[BioC] question from any of TopGO, gage, sigpathway, GSVA, GOstat users

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Mar 12 16:19:26 CET 2012


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.


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

More information about the Bioconductor mailing list