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SUMMARY: We present GeneNet Toolbox for MATLAB (also available as a set of standalone applications for Linux). The toolbox, available as command-line or with a graphical user interface, enables biologists to assess connectivity among a set of genes of interest ('seed-genes') within a biological network of their choosing. Two methods are implemented for calculating the significance of connectivity among seed-genes: 'seed randomization' and 'network permutation'. Options include restricting analyses to a specified subnetwork of the primary biological network, and calculating connectivity from the seed-genes to a second set of interesting genes. Pre-analysis tools help the user choose the best connectivity-analysis algorithm for their network. The toolbox also enables visualization of the connections among seed-genes. GeneNet Toolbox functions execute in reasonable time for very large networks (∼10 million edges) on a desktop computer. AVAILABILITY AND IMPLEMENTATION: GeneNet Toolbox is open source and freely available from http://avigailtaylor.github.io/gntat14. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: avigail.taylor@dpag.ox.ac.uk.

Original publication

DOI

10.1093/bioinformatics/btu669

Type

Journal article

Journal

Bioinformatics

Publication Date

01/02/2015

Volume

31

Pages

442 - 444

Keywords

Algorithms, Computational Biology, Computer Graphics, Databases, Genetic, Gene Expression Regulation, Gene Regulatory Networks, Humans, Information Storage and Retrieval, Metabolic Networks and Pathways, Sequence Analysis, DNA, Software, User-Computer Interface