List of Genes According to Ontologies

Question

[fusion.slope]

Hello,

I was wondering if there is a website in which I can retrieve the list of genes for each ontology.

For example for the biological process "Regulation of Gene Expression," I would like to have all the list that belong to this ontology etc..

Thanks in advance

Answer 1

[Pierre Lindenbaum]

I recently wrote a small tool to fetch all the children of a given term in GO: http://lindenb.github.io/jvarkit/GoUtils.html

there is an example to fetch all the associated genes:

Use GO annotation to retrieve genes associated to GO:0005216 ‘ion channel activity’

join -t $'\t' -1 1 -2 2 \
    <(java -jar dist/goutils.jar -A 'GO:0005216' | cut -f 1 | sort | uniq) \
    <(wget -q -O - "http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD" | gunzip -c | grep -v '^!' | cut -f3,5 | uniq | LC_ALL=C sort -t $'\t' -k2,2) |\
sort -t $'\t' -k2,2 |\
grep SCN5A -A 10 -B 10

(...)
GO:0086006  SCN2B
GO:0005244  SCN3A
GO:0005248  SCN3A
GO:0005248  SCN3A
GO:0005248  SCN3B
GO:0086006  SCN3B
GO:0005248  SCN4A
GO:0005248  SCN4A
GO:0005248  SCN4B
GO:0086006  SCN4B
GO:0005244  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0086006  SCN5A
GO:0086060  SCN5A
GO:0086061  SCN5A
GO:0086062  SCN5A
GO:0086063  SCN5A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN8A
GO:0005248  SCN8A
GO:0005248  SCN9A
GO:0005248  SCN9A
GO:0005248  SCN9A
GO:0005272  SCNN1A
(...)

Answer 2

[EagleEye]

With 'prepare_database' module in GeneSCF. you can download organism/species specific genes for corresponding process as a simple text in table format. Example:

Process1    gene1,gene2,gene3
Process2    gene4,gene6,gene2

Discussion on Biostar with example usage.