On Wed, Apr 18, 2012 at 10:01 AM, Yadav Sapkota <ysapkota@ualberta.ca>wrote:

> 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.
>

Hi Yadav,

You can try package ggbio, to plot your interaction in a circular view as
links and colored by P-value or any other score, or use extra track to to
show P-value.
You need aggregate the information and score you need into a GRanges object
and extra column including your score and linked gene position(as GRanges),
the use layout_circle to build circular view one by one,  other choice
including Manhattan plot, showing arches in Manhattan is tricky, though
still possible with ggbio too.
a simple example:

library(ggbio)
example(layout_circle)

or some case studies here(ignore the error, it works now, need to be
updated)
http://tengfei.github.com/ggbio/blog/2012/04/12/circle/

HTH

Tengfei




> I would appreciate if anyone knows anything like this.
>
> Regards,
> --
> Yadav Sapkota
> PhD Candidate
> Dept. of Laboratory Medicine and Pathology, UofA
> Cross Cancer Institute
> 11560 University Avenue, Edmonton AB T6G 1Z2
> Phone: 780-5778092
>
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-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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