Performing GO enrichment analyis on DE genes
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13 months ago
Light92 ▴ 60

Good morning to everyone,

To complete a DE genes analysis, at the end of my pipeline (during which I adopted DESEQ2 and edgeR methods, to compare results), I'd like to perform a GO enrichment analysis.

My main problem is that the GO terms aren't available on databases online, since I'm using a genome which is incomplete and only partially annotated. I'd like to use GO terms from that one.

I've tried to use the function goana from R, which I slightly changed to make it accept an external database, but it isn't working on my specific results, like I explained here.

I was considering topGo but it seems quite hard to adapt it to this purpose... I'd also be interested in something similar for KEGG analysis (for which I had thought of kegga from Bioconductor, but I guess I'm going to have similar issues).

Any suggestions there? What could I use which is free (I'm not going to buy BLAST2GO). Thanks in advance!

de go enrichment rnaseq • 294 views
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What you need to do is create your own set of GO annotations by transferring annotations from annotated species using orthology.

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This is similar to what I wanted to do in case there is no alternative. More specifically, I'm working on domesticated olive tree and I could try by blasting domestic olive tree genes against Olea europaea var. sylvestris ones, so that I could use the GO annotations of the latter once I know the correspondance between domestic genes and wild ones...

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