, b4147, b0023, b0171, b3636, b3309, b3320, b4203, b3297, b4059, b3986, b3357, b3298, b3305, b3169, b3165, b3987, b0474, b3308, b3988, b3341, b3316, b3306, b3985, b2607
GO:0015934 0.0000000 14/14 cellular_component: large ribosomal subunit b3315, b3310, b3983, b3302, b3986, b1089, b3317, b3294, b3319, b3301, b3984, b1717, b3636, b3985
GO:0015935 0.0000000 12/12 cellular_component: small ribosomal subunit b3321, b3298, b3296, b2609, b3230, b3316, b3307, b3342, b0023, b3341, b3303, b0169
GO:0000049 0.0000000 15/46 molecular_function: tRNA binding b3260, b3321, b3341, b3313, b3298, b3185, b3590, b3230, b3308, b3704, b3984, b3342, b3871, b3316, b3636
GO:0070180 0.0000000 9/9 molecular_function: large ribosomal subunit rRNA binding b1716, b3310, b3231, b3983, b4203, b3305, b3309, b2606, b3985
GO:0003746 0.0000000 7/8 molecular_function: translation elongation factor activity b3980, b3590, b2171, b4147, b3340, b0170, b3339
GO:0043022 0.0000000 10/28 molecular_function: ribosome binding b3986, b1203, b3185, b1718, b4147, b2597, b0436, b0884, b3985, b2608
GO:0005515 0.0000000 54/1066 molecular_function: protein binding b3980, b3637, b3168, b3170, b3185, b3590, b1718, b3319, b2597, b3984, b4200, b3591, b3871, b3303, b3296, b3732, b0169, b4201, b3310, b3321, b1203, b3261, b3300, b4202, b3342, b0436, b0884, b3301, b3315, b3983, b3067, b1274, b3317, b1089, b3295, b3309, b3339, b3320, b3734, b4203, b3297, b4059, b3986, b3357, b3298, b3169, b3318, b3987, b0474, b3988, b3341, b0170, b3985, b2608
GO:0070181 0.0000000 6/7 molecular_function: small ribosomal subunit rRNA binding b3297, b3311, b4202, b4200, b0023, b3165
GO:0006414 0.0000000 6/7 biological_process: translational elongation b3980, b2171, b4147, b3340, b0170, b3339
GO:0003924 0.0000003 8/26 molecular_function: GTPase activity b3980, b3168, b3986, b3590, b3340, b3871, b3985, b3339
GO:0017148 0.0000016 6/14 biological_process: negative regulation of translation b1716, b3231, b2185, b3319, b3341, b3985
GO:0006417 0.0000033 7/25 biological_process: regulation of translation b3319, b3165, b2597, b3984, b3296, b3306, b3985
GO:0046677 0.0000080 12/101 biological_process: response to antibiotic b3980, b3315, b3311, b3296, b3305, b3319, b3987, b3342, b3988, b3303, b3636, b3339
GO:0006413 0.0000170 4/6 biological_process: translational initiation b1718, b3168, b3936, b0884
GO:0048027 0.0000170 4/6 molecular_function: mRNA 5’-UTR binding b4202, b3296, b4200, b3297
GO:0003729 0.0000201 5/13 molecular_function: mRNA binding b1716, b3231, b3314, b3341, b0911
GO:0046961 0.0000518 4/8 molecular_function: proton-transporting ATPase activity, rotational mechanism b3734, b3736, b3735, b3732
GO:0008097 0.0000628 3/3 molecular_function: 5S rRNA binding b3304, b3308, b2185
GO:1990145 0.0000628 3/3 biological_process: maintenance of translational fidelity b3303, b3296, b3342
GO:0006754 0.0000814 4/9 biological_process: ATP biosynthetic process b3734, b3736, b3735, b3732
GO:0046933 0.0000814 4/9 molecular_function: proton-transporting ATP synthase activity, rotational mechanism b3734, b3736, b3735, b3732
GO:0015986 0.0000814 4/9 biological_process: ATP synthesis coupled proton transport b3734, b3736, b3735, b3732
