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

Taylor, Avigail, Steinberg, Julia, Andrews, Tallulah S. and Webber, Caleb ORCID: https://orcid.org/0000-0001-8063-7674 2015. GeneNet toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks. Bioinformatics 31 (3) , pp. 442-444. 10.1093/bioinformatics/btu669

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Abstract

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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Publisher:	Oxford University Press
ISSN:	1367-4803
Date of First Compliant Deposit:	22 October 2020
Date of Acceptance:	6 October 2014
Last Modified:	06 May 2023 04:22
URI:	https://orca.cardiff.ac.uk/id/eprint/135802

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