GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 25319962.
- Also identified by DOI 10.1093/bioinformatics/btu669 and PMC identifier 4308667.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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. GeneNet Toolbox is open source and freely available from http://avigailtaylor.github.io/gntat14. Supplementary data are available at Bioinformatics online. avigail.taylor@dpag.ox.ac