GO:0042254 0.0001194 5/19 biological_process: ribosome biogenesis b3170, b1088, b3871, b3985, b2608
GO:0003743 0.0001462 3/4 molecular_function: translation initiation factor activity b0884, b3168, b1718
GO:0046940 0.0002804 3/5 biological_process: nucleoside monophosphate phosphorylation b0910, b0474, b0171
GO:0006353 0.0004760 3/6 biological_process: DNA-templated transcription, termination b3319, b3296, b3169
GO:0045261 0.0004760 3/6 cellular_component: proton-transporting ATP synthase complex, catalytic core F(1) b3734, b3735, b3732
GO:0005525 0.0006265 7/58 molecular_function: GTP binding b3980, b3168, b1203, b3590, b3340, b3871, b3339
GO:0045947 0.0007425 3/7 biological_process: negative regulation of translational initiation b3296, b2597, b3984
GO:0003899 0.0007425 3/7 molecular_function: DNA-directed 5’-3’ RNA polymerase activity b3988, b3987, b3295
GO:0009242 1.361e-21 11/19 biological_process: colanic acid biosynthetic process b2061, b2059, b2054, b2058, b2049, b2060, b2057, b2053, b2052, b2050, b2055
GO:0009103 0.0000000 11/72 biological_process: lipopolysaccharide biosynthetic process b2059, b2048, b2056, b2054, b2051, b2058, b2049, b2060, b2057, b2050, b2055
GO:0045228 0.0000000 7/10 biological_process: slime layer polysaccharide biosynthetic process b2059, b2056, b2054, b2058, b2057, b2050, b2055
GO:0000271 0.0000002 4/11 biological_process: polysaccharide biosynthetic process b2049, b2061, b2062, b2060
GO:0004615 0.0000414 2/2 molecular_function: phosphomannomutase activity b3176, b2048
GO:0042351 0.0000414 2/2 biological_process: ‘de novo’ GDP-L-fucose biosynthetic process b2053, b2052
GO:0071704 0.0000928 2/3 biological_process: organic substance metabolic process b3176, b2048
GO:0016413 0.0000928 2/3 molecular_function: O-acetyltransferase activity b2058, b2054
GO:0046377 0.0000928 2/3 biological_process: colanic acid metabolic process b2062, b2056
GO:0009298 0.0000928 2/3 biological_process: GDP-mannose biosynthetic process b2049, b2048
GO:0036065 0.0001646 2/4 biological_process: fucosylation b2050, b2055
GO:0070401 0.0002565 2/5 molecular_function: NADP+ binding b2053, b2052
GO:0015627 8.905e-23 10/12 cellular_component: type II protein secretion system complex b3326, b3333, b3331, b3325, b3324, b3329, b3328, b3334, b3327, b3330
GO:0015628 0.00e+00 10/14 biological_process: protein secretion by the type II secretion system b3326, b3333, b3331, b3325, b3324, b3329, b3328, b3334, b3327, b3330
GO:0015031 0.00e+00 11/67 biological_process: protein transport b3326, b3333, b3331, b3325, b3324, b3332, b3329, b3328, b3334, b3327, b3330
GO:0016021 2.00e-07 13/966 cellular_component: integral component of membrane b3333, b3331, b3325, b3324, b3332, b3322, b3329, b3328, b3335, b3334, b3327, b3323, b3330
GO:0016020 3.00e-07 14/1299 cellular_component: membrane b3326, b3333, b3331, b3325, b3324, b3332, b3322, b3329, b3328, b3335, b3334, b3327, b3323, b3330
GO:0005886 1.40e-06 13/1139 cellular_component: plasma membrane b3326, b3333, b3331, b3324, b3332, b3322, b3329, b3328, b3335, b3334, b3327, b3323, b3330
GO:0009306 1.38e-05 3/13 biological_process: protein secretion b3332, b3327, b3325
GO:0015976 1.941e-13 5/11 biological_process: carbon utilization b3394, b3395, b3392, b3393, b3391
