Question: Network statistics on Protein Interaction Networks
0
gravatar for jt539
4 months ago by
jt5390
jt5390 wrote:

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

R gene • 231 views
ADD COMMENTlink modified 4 months ago by Jean-Karim Heriche19k • written 4 months ago by jt5390

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

ADD REPLYlink modified 4 months ago • written 4 months ago by natasha.sernova3.5k
2
gravatar for Jean-Karim Heriche
4 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche19k wrote:

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.

ADD COMMENTlink written 4 months ago by Jean-Karim Heriche19k
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