How to extract known pathways from protein protein interaction network?

Question

[jack]

Hi,

Given physical protein protein interaction like String and KEGG pathway. I would like to know how many of KEGG pathways or signaling pathways exist in PPI network. Is there any tool to extract known pathways(either entire or partial) from PPI network ?

[andrew]

Your question is not clear. Are you asking if one can extract an ENTIRE pathway from a PPI network? Or are you looking for even PARTIAL pathways from a PPI network - if so, what threshold would you use for inclusion or exclusion? Please restate your question more clearly.

[jack]

Either entire or partial is fine.

Answer 1

[natasha.sernova]

See my answer to the following post:

C: Pathway annotation using sequence alignment

it gives KEGG links.

There are a lot of papers about ppi, try to search KEGG.

I’ve provided some necessary links in my post above:

But it is not quite clear whose proteins you study.

STRING may also be helpful.

There are some random examples below (I searched NCBI for “KEGG AND ppi”):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022245/pdf/1745-6150-9-5.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851814/pdf/1752-0509-7-S2-S8.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300222/pdf/pone.0116347.pdf

But this link https://omictools.com/ppis-category

is more general, it relates to many areas.

And look at the right panel - there are a lot of similar questions:answers there,

it may be helpful too.