KEGG pathway and module enrichment for non-model fungi

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6.9 years ago

sbchua.1990 ▴ 50

Hi, I am working on transcriptome of non-model fungi species. I have retrieved KOs from KEGG website and would like to perform enrichment analysis for biological interpretation.

Any suggestion on softwares that can be used?

I am new to transcriptome analysis. Correct me if I am wrong. When we perform enrichment analysis, we need to compare our KO list retrieved from DEGs against KO list retrieved from 'standard database' right? In my case, as there is no genome available for the species, should I use the KO list retrieved from transcriptome backbone (assemble from all raw read from my experiment) as 'standard database' ?

gene blast RNA-Seq • 2.0k views

ADD COMMENT • link 6.9 years ago by sbchua.1990 ▴ 50

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You can try goseq, if you have your KO-to-gene data in correct format.

And yes, you'll have to use your whole assembly as a background.

ADD REPLY • link 6.9 years ago by Benn 8.3k

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How did you solve your problem?

ADD REPLY • link 6.5 years ago by Ric ▴ 430

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