Question: Go Enrichment From Protein Id
1
gravatar for Phil S.
5.0 years ago by
Phil S.660
Stuttgart, Germany
Phil S.660 wrote:

Hi,

I know there are databases like biomaRt and DAVID to do enrichment Analysis for gene IDs. Is there also a tool doing the same thing with protein IDs. Preferrably for e.coli ;)

Thank you!

Best

Phil

enrichment protein go • 3.7k views
ADD COMMENTlink modified 5.0 years ago by Pablacious610 • written 5.0 years ago by Phil S.660
3
gravatar for Arnaud Ceol
5.0 years ago by
Arnaud Ceol840
Milan, Italy
Arnaud Ceol840 wrote:

Hi Phil,

if you're working on bacteria, I think you can anyway forget about DAVID and Biomart. You may have a look at Cytoscape and its plugins. BINGO for instance is a nice one to do GO enrichment. I use it most of the time with Uniprot protein IDs, but you should be anyway able (encouraged) to load yourself the annotation file.

links: Cytoscape: http://cytoscape.org/, plugins for enrichment analyses: http://apps.cytoscape.org/apps/with_tag/enrichmentanalysis

best,

Arnaud

ADD COMMENTlink written 5.0 years ago by Arnaud Ceol840

Thank you all for your suggestions. I guess I will give them all a try...

ADD REPLYlink written 5.0 years ago by Phil S.660
1
gravatar for Xingyu Yang
5.0 years ago by
Xingyu Yang260
Atlanta
Xingyu Yang260 wrote:

DAVID accept refseq and serval other kind of protein IDs. You can convert your protein IDs into the ids DAVID accepted. And you can also convert your protein IDs to their corresponding genes IDs.

All these above depends on whether your IDs (proteins/ genes) are well annotated. If not, you might like to first annotate your protein and find their ortholog genes whose ID are available in DAVID.

If you don't want to convert or annotate them, you can also try to leave them DAVID and let DAVID to autodetect you ids(in most cases, it doesn't work). Good luck with it.

Could please share what kind protein IDs you have ? Then, other people can better help you.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Xingyu Yang260
1
gravatar for Pablacious
5.0 years ago by
Pablacious610
Cambridge, UK
Pablacious610 wrote:

For E. coli I would use EcoCyc from SRI. It is probably one of the most comprehensive and curated resources when it comes to E. coli. It has a module for doing enrichment analysis through its smart tables, see here http://ecocyc.org/PToolsWebsiteHowto.shtml#node_toc_node_sec_7.5.1

It might be more pathway related enrichment analysis than GO based, but in any case you might find the result useful, or complementary to the GO-based analysis.

ADD COMMENTlink written 5.0 years ago by Pablacious610
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