GO:0006308 0 5/11 biological_process: DNA catabolic process b3394, b3395, b3392, b3393, b3391
GO:0009246 2.322e-22 11/13 biological_process: enterobacterial common antigen biosynthetic process b3791, b3786, b3788, b3787, b3785, b3789, b3793, b3790, b3784, b3794, b3792
GO:0009103 0.0000000 13/72 biological_process: lipopolysaccharide biosynthetic process b2034, b2039, b2033, b2036, b2032, b3788, b3785, b2035, b2038, b2041, b2040, b3784, b2037
GO:0009243 0.0000000 6/6 biological_process: O antigen biosynthetic process b2039, b2038, b2041, b2040, b3784, b2037
GO:0045226 0.0000000 6/12 biological_process: extracellular polysaccharide biosynthetic process b3788, b2038, b3789, b2041, b2040, b2039
GO:0019305 0.0000000 4/4 biological_process: dTDP-rhamnose biosynthetic process b2038, b2041, b2039, b2040
GO:0000271 0.0000302 3/11 biological_process: polysaccharide biosynthetic process b3787, b3791, b3789
GO:0008879 0.0000567 2/2 molecular_function: glucose-1-phosphate thymidylyltransferase activity b3789, b2039
GO:0008460 0.0000567 2/2 molecular_function: dTDP-glucose 4,6-dehydratase activity b3788, b2041
GO:0009225 0.0001272 2/3 biological_process: nucleotide-sugar metabolic process b3788, b2041
GO:0048476 2.422e-10 5/5 cellular_component: Holliday junction resolvase complex b1860, b1861, b3811, b2894, b1863
GO:0006310 0.0000000 9/107 biological_process: DNA recombination b0962, b1860, b3652, b2892, b1861, b3822, b3811, b2894, b1863
GO:0004386 0.0000000 6/28 molecular_function: helicase activity b3652, b0962, b1860, b1861, b3822, b3162
GO:0003678 0.0000001 5/15 molecular_function: DNA helicase activity b3652, b0962, b1860, b1861, b3822
GO:0032508 0.0000001 5/16 biological_process: DNA duplex unwinding b3652, b0962, b1860, b1861, b3822
GO:0000725 0.0000007 4/10 biological_process: recombinational repair b1863, b1861, b0962, b1860
GO:0006281 0.0000008 7/80 biological_process: DNA repair b3652, b2892, b0962, b1860, b1861, b3822, b1863
GO:0009378 0.0000012 3/3 molecular_function: four-way junction helicase activity b3822, b1861, b1860
GO:0009314 0.0000197 5/50 biological_process: response to radiation b3652, b1861, b3162, b1863, b2894
GO:0003676 0.0000241 6/89 molecular_function: nucleic acid binding b2892, b3652, b3822, b3162, b1866, b1863
GO:0016787 0.0000242 12/477 molecular_function: hydrolase activity b0962, b1860, b3650, b3652, b2892, b1861, b3822, b3162, b1865, b3183, b1863, b3812
GO:0046688 0.0000755 3/12 biological_process: response to copper ion b4137, b4136, b2893
GO:0009379 0.0000877 2/2 cellular_component: Holliday junction helicase complex b1861, b3652
GO:0009037 0.0000877 2/2 molecular_function: tyrosine-based site-specific recombinase activity b3811, b2894
GO:0071139 0.0000877 2/2 biological_process: resolution of recombination intermediates b3811, b2894
GO:0007059 0.0001188 3/14 biological_process: chromosome segregation b3183, b3811, b2894
GO:0009009 0.0001964 2/3 molecular_function: site-specific recombinase activity b3811, b2894
GO:0003677 0.0002000 11/496 molecular_function: DNA binding b0962, b1860, b3652, b3183, b4135, b1861, b1864, b3822, b3649, b3811, b2894
GO:0005737 0.0004117 14/848 cellular_component: cytoplasm b1863, b1860, b3650, b3183, b4137, b1861, b1864, b3822, b3162, b1866, b3648, b3811, b2894, b3809
