integrated pathway identification

[adrian]

hello group,

What are the pathway analyses tools that can identify pathways affected given mutation, expression, methylation and copy number data, for example TCGA type data. I came across Paradigm but I am not clear if it can take all 4 data types. Thanks a lot for pointing some tools.

[bigmw]

You may conduct pathway analysis within each data type using GAGE, then summarize the p-values using some meta-test procedure.
To visualize the integrated datasets on pathways, you can try Pathview. It is a a tool set for pathway based data integration and visualization.

For details please check the Bioconductor package and documentations:

http://bioconductor.org/packages/release/bioc/html/gage.html

http://bioconductor.org/packages/release/bioc/html/pathview.html