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Bioinformatics. 2013 Oct 1;29(19):2509-11. doi: 10.1093/bioinformatics/btt430. Epub 2013 Aug 13.

SubNet: a Java application for subnetwork extraction.

Author information

1
Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.

Erratum in

  • Bioinformatics. 2013 Nov 15;29(22):2958. Lemetre, Christophe [added].

Abstract

SUMMARY:

The extraction of targeted subnetworks is a powerful way to identify functional modules and pathways within complex networks. Here, we present SubNet, a Java-based stand-alone program for extracting subnetworks, given a basal network and a set of selected nodes. Designed with a graphical user-friendly interface, SubNet combines four different extraction methods, which offer the possibility to interrogate a biological network according to the question investigated. Of note, we developed a method based on the highly successful Google PageRank algorithm to extract the subnetwork using the node centrality metric, to which possible node weights of the selected genes can be incorporated.

AVAILABILITY:

http://www.zdzlab.org/1/subnet.html

PMID:
23946504
PMCID:
PMC3777115
DOI:
10.1093/bioinformatics/btt430
[Indexed for MEDLINE]
Free PMC Article

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