Question: How to extract known pathways from protein protein interaction network?
0
gravatar for jack
13 months ago by
jack730
Germany
jack730 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 • 618 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by jack730

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 13 months ago by andrew450

Either entire or partial is fine.

ADD REPLYlink written 13 months ago by jack730
1
gravatar for natasha.sernova
13 months ago by
natasha.sernova3.1k
natasha.sernova3.1k 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 13 months ago • written 13 months ago by natasha.sernova3.1k
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