I discovered a few hundred mRNAs that are co-immunoprecipitated with my protein of interest using RIP-Seq. Now I want to find similarities based on sequence, structure, motifs etc. which could eventually help me to identify a general mechanism underlying this Protein-RNA interaction. Do you have any suggestions which kind of tools I can use?
Hi Clemens, I guess you could use GO and KEGG enrichment, either using a hypergeometric test like FIsher's exact or gene set enrichment (which some people prefer because it doesn't use a threshold). There are tons of online tools for this (e.g. GSEA from Broad) or you can use one of the many R packages... Alternatively, you could also get the annotations from PFAM yourself and look for overrepresentation. Hope this helped, S
for functional classes I recommend EnrichR (http://amp.pharm.mssm.edu/Enrichr/) but I understand that you are more interested in sequence or structural motifs that explain protein/RNA interactions. Here PFOLD might help (http://www.daimi.au.dk/~compbio/rnafold/) to begn with and you can see many more here: http://pridb.gdcb.iastate.edu/RPISeq/links.php but I have not used them.
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