GO:0009408 1.429e-17 16/55 biological_process: response to heat b0437, b3686, b4142, b0015, b0014, b2592, b0439, b3932, b3400, b0473, b2614, b3401, b4143, b0881, b3931, b3687
GO:0009086 0.0000000 10/15 biological_process: methionine biosynthetic process b3829, b0260, b4013, b3940, b3433, b4019, b3939, b0261, b3941, b3828
GO:0051082 0.0000000 10/21 molecular_function: unfolded protein binding b4142, b0015, b0014, b0438, b0473, b2614, b3401, b4143, b0492, b1000
GO:0008652 0.0000000 14/100 biological_process: cellular amino acid biosynthetic process b3940, b2319, b4013, b3829, b4024, b3433, b4019, b3939, b0004, b0002, b0261, b0003, b3941, b3828
GO:0006457 0.0000000 9/26 biological_process: protein folding b4142, b0015, b0014, b0438, b0473, b2614, b3401, b4143, b1000
GO:0042026 0.0000000 6/9 biological_process: protein refolding b0015, b2592, b4143, b3401, b0492, b1000
GO:0004176 0.0000000 6/9 molecular_function: ATP-dependent peptidase activity b0437, b0438, b3932, b0882, b0439, b3931
GO:0051087 0.0000000 6/10 molecular_function: chaperone binding b4142, b0015, b0014, b0473, b2614, b0881
GO:0051085 0.0000000 5/5 biological_process: chaperone cofactor-dependent protein refolding b4142, b0015, b0014, b4143, b1000
GO:0009088 0.0000000 5/6 biological_process: threonine biosynthetic process b3940, b3433, b0004, b0002, b0003
GO:0005829 0.0000001 32/1032 cellular_component: cytosol b2319, b3433, b3932, b2614, b0003, b3941, b4143, b2745, b4142, b3399, b3401, b0439, b3931, b3940, b3829, b4024, b4019, b0015, b0014, b2747, b2942, b0882, b0492, b3687, b0004, b2592, b3259, b0438, b2320, b3400, b0473, b0437
GO:0009090 0.0000003 4/4 biological_process: homoserine biosynthetic process b3940, b0002, b4024, b3433
GO:0005737 0.0000004 28/848 cellular_component: cytoplasm b3932, b2614, b0003, b4143, b3828, b1000, b4013, b4142, b3939, b3401, b0439, b2744, b3931, b3940, b4024, b4019, b0015, b0014, b2942, b0882, b3687, b2743, b3686, b2592, b3259, b2320, b0473, b0437
GO:0009376 0.0000007 4/5 cellular_component: HslUV protease complex b3931, b3932, b0438, b0437
GO:0030163 0.0000044 4/8 biological_process: protein catabolic process b0881, b3932, b0438, b0439
GO:0004072 0.0000097 3/3 molecular_function: aspartate kinase activity b3940, b0002, b4024
GO:0034605 0.0000105 4/10 biological_process: cellular response to heat b2592, b0882, b0439, b3400
GO:0009089 0.0000213 4/12 biological_process: lysine biosynthetic process via diaminopimelate b3940, b0002, b4024, b3433
GO:0043335 0.0000228 3/4 biological_process: protein unfolding b3931, b0882, b0438
GO:0046983 0.0000387 4/14 molecular_function: protein dimerization activity b2319, b0438, b2320, b3433
GO:0065003 0.0000440 3/5 biological_process: protein-containing complex assembly b0015, b0014, b2614
GO:0044183 0.0000440 3/5 molecular_function: protein binding involved in protein folding b0014, b0473, b3401
GO:0035999 0.0000754 3/6 biological_process: tetrahydrofolate interconversion b3829, b3941, b4019
GO:0016887 0.0001238 8/114 molecular_function: ATPase activity b2592, b0014, b0438, b0882, b0473, b4143, b0439, b3931
GO:0005524 0.0001261 16/441 molecular_function: ATP binding b3940, b4024, b4142, b0015, b0014, b2592, b0002, b0438, b2942, b3932, b0882, b0473, b4143, b0003, b0439, b3931
