I have a list of differentially expressed genes in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have 2 options:
- BLAST my DE genes against a database with GO terms (human/mouse) to look for orthologs
- Use a program that assigns GO from BLAST results, such as Blast2GO
I've been trying with Blast2GO recently, but find if very slow and generally lacking. Does anyone have any experience doing GO in Xenopus or other non-model organisms?
Use Interproscan (http://www.ebi.ac.uk/Tools/pfa/iprscan/). It will fetch the GO terms as well as the pathway information from KEGG.
Thanks for the link. Do you know any similar tool (but not BLAST2GO) that will do something similar with nucleotide sequence?
You can use interproscan for nucleotide sequences as well. But here are few options:-
Annot8r:- http://www.nematodes.org/bioinformatics/annot8r/
http://www.biomedcentral.com/1471-2105/6/151#sec2
I hope this helps..
Trinotate ( http://trinotate.sourceforge.net/ ) uses both nucleotide sequences and protein sequences to generate its annotation report, which is quite complete. I recommend it.
going Blast2go way is a little slow - particularly if you want to look at around a 1000 genes, you are looking at about 4 to 5 days of Blasting to annotate the genes. Another method is to use a local blast version and generate an xml output which you can use in Blast2go - which will be much quicker. Then use blast2go to assign goterms and do an interpro scan to merge the results.
Once you have the results, you can export the results from Blast2go in a table format which will contain go terms and the genes e..g
GO1 gene1
GO1 gene2
GO2 gene2
etc
Using this table you can generate an incidence matrix and construct a bipartite graph of this incidence matrix to visualize your genes in a form of a network. Then you can look at various graph analysis methods like shortest paths, communities, clusters etc to find genes of interest - depending on your question.
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