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, -- Yadav Sapkota PhD Candidate Dept. of Laboratory Medicine and Pathology, UofA Cross Cancer Institute 11560 University Avenue, Edmonton AB T6G 1Z2 Phone: 780-5778092 [[alternative HTML version deleted]]

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

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]