Question: Compute Distance Between The Two Sets Of Disease Associated Genes On Protein-Protein Interaction Network
2
gravatar for dcolinmorgan
5.6 years ago by
dcolinmorgan100
SciLifeLab, Stockholm
dcolinmorgan100 wrote:

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

ppi distance • 3.2k views
ADD COMMENTlink modified 5.6 years ago by miquelduranfrigola760 • written 5.6 years ago by dcolinmorgan100
2

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

ADD REPLYlink written 5.6 years ago by David Westergaard1.4k
2
gravatar for Sudeep
5.6 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

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

ADD COMMENTlink written 5.6 years ago by Sudeep1.6k
1
gravatar for jackuser1979
5.6 years ago by
jackuser1979860
US
jackuser1979860 wrote:

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

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by jackuser1979860
1
gravatar for miquelduranfrigola
5.6 years ago by
Barcelona
miquelduranfrigola760 wrote:

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

Functions like shortest_path or all_shortest_path should do the thing.

ADD COMMENTlink written 5.6 years ago by miquelduranfrigola760
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