Questions about non-model organisms gene enrichment analysis
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yuhang • 0
@1b2a94a4
Last seen 4 weeks ago
Hong Kong

Hi, I am doing the RNA-Seq data analysis of a non-model organism these days, and a few questions occurred to me. The non-model organism doesn't have a orgDb, so I have to use the org.Hs.eg.db. When we do ORA for gene function enrichment, we need the 'Gene Ratio' and 'Background Gene Ratio' to confirm the significance of a specific GO term or KEGG pathway. Since different species have different gene numbers, is the significance of a GO term based on the human 'Background Gene Ratio' still meaningful for the non-model organism?

Looking forward to your help!

non-model enrichment organisms analysis • 172 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

I didn't read much past this point

The non-model organism doesn't have a orgDb, so I have to use the org.Hs.eg.db

Because nothing past that statement is relevant. You cannot just slot the annotation data for one species in for another and expect things to work.

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Thanks a lot for your reply! I am analyzing the RNAseq data of a non-model organism that doesn't have an annotation database, someone advised me to use the annotation database of humans instead. I think it maybe not make sense.

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So how did you solve the problem? I am aldo facing the same problem. What is the solution for non modrl organism?

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@ afsanarupa1: Please start a new thread, and then provide information on which non-model organism you are working with, together with a list of (say) 10 representative gene ids, and the code you already tried.

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