Look Up Go Terms For A Given Gene Symbol

Question

[BioStarUser99]

I'm trying to use library("GO.db") in R. How do you look up all GO terms for a given gene symbol (Hugo). For example, how would I look up all:

1. Cellular component
2. Molecular Function
3. Biological Process

That BRAF is involved in?

Thanks!

Answer 1

[Charles Warden]

AmiGO should work:

http://www.geneontology.org/

One human BRAF result as an example:

http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=UniProtKB:H7C560&session_id=5200amigo1387913223

[BioStarUser99]

Hi, thanks for the quick response. I am trying to do this in R so I found RamiGO: http://www.bioconductor.org/packages/release/bioc/vignettes/RamiGO/inst/doc/RamiGO.pdf However, I don't see how to look up gene symbols in this package. ??

[Charles Warden]

I'm not very familiar with the R/Bioconductor GO packages.

If I have a non-standard task, I typically just parse the raw files from GO. Each category is typically a line in the text file. Searching each line for your gene of interest will tell you which categories the gene is in.

For standard GO analysis, there are lots of tools that are easy to use. You may know them already, but I have some links that I have found to be useful here:

http://cdwscience.blogspot.com/2013/03/bioinformatics-101-pathway-analysis.html

[BioStarUser99]

I don't think this will work in this case. e.g. I looked at http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo and there is no mapping for gene symbols to entries.

[Charles Warden]

GO provides a lot of files...you want a gene association one.

I found this one when I searched today::

http://www.geneontology.org/gene-associations/gene_association.goa_human.gz

ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/

It looks like I may have not been precise when I described the file format (one line per category). You are welcome to use the GO files in my BD-Func package (which should match the format I described), but this isn't a comprehensive list of all GO categories:

http://sourceforge.net/projects/bdfunc/