Questions about non-model organisms gene enrichment analysis
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yuhang • 0
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 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 • 135 views
Entering edit mode
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

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.

Entering edit mode

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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