Compute Distance Between The Two Sets Of Disease Associated Genes On Protein-Protein Interaction Network

Question

[dcolinmorgan]

I am looking for a way to compare entire subnetworks within the context of encompassing PPI, say Y2H, and calculating how far (shortest path) each node of a disease subnetwork is against each node of another disease subnetwork, and averaging this number over the span of the entire subnetwork - to get a distance between two gwas disease gene sets

[David Westergaard]

If you want to learn how to write your own code, Think Complexity has a section on working with graphs.

Answer 1

[Sudeep]

Take a look at R package igraph, on the simplest case (assuming that there are no node/edge intersections between both the subnetworks) you can do it quite easily by calling shortest.paths or get.shortest.paths functions and calculating average of the edge weights/number of edges

Answer 2

[jackuser1979]

You can use cytoscape for network analysis

http://www.cytoscape.org/

You can use subnetworkcreator plugin in cytoscape for subnetwork analysis

http://apps.cytoscape.org/apps/subnetworkcreator

Also you can use NetworKPrioritizer plugin

http://www.networkprioritizer.de/

see more on their publication: http://bioinformatics.oxfordjournals.org/content/29/11/1471

Also see, iCTNEt cytoscape plugin-incorporates phenotype-SNP associations from the genome-wide association studies (GWAS)

http://sites.cs.queensu.ca/ictnet/UserInformation/download.php

refer to their publication: http://www.biomedcentral.com/1471-2105/12/380

Answer 3

[miquelduranfrigola]

If you are a python programmer, networkx is extremely easy to use.

Functions like shortest_path or all_shortest_path should do the thing.