Hello all,
Can some help me in identifying the complete list of genes that are associated with a particular GO accessions number (for eg: GO:0005515) ?
I have a large number of GO accessions numbers. Is there any tool/database for doing the above task?
Thanks in advance, Prasad
2 answers
1st solution:
See: QuickGO can supply GO term information and GO annotation data via REST web services. http://www.ebi.ac.uk/QuickGO/WebServices.html
goid GO identifiers either directly or indirectly (descendent GO identifiers) applied in annotations
example:
$ curl -s 'http://www.ebi.ac.uk/QuickGO/GAnnotation?goid=GO:0005515&format=tsv' | awk -F ' ' '($4!="-")' | head -n 3 | ~/src/variationtoolkit/bin/verticalize
>>> 2
$1 DB UniProtKB
$2 ID A0A097
$3 Splice -
$4 Symbol Tbeta-a
$5 Taxon 7955
$6 Qualifier -
$7 GO ID GO:0003779
$8 GO Name actin binding
$9 Reference GO_REF:0000002
$10 Evidence IEA
$11 With InterPro:IPR001152
$12 Aspect Function
$13 Date 20120616
$14 Source InterPro
<<< 2
>>> 3
$1 DB UniProtKB
$2 ID A0A097
$3 Splice -
$4 Symbol Tbeta-a
$5 Taxon 7955
$6 Qualifier -
$7 GO ID GO:0003779
$8 GO Name actin binding
$9 Reference GO_REF:0000002
$10 Evidence IEA
$11 With InterPro:IPR016323
$12 Aspect Function
$13 Date 20120616
$14 Source InterPro
<<< 3
2nd solution:
use NCBI esearch with db=gene and the GO modifier:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=%225515%22[GO]
You don't mention whether you want programmatic access or not. For web-based access, you can go to Amigo from the Gene Ontology folks themselves. For example:
http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0005515
From that page, you can filter by species, evidence, etc.
For programmatic access, Pierre's answers are great. As another alternative, my group maintains mygene.info, which is optimized for fast JSON queries (suitable for AJAX applications). For example:
http://mygene.info/query?q=go:GO\:0005515
The downside is that it only supports nine of the most common species.
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