GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks - PubMed (original) (raw)

GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks

Avigail Taylor et al. Bioinformatics. 2015.

Abstract

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.

© The Author 2014. Published by Oxford University Press.

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