[BioC] (no subject)

McGee, Monnie mmcgee at mail.smu.edu
Fri Jul 17 17:21:25 CEST 2009

Dear Anupam,

I am responding to you message about finding signaling pathways to which a list of over/under expressed genes belong.

There are several tools for this: Reactome, OntoExpress, PathExpress, CLASSIFI (requires clustering of the genes using some type of clustering tool before use).  
Most of these are available online, and some are actually websites to which you submit your list and then wait for a response.  You can find any of these by searching for them using any Internet search engine.

Bioconductor has a several packages that contain functions to do find pathway membership.  GOstats and goTools come to mind immediately.   There are probably others.

I hope that gets your started.  

Best Regards,
Monnie McGee

>Message: 6
>Date: Thu, 16 Jul 2009 19:40:45 +0530
>From: anupam sinha <anupam.contact at gmail.com>
>Subject: [BioC] Checking for pathway membership
>To: Bioconductor at stat.math.ethz.ch
 >       <82ec54570907160710i56ebd0b5pe3817053cd4817bb at mail.gmail.com>
>Content-Type: text/plain
>Hi all,
>         A rather naive query from a novice. I have a list of
>over-expressed and under-expressed human genes(gene names) from a microarray
>experiment.What I want is basically to find the signalling pathways in which
>these genes are involved and interaction between these genes themselves. Can
>anyone help me out ??? Thanks in advance.
>Anupam Sinha

Monnie McGee, PhD
Associate Professor
Statistical Science
Southern Methodist University
Office: 214-768-2462
Fax: 214-768-4035
Website: http://faculty.smu.edu/mmcgee

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