Question: GO enrichment analysis using non model organism
1
gravatar for dago
5.9 years ago by
dago2.6k
Germany
dago2.6k wrote:

Hi everybody,

I have proteome data for a non model organism, and I would like to performe gene onthology (GO) enrichment analysis.

I would like to perform the enrichment for the up-regualted proteins using the all proteins encoded in the genome as background dataset. I downloaded the GO annotation for each protein directly from Uniprot and now I am kind of lost among the many tools available for doing the analysis.

I am looking for web tools or R-Bioconductor tools more appropriate form my purpose, because it seemed to my that most of the tools deal with model organism.

Any advice will be greatly appreciated. 

proteome genome bioconductor R gene • 6.5k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 5.9 years ago by dago2.6k

What is the organism you are working on?

ADD REPLYlink written 5.9 years ago by Renesh1.9k
3
gravatar for dago
5.9 years ago by
dago2.6k
Germany
dago2.6k wrote:

An update.

I used the Bioconductor package topGO and I think it is a great tool for performing enrichment for non model organisms.

ADD COMMENTlink written 5.9 years ago by dago2.6k

Could please you share you code how you did it with topGO?

ADD REPLYlink written 2.9 years ago by Ric300
3
gravatar for Renesh
5.9 years ago by
Renesh1.9k
United States
Renesh1.9k wrote:

If you are working on plant, use agriGO enrichment tool. It has most of the species listed. It supports gene IDs for performing GO enrichment. You can also try BinGO plugin of cytoscape.

If you organism is not listed in their default database, you can perform blast homology search of your proteins with closely related organims available in their database. Use these top hits resulted from blast for performing Go enrichment.

ADD COMMENTlink written 5.9 years ago by Renesh1.9k
0
gravatar for dago
5.9 years ago by
dago2.6k
Germany
dago2.6k wrote:

I work with bacteria and I found the .goa file for the GO annotation on the Uniprot FTP server

ADD COMMENTlink written 5.9 years ago by dago2.6k
0
gravatar for Renesh
5.9 years ago by
Renesh1.9k
United States
Renesh1.9k wrote:

Use BinGO http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

You dont need to have GO IDs in BinGO. You should have gene IDs listed in their database. Check for your bacteria, if it is available there. If not then do as i suggested in above post.

ADD COMMENTlink written 5.9 years ago by Renesh1.9k
0
gravatar for dago
5.9 years ago by
dago2.6k
Germany
dago2.6k wrote:

Indeed, BINGO seems to be quite interesting.

I read on its website that it is possible to performe analysis on Custom dataset (http://www.psb.ugent.be/cbd/papers/BiNGO/Customize.html), which would be what I need.

Do you have any idea how I can create my own ontology file or download an ontology file useful for bacteria?

 

Thanks again for your help

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by dago2.6k
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