GO:0005515 0.0001322 27/1066 molecular_function: protein binding b2319, b3932, b2614, b4143, b1000, b4142, b0999, b3401, b0439, b3931, b2748, b3829, b0015, b0014, b2942, b0882, b0492, b2746, b3687, b3686, b2592, b3259, b0438, b3400, b0473, b0881, b0437
GO:0042802 0.0003303 15/429 molecular_function: identical protein binding b3686, b4142, b2747, b2592, b0438, b2942, b2746, b3932, b0473, b4143, b3401, b0437, b3931, b3687, b2748
GO:0009067 0.0003409 2/2 biological_process: aspartate family amino acid biosynthetic process b3940, b0002
GO:0004412 0.0003409 2/2 molecular_function: homoserine dehydrogenase activity b3940, b0002
GO:0006986 0.0003409 2/2 biological_process: response to unfolded protein b2592, b0882
GO:0036506 0.0003409 2/2 biological_process: maintenance of unfolded protein b0492, b3401
GO:0050667 0.0003409 2/2 biological_process: homocysteine metabolic process b3829, b4019
GO:0008705 0.0003409 2/2 molecular_function: methionine synthase activity b3829, b4019
GO:1990220 0.0003409 2/2 cellular_component: GroEL-GroES complex b4142, b4143
GO:0019068 0.0003409 2/2 biological_process: virion assembly b4142, b4143
GO:0019904 0.0004433 3/11 molecular_function: protein domain specific binding b3932, b3931, b2614
GO:0006520 0.0005401 4/28 biological_process: cellular amino acid metabolic process b3940, b0004, b0002, b3433
GO:0006508 0.0005481 7/108 biological_process: proteolysis b0437, b0438, b3932, b0882, b0439, b0881, b3931
GO:0008706 8.399e-10 4/4 molecular_function: 6-phospho-beta-glucosidase activity b1734, b2716, b3721, b2901
GO:0103047 0.0000000 4/4 molecular_function: methyl beta-D-glucoside 6-phosphate glucohydrolase activity b1734, b2716, b3721, b2901
GO:1902815 0.0000001 3/3 biological_process: N,N’-diacetylchitobiose import b1736, b1737, b1738
GO:0008422 0.0000003 3/4 molecular_function: beta-glucosidase activity b2901, b3721, b2716
GO:0004553 0.0000012 4/25 molecular_function: hydrolase activity, hydrolyzing O-glycosyl compounds b1734, b2901, b3721, b2716
GO:0016052 0.0000017 3/7 biological_process: carbohydrate catabolic process b2901, b3721, b2716
GO:0005975 0.0000056 6/154 biological_process: carbohydrate metabolic process b1733, b2716, b1734, b4090, b3721, b2901
GO:0016798 0.0000078 4/40 molecular_function: hydrolase activity, acting on glycosyl bonds b1734, b2901, b3721, b2716
GO:0034219 0.0000095 4/42 biological_process: carbohydrate transmembrane transport b1738, b1736, b3722, b1737
GO:0090566 0.0000211 2/2 molecular_function: protein-phosphocysteine-N,N’-diacetylchitobiose phosphotransferase system transporter activity b1736, b1738
GO:0009401 0.0000313 4/57 biological_process: phosphoenolpyruvate-dependent sugar phosphotransferase system b1738, b1736, b3722, b1737
GO:0008982 0.0001291 3/30 molecular_function: protein-N(PI)-phosphohistidine-sugar phosphotransferase activity b1738, b3722, b1737
GO:0061720 0.0001313 2/5 biological_process: 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde b3882, b3881
GO:1902777 0.0001313 2/5 biological_process: 6-sulfoquinovose(1-) catabolic process b3882, b3881
GO:0008643 0.0003177 4/104 biological_process: carbohydrate transport b1738, b1736, b3722, b1737
