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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308667 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btu669 | DOI Listing |
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GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.
Bioinformatics
February 2015
MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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'.
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