I am looking for a software to do pfam enrichment analysis for my differential expressed genes from RNAseq. I have the differentially expressed gene list, and the annotaiton (GO, pfam, KEGG) of the genes in the genome. I did the GO enrichment analysis using GOseq. However, Goseq cannot do pfam. I wonder if there is a similar software for any annotation term that I want to analyze, particularly pfam.
The species I am working on is not model species. So I am looking for a software that allows me to upload my own annotation file.
Thank you very much.
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Yunqing Yu •
Have you tried Enrichr?
Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016;
In my understanding, Enrichr does only work for model organisms. Unfortunately, most online enrichment tools are working for model organisms only. I guess for people working only with well annotated organisms, it is often difficult to imagine the hardships we are going though...
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This might be a bit bold as an answer, but AFAIK and as unlikely as it might seem, such an online-tool does not exist, please prove me wrong though! All online-tools I know work with pre-annotated genes only, it seems as supporting the minority of NOMO researchers is not a prime concern. One could use a standard F-test or Chi-square test online tools but they often offer only limited contingency tables and are not adept to the requirements genome-wide analysis.
Assuming, the term relationships in PFAM can be ignored, I would do a Chi-square test in R locally, taking the genomic distribution of PFAM terms as background distribution. Hope this works out. Or check GSEA as an alternative.
Edit: I think I got the (false?) impression that you were looking for an online tool because you wrote "upload". If any tool would do, then R f-test/or Chi-square would be valid.
Btw, don't get me wrong, these tools are great. If one can get their hands on PFAM terms assigned to genes in a non-model organism and make gene-sets, testing for enrichment is possibly easy-breezy.