Question: How to extract known pathways from protein protein interaction network?
0
gravatar for jack
10 days ago by
jack680
Germany
jack680 wrote:

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 ?

protein network pathway • 160 views
ADD COMMENTlink modified 9 days ago • written 10 days ago by jack680

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.

ADD REPLYlink written 9 days ago by andrew410

Either entire or partial is fine.

ADD REPLYlink written 9 days ago by jack680
1
gravatar for natasha.sernova
9 days ago by
natasha.sernova2.6k
natasha.sernova2.6k wrote:

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.

ADD COMMENTlink modified 9 days ago • written 9 days ago by natasha.sernova2.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1357 users visited in the last hour