SubNet: a Java application for subnetwork extraction | Zendy

Quanwei Zhang | Zendy; Zhengdong D. Zhang | Zendy

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SubNet: a Java application for subnetwork extraction

Author(s) -

Quanwei Zhang,

Zhengdong D. Zhang

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt430

Subject(s) - subnet , subnetwork , computer science , java , node (physics) , metric (unit) , set (abstract data type) , centrality , data mining , information retrieval , computer network , programming language , operations management , mathematics , structural engineering , combinatorics , engineering , economics

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.

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