[BioC] Gene-gene interaction analysis

[Sean Davis]

On Wed, Apr 18, 2012 at 12:17 PM, Wolfgang Huber <whuber at embl.de> wrote:
> Apr/18/12 5:01 PM, Yadav Sapkota scripsit::
>>
>> Hi,
>>
>> I am looking for a tool or R package that can take SNPs or DE genes with
>> their p-values and build a graphical representation showing possible
>> gene-gene interactions using prior knowledge from protein interactions
>> databases such as KEGG with some scores for the interaction. I know this
>> can be done in Ingenuity Pathway Analysis but I am looking for something
>> open-source.
>>
>> I would appreciate if anyone knows anything like this.
>>
>> Regards,
>
>
> Dear Yadav
>
> the BioNet and HTSanalyzeR packages on Bioconductor are good places to
> start. Ex-Bioc, there is String: http://string-db.org, and Reactome offers a
> GUIs for painting their networks with colours representing scores such as
> p-values: http://www.reactome.org/ReactomeGWT/entrypoint.html -> Analyse
> Expression Data.

And the RCytoscape packages opens up many opportunities here, also.

Sean