Enrichment analysis of Differentially expressed genes
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3.1 years ago
Ambika ▴ 40

Hello everyone,

I used STAR-HTseq-DESeq2 pipleline to analyse my RNAseq data and now I have list of differentially expressed genes. I want to do the enrichment analysis of the list of genes obtained from DEseq2. I tried to use DAVID but it didn't work for me since I am working with non-model organism (fungi). Could you please suggest any other programs that are good for enrichment analysis with non model organisms.

Thank you, Ambika

RNA-Seq Enrichment analysis • 1.2k views
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Is there a published genome for your organism? Is it annotated?

edit: just as a side note, HTSeq is not needed here, because STAR can output counts with the parameter --quantMode GeneCounts.

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No it is not published and not annotated

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3.1 years ago
h.mon 32k

Are you still working with the same fungi as here: Extract exon Intron reads from RNA seq data ? You have an assembled draft genome, a gtf with predicted genes, and mapped your RNAseq to this draft genome? Assuming so, you will have to annotate this genome somehow. A quick and dirty annotation would just be blasting / diamonding the Augustus predicted genes against UniProt, to associate each gene with a UniProt identifier. Then you could use DAVID.

Another quick and dirty option would be to map your RNAseq to a close, annotated genome - in case one exists. Tthis way you can leverage the existing annotation to perform enrichment analysis.

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Yes you are right I have an assembled draft genome. Right now I am trying to blast my draft genome using Blast2Go and looks like it will take forever. I will try the other idea you said using UniProt. Thank you h.mon for helping.

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Hi, h.mon, I was looking on how can I associate each identified gene with UniProt identifier, but I am lost. Can you suggest a way I can do that.

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