[BioC] Gene-gene interaction analysis

[Wolfgang Huber]

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.

I am sure there are many more good options.

Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber