[Bioperl-l] How to make a network graphic using my genes in pathways?

Sean Davis sdavis2 at mail.nih.gov
Wed Apr 2 07:33:38 EDT 2008


On Tue, Apr 1, 2008 at 10:14 PM, Jinyan Huang <hiekeen at gmail.com> wrote:
> I have 20 pathways. My interesting genes are in these pathways. There
>  are some genes overlaps in these pathways. How can I make a graphic
>  network using these genes? It means connecting these pathways through
>  these overlap genes. What kind of software can I use?

R/Bioconductor has tools for working with graphs and pathways.
Cytoscape is another open-source graphical solution.  Ingenuity is, of
course, not free.  If you are looking at a perl solution, you can look
at the various graph modules and their integration with the Graphviz
libraries.

SEan


More information about the Bioperl-l mailing list