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!
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exin
2 answers
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.
How about DAVID ( https://david.ncifcrf.gov/ ) or TargetMine ( https://targetmine.mizuguchilab.org/ ) ?
Both have domain enrichment analysis function(s).
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".
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