Network statistics on Protein Interaction Networks

Question

[jt539]

Hi all,

I have a list of genes and want to know what possible interaction networks may lie between them. What resources should I be using for this?

For the database side of things, KEGG seems to be my best shot... but you have to pay for it, right? For the programming side of things, the "KEGGgraph" package seems incredibly useful as it does lots of stats for you. Any other suggestions?

Many thanks

Jake

[natasha.sernova]

https://www.bioconductor.org/packages/devel/bioc/manuals/KEGGgraph/man/KEGGgraph.pdf

Are you sure it is not free?

This post is 7 years old, A: Pathway Analysis In R

but what is a current situation? By the way, in this post people described

other approaches of PPI you are looking for.

Try this link below for KEGG graph. It looks free?

http://bioconductor.org/packages/release/bioc/html/KEGGgraph.html

Answer 1

[Jean-Karim Heriche]

What you want is the solution to a problem called subgraph extraction. For example, given a protein-protein interaction graph, find the subgraph that contains a given list of proteins/genes. There are many algorithms for this depending on what you want from the subgraph. In the past I've used limited random walks to extract relevant sugbraphs. You'll find an implementation in my perl module Algorithm::Graph.