GO:0006097 6.176e-09 4/8 biological_process: glyoxylate cycle b4015, b4014, b2976, b4016
GO:0019154 1.00e-07 3/3 molecular_function: glycolate dehydrogenase activity b2979, b4468, b4467
GO:0046296 6.00e-07 3/6 biological_process: glycolate catabolic process b2979, b4468, b4467
GO:0006099 1.00e-06 4/29 biological_process: tricarboxylic acid cycle b4015, b4014, b2976, b4016
GO:0004474 1.49e-05 2/2 molecular_function: malate synthase activity b4014, b2976
GO:0030267 3.35e-05 2/3 molecular_function: glyoxylate reductase (NADP) activity b3553, b1033
GO:0016618 3.35e-05 2/3 molecular_function: hydroxypyruvate reductase activity b3553, b1033
GO:0042128 2.939e-20 14/20 biological_process: nitrate assimilation b1466, b2206, b1224, b1227, b1225, b1467, b1468, b3366, b1226, b3365, b1223, b1465, b4070, b3367
GO:0017004 0.0000000 9/13 biological_process: cytochrome complex assembly b2196, b4074, b2200, b2199, b2201, b2194, b2195, b2198, b2197
GO:0055114 0.0000000 28/448 biological_process: oxidation-reduction process b2204, b1224, b2542, b4072, b4070, b2205, b2538, b2539, b1227, b1465, b2202, b2711, b1225, b1467, b2710, b3368, b2540, b3867, b2436, b2206, b2541, b1468, b2195, b3366, b4071, b3365, b2203, b2194
GO:0008940 0.0000000 7/7 molecular_function: nitrate reductase activity b2206, b1224, b1225, b1467, b1227, b1468, b1465
GO:0019645 0.0000000 8/15 biological_process: anaerobic electron transport chain b1227, b1467, b1468, b4071, b1465, b4073, b4072, b4070
GO:0015886 0.0000000 7/9 biological_process: heme transport b2196, b4074, b2200, b2199, b2201, b2198, b2197
GO:0009061 0.0000000 11/49 biological_process: anaerobic respiration b2206, b1225, b1224, b1227, b1467, b1468, b3366, b3365, b1465, b2203, b2202
GO:0020037 0.0000000 10/39 molecular_function: heme binding b2196, b4074, b2199, b1227, b4071, b3365, b1465, b2202, b4070, b2197
GO:0009325 0.0000000 6/6 cellular_component: nitrate reductase complex b1224, b1225, b1467, b1227, b1468, b1465
GO:0016491 0.0000000 22/356 molecular_function: oxidoreductase activity b1224, b2542, b4072, b4070, b2538, b2539, b1227, b1465, b2711, b1225, b1467, b2710, b3368, b3867, b2436, b2206, b2541, b1468, b2195, b3366, b4071, b3365
GO:0006779 0.0000000 7/15 biological_process: porphyrin-containing compound biosynthetic process b2436, b3997, b3805, b3368, b3804, b3802, b3867
GO:0051536 0.0000001 13/146 molecular_function: iron-sulfur cluster binding b2538, b2204, b2206, b1224, b1225, b1467, b1468, b3365, b4072, b2540, b3867, b2205, b2208
GO:0006782 0.0000002 5/9 biological_process: protoporphyrinogen IX biosynthetic process b2436, b3997, b3805, b3804, b3867
GO:0042126 0.0000004 4/4 biological_process: nitrate metabolic process b1467, b1224, b1468, b1225
GO:0018378 0.0000004 4/4 biological_process: cytochrome c-heme linkage via heme-L-cysteine b4076, b4074, b2194, b4075
GO:0008695 0.0000004 4/4 molecular_function: 3-phenylpropionate dioxygenase activity b2540, b2538, b2539, b2542
GO:0046872 0.0000004 26/692 molecular_function: metal ion binding b2204, b1224, b3998, b4072, b4070, b2205, b2208, b4075, b2538, b1227, b1465, b2202, b3996, b1225, b1467, b2710, b2540, b2436, b3867, b2206, b2194, b1468, b4071, b3365, b2203, b2197
GO:0019380 0.0000005 5/11 biological_process: 3-phenylpropionate catabolic process b2538, b2539, b2541, b2542, b2540
