SubNet: A Java application for subnetwork extraction

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2509-2511
Number of pages3
JournalBioinformatics
Volume29
Issue number19
DOIs
StatePublished - 2013

Fingerprint

Java
Complex networks
Graphical user interfaces
Vertex of a graph
PageRank
Genes
Centrality
Biological Networks
Graphical User Interface
Weights and Measures
Complex Networks
Pathway
Gene
Metric
Module

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

SubNet : A Java application for subnetwork extraction. / Zhang, Quanwei; Zhang, Zhengdong.

In: Bioinformatics, Vol. 29, No. 19, 2013, p. 2509-2511.

Research output: Contribution to journalArticle

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