Functional annotation of DESeq2 results?
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8 months ago
snow4964 ▴ 10

To give context to my methods so far, I have run a differential expression analysis of nonmodel organisms using DESeq2. I was able to use the coding sequences (cds) from a genome published on Ensembl as my reference for DESeq2, though the organism is not functionally annotated.

Is there a way I can create a function annotation or discover gene ontology and connect that to my DESeq2 results? I was considering BLASTing the cds fasta, but I am not sure if this is a viable method.

RNA-Seq rna-seq gene R • 438 views
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To give an update, my reference was blasted using uniprot's database and the additional information was gathered using biomaRt. It provided enough information to have a predicted annotation with functional support

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8 months ago

I'm not sure if this could be possible but as an explorative analysis you might be able to use the functional annotation of a closely related organism.

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Thank you for the suggestion, though I am not sure if that is possible. I am working with Rotiferan data and there does not seem to be too many, if any, functional annotations of closely related organisms. I have been considering using C. elegans and D. melanogaster and overlapping/comparing them, if possible, because I am interested in a group of highly conserved genes

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