Dear all, I have a list of proteins, predicted from miRNA. There is now P-value associated with any protein and there are some proteins that occur several time in my list. I wondered how I can "compare" two such lists in terms of their ontology or KEGG pathways.

Hi, On Mon, Mar 12, 2012 at 7:52 AM, Ali Mohammadian <nrcgeb at="" gmail.com=""> wrote: > Dear all, > > I have a list of proteins, predicted from miRNA. There is now P-value > associated with any protein and there are some proteins that occur > several time in my list. I wondered how I can "compare" two such lists > in terms of their ontology or KEGG pathways. Out of curiosity, how does one protein appear multiple times in your list? I mean, does it appear multiple times per miRNA? (I'm assuming the data you have is a list of differentially expressed proteins after some miRNA transfection or something, so that sounds weird?) In any event, I think topGO can plot GO "profile" plots for different gene lists against each other, no? One way to compare the two lists is to simply "eyeball" those bar charts ... I reckon you can start there. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact