Tool/algorithm to assess the effect of several mutations

Question

[roy.granit]

Searching for a tool that could (try to) predict which pathways are predicted to be affected by several mutation co-occurring in a certain tumor.

e.g. mutated PTEN would active the PI3K pathway, and HER2 mutated would also active the MAPK pathway

Thanks!

Answer 1

[Cyriac Kandoth]

Here are related tools with varying levels of "ease of use". Good luck!

• http://compbio.cs.brown.edu/projects/multi-dendrix/
• http://compbio.cs.brown.edu/projects/hotnet2/
• http://cbio.mskcc.org/tools/memo/
• http://cbio.mskcc.org/tools/netbox/

Answer 2

[Jean-Karim Heriche]

I would look into Boolean network modelling of pathways. There may be cytoscape plug-ins for this.

[roy.granit]

Thanks, good idea

Answer 3

[Sean Davis]

netsig is a new one.

[roy.granit]

Thanks, will check it out..