[BioC] GOstats with Reactome database?

Robin Haw Robin.Haw at oicr.on.ca
Mon Aug 15 23:37:24 CEST 2011

Dear Martin and Jose,

We, at Reactome, would be encouraged by the development of Gostats to use
our pathway data. If you would like to discuss this further, please let me

Likewise, if there are any other BioConductor developers interested in
using Reactome as a source of pathway data, drop me an email. In the
meantime, we do provide a "Reactome Pathway Gene Set" and other annotation
data at http://www.reactome.org/download/.


Robin Haw, PhD
Scientific Associate and Outreach Coordinator (Reactome)

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
Tel:         647-260-7985
Toll-free: 1-866-678-6427

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On 11-08-15 1:21 PM, "J.delasHeras at ed.ac.uk" <J.delasHeras at ed.ac.uk> wrote:

>Quoting Martin Morgan <mtmorgan at fhcrc.org> on Mon, 15 Aug 2011 10:11:50
>> On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote:
>>> Dear all,
>>> with the demise of KEGG (well, at least without subscription), I was
>>> wondering whether there are any plans to get GOstats working with the
>>> Reactome database, or whether there is an "easy" way to persuade
>>> to work with it.
>> Hi Jose --
>> Yes, we intend to revise the GOstats, GSEABase, and perhaps other
>> packages to work more flexibly with Reactome & other data base
>> packages. Whether this will be accomplished this release is not clear.
>> Martin
>>> Any ideas?
>>> Jose
>Hi Martin,
>that's great news. I have become a bit of a fan of GOstats recently
>and would love to use a similar approach with other databases.
>Very grateful for all your work.
>Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
>The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507090
>Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
>Swann Building, Mayfield Road
>University of Edinburgh
>Edinburgh EH9 3JR
>The University of Edinburgh is a charitable body, registered in
>Scotland, with registration number SC005336.
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