GO:0051539 0.0000006 11/117 molecular_function: 4 iron, 4 sulfur cluster binding b2204, b2206, b1224, b1225, b1467, b1468, b3365, b4072, b3867, b2205, b2208
GO:0019439 0.0000012 5/13 biological_process: aromatic compound catabolic process b2538, b2539, b2541, b2542, b2540
GO:0015232 0.0000018 4/6 molecular_function: heme transporter activity b2196, b4074, b2200, b2199
GO:0009055 0.0000023 9/83 molecular_function: electron transfer activity b2206, b1225, b1224, b1227, b1467, b2710, b4071, b1465, b2202
GO:0044799 0.0000115 3/3 cellular_component: NarGHI complex b1224, b1225, b1227
GO:0042279 0.0000115 3/3 molecular_function: nitrite reductase (cytochrome, ammonia-forming) activity b4070, b4072, b4071
GO:0031235 0.0000523 3/5 cellular_component: intrinsic component of the cytoplasmic side of the plasma membrane b1224, b2198, b1225
GO:0031237 0.0001407 3/7 cellular_component: intrinsic component of periplasmic side of plasma membrane b2194, b2197, b2195
GO:0006783 0.0002079 3/8 biological_process: heme biosynthetic process b2436, b3997, b3805
GO:0051131 0.0003822 2/2 biological_process: chaperone-mediated protein complex assembly b1226, b1466
GO:0018063 0.0003822 2/2 biological_process: cytochrome c-heme linkage b2196, b2197
GO:0016966 0.0003822 2/2 molecular_function: nitric oxide reductase activity b4070, b2710
GO:0009344 0.0003822 2/2 cellular_component: nitrite reductase complex [NAD(P)H] b3365, b3366
GO:0008942 0.0003822 2/2 molecular_function: nitrite reductase [NAD(P)H] activity b3365, b3366
GO:0006780 0.0003822 2/2 biological_process: uroporphyrinogen III biosynthetic process b3997, b3804
GO:0019700 5.884e-20 8/8 biological_process: organic phosphonate catabolic process b4100, b4101, b4096, b4095, b4092, b4099, b4098, b4097
GO:1904176 0.00e+00 5/5 cellular_component: carbon phosphorus lyase complex b4100, b4101, b4099, b4098, b4097
GO:0019634 0.00e+00 4/4 biological_process: organic phosphonate metabolic process b4100, b4101, b4094, b4099
GO:0061694 0.00e+00 4/4 cellular_component: alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex b4100, b4101, b4096, b4099
GO:0061693 0.00e+00 4/4 molecular_function: alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity b4100, b4101, b4096, b4099
GO:0015716 5.95e-05 2/4 biological_process: organic phosphonate transport b4101, b4102
GO:0009401 5.831e-11 9/57 biological_process: phosphoenolpyruvate-dependent sugar phosphotransferase system b2094, b2093, b4194, b4193, b4565, b4304, b4302, b4195, b2095
GO:0019402 0.0000000 5/5 biological_process: galactitol metabolic process b2094, b2096, b2093, b2091, b2095
GO:0005975 0.0000000 10/154 biological_process: carbohydrate metabolic process b4198, b3582, b3581, b2096, b4196, b4197, b3583, b4301, b3580, b2095
GO:0019854 0.0000000 4/5 biological_process: L-ascorbic acid catabolic process b4197, b3581, b4198, b4196
GO:0019852 0.0000011 3/3 biological_process: L-ascorbic acid metabolic process b4198, b3582, b4197
GO:0019404 0.0000011 3/3 biological_process: galactitol catabolic process b2096, b2091, b2095
GO:0015796 0.0000011 3/3 biological_process: galactitol transport b2094, b2093, b4304
