Pathway based analysis of mutated genes

Question

[Camilo Andres]

Hello! I would like to do a kind of pathway based analysis of mutated genes. I have a VCF file from breast cancer samples sequenced by targeted ngs and I am looking for some kind of tool that allows me to see a diagram that shows me the pathways my mutated genes are and ideally the processes they are related to (I don't know, something like this and somehow shows me which my mutated genes are). I think this might be achievable by cyctoscape but I am not too sure how to do this. Any help will be very useful.

PD: I am able to use R, I would be very grateful if somebody could help me

Answer 1

[skiesareforflying]

You can try DAVID https://david.ncifcrf.gov/ it can give you KEGG pathways which overlap a given gene list and annotates the diagram with a red star next to the target genes.

Not sure what your data looks like, but if you have a lot of mutations you might want to filter the genes based on some statistical metric, or limit to only pathogenic mutations or something.

[Camilo Andres]

Many thanks, I'm gonna try DAVID. My data is from breast cancer with no a lot of mutations per sample and has been already filtered by pathogenicity of the variants, so I think it should work. Thank you!