GO analysis of a gene set

Question

[sumudu_rangika]

Hi,

My analysis is about whole genome sequencing (Illumina Miseq) of 8 isolates of a parasitic species belongs to two different sub-strains.

I'm concerned with highly variable gene copy numbers among the two sub-strains. I want to do a gene ontology analysis of the set of genes with highly variable copy numbers among the two. This is where I faced the problem. I tried using PANTHER, AMIGO2, GO Consortium but unable to come up with a result. My species is Leishmania donovani and the said databases use Leishmania major genome.

If anyone familiar with GO analysis please advice how to perform it correctly and good tools to use with my species, since I'm new to this type of analysis.

Thanks in advance Rangi

Answer 1

[Jean-Karim Heriche]

The way to do this is to transfer annotations by orthology, i.e. assign to L. donovani genes the GO terms from their L. major orthologs. You can then proceed with enrichment analysis.

[ivivek_ngs]

Totally a spot on answer, about using the orthologs. OP should be able to work it out now.

Answer 2

[dago]

Basically you want to assign GO to your list of genes, is that right? You could look Blast2GO, as also reported in this other post:

How can I do GO enrichment analysis for bacteria genome? (biomaRt is not support bacteria anymore)

Otherwise you can look if your organism is in QuickGO db. Hope this helps.