GO:0015882 0.0000011 3/3 biological_process: L-ascorbic acid transmembrane transport b4194, b4193, b4195
GO:0090585 0.0000011 3/3 molecular_function: protein-phosphocysteine-L-ascorbate-phosphotransferase system transporter activity b4194, b4193, b4195
GO:0008643 0.0000034 7/104 biological_process: carbohydrate transport b2094, b2093, b4193, b4565, b4304, b4302, b3579
GO:0019324 0.0000050 3/5 biological_process: L-lyxose metabolic process b3580, b3582, b3583
GO:0034219 0.0000070 5/42 biological_process: carbohydrate transmembrane transport b2094, b3577, b2093, b4565, b3578
GO:0019323 0.0000286 3/9 biological_process: pentose catabolic process b4301, b4198, b3583
GO:0090584 0.0000809 2/2 molecular_function: protein-phosphocysteine-galactitol-phosphotransferase system transporter activity b2094, b2093
GO:0033982 0.0000809 2/2 molecular_function: 3-dehydro-L-gulonate-6-phosphate decarboxylase activity b3581, b4196
GO:0034015 0.0000809 2/2 molecular_function: L-ribulose-5-phosphate 3-epimerase activity b3582, b4197
GO:0016832 0.0001054 3/14 molecular_function: aldehyde-lyase activity b2096, b4198, b3583
GO:0008742 0.0001814 2/3 molecular_function: L-ribulose-phosphate 4-epimerase activity b4198, b3583
GO:0004590 0.0001814 2/3 molecular_function: orotidine-5’-phosphate decarboxylase activity b3581, b4196
GO:2001059 0.0003212 2/4 biological_process: D-tagatose 6-phosphate catabolic process b2096, b2095
GO:0009401 1.118e-12 8/57 biological_process: phosphoenolpyruvate-dependent sugar phosphotransferase system b1101, b2415, b2417, b2429, b2416, b2715, b4240, b1621
GO:0008643 0.0000000 8/104 biological_process: carbohydrate transport b1101, b2415, b2417, b2429, b2416, b2715, b4240, b1621
GO:0090563 0.0000000 5/20 molecular_function: protein-phosphocysteine-sugar phosphotransferase activity b1101, b2429, b2715, b4240, b1621
GO:0016301 0.0000000 8/166 molecular_function: kinase activity b1101, b2296, b2417, b2429, b2416, b2715, b4240, b1621
GO:0016310 0.0000000 8/169 biological_process: phosphorylation b1101, b2296, b2417, b2429, b2416, b2715, b4240, b1621
GO:0008982 0.0000000 5/30 molecular_function: protein-N(PI)-phosphohistidine-sugar phosphotransferase activity b1101, b2429, b2715, b4240, b1621
GO:0016740 0.0000055 9/576 molecular_function: transferase activity b1101, b2297, b2296, b2417, b2429, b2416, b2715, b4240, b1621
GO:0006085 0.0000179 2/2 biological_process: acetyl-CoA biosynthetic process b2297, b2296
GO:0090564 0.0000179 2/2 molecular_function: protein-phosphocysteine-glucose phosphotransferase system transporter activity b1101, b1621
GO:0019413 0.0000179 2/2 biological_process: acetate biosynthetic process b2297, b2296
GO:0006083 0.0000402 2/3 biological_process: acetate metabolic process b2297, b2296
GO:0015771 0.0000402 2/3 biological_process: trehalose transport b2715, b4240
GO:0090589 0.0000402 2/3 molecular_function: protein-phosphocysteine-trehalose phosphotransferase system transporter activity b2715, b4240
GO:1904659 0.0001599 2/6 biological_process: glucose transmembrane transport b1101, b1621
GO:0034219 0.0002684 3/42 biological_process: carbohydrate transmembrane transport b2429, b2715, b4240

DELETE ALL nodes & edges

MATCH ()-[r]-() DELETE r; # DELETE ALL RELATIONSHIPS
MATCH (n) DELETE n;       # DELETE ALL NODES