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Question: Tool suggestions for bulk domain analyses?
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I'm exploring the potential function of a cell-type in a non-model organism.

After scRNA-Seq, I obtained 300+ differentially expressed genes in this cell type. Besides GO-term analyses, I'm interested in looking at what domains are enriched. I don't know of such a such tool and haven't been able to find one with some briefing googling. Pfam/SMART seem to do 1 sequence at a time. Any suggestions?

Other suggestions that are not GO/domain-analyses welcome too!

ADD COMMENTlink 11 months ago exin • 50 • updated 11 months ago fishgolden • 390
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If your sequences are not already annotated with domains, you could annotate them with the PFAM HMMs using the pfam_scan.pl tool. Once you have the annotations you can write a script for enrichment analysis using Fisher's exact test.

ADD COMMENTlink 11 months ago Jean-Karim Heriche 19k
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Thank you Jean-Karim!!

ADD REPLYlink 11 months ago
exin
• 50
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How about DAVID ( https://david.ncifcrf.gov/ ) or TargetMine ( https://targetmine.mizuguchilab.org/ ) ?

Both have domain enrichment analysis function(s).

ADD COMMENTlink 11 months ago fishgolden • 390
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Thanks, but they both seem to require geneIDs as input, which I don't have, it's a non-model organism.

ADD REPLYlink 11 months ago
exin
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Oh, sorry. I thought you have id of transcripts or genes somehow because you could do DE analysis. BTW, Pfam website accepts multiple sequences with "search"->"batch search".

ADD REPLYlink 11 months ago
fishgolden
• 390
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Oh sweet! Thank you!! :)

ADD REPLYlink 11 months ago
exin
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