Question

Alternative tools to perform GO enrichment on DE genes

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Raito92 ▴ 60

@raito92-20399

Last seen 2.4 years ago

Italy

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!

go de enrichment rnaseq goana • 2.6k views

ADD COMMENT • link updated 4.6 years ago by Gordon Smyth 52k • written 4.6 years ago by Raito92 ▴ 60

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Posts have been cross-posted on Biostars:

ADD REPLY • link 4.6 years ago Kevin Blighe ★ 4.0k

Gordon Smyth · Answer 1 · 2020-04-15

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Gordon Smyth 52k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

I suggested kegga to you about a year ago as the easiest way to do GO analysis with your own database. You can input your own GO database to kegga as a data.frame. There is little point in trying lots of different GO tools because they essentially all the use same statistical method and hence should give the same result.

If the genome is only partly annotated, where are you getting the GO annotation from?

ADD COMMENT • link 4.6 years ago Gordon Smyth 52k

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Hello, thank you for your answer!

The real problem as I said is that I'm trying to use the GO annotation of a genome which isn't available online, because it's only a beta version. Only its wild counterpart is. This makes using the default functions goana and kegga harder for anyone who isn't skilled in programming. KEGG annotation isn't even available at all, not even in a beta version, so I had to do somehow a cross reference and use the wild species instead. I just picked the corresponding KEGG wild terms on which the basis of the genes were annotated.

You can input your own GO database to kegga as a data.frame

Could you expand on this? I'm not experienced in programming. Is it possible to easily use an external database rather than online ones, and basically do the same for goana?

Thanks in advance!

ADD REPLY • link updated 4.6 years ago by Gordon Smyth 52k • written 4.6 years ago by Raito92 ▴ 60

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Another alternative tool for enrichment analysis is PathfindR. You can use “KEGG”, “Reactome”, “BioCarta”, “GO-All”, “GO-BP”, “GO-CC”, “GO-MF” or custom genesets as protein interaction networks. Please check details in here: https://github.com/egeulgen/pathfindR

ADD REPLY • link 4.6 years ago rekren ▴ 20

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Thanks, I'll try this too!

ADD REPLY • link 4.6 years ago Raito92 ▴ 60

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Just read the kegga documentation by typing help("kegga"). Or see

https://support.bioconductor.org/p/76482/

for an example.

ADD REPLY • link 4.6 years ago Gordon Smyth 52k

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I will try, thanks for your help!

ADD REPLY • link 4.6 years ago Raito92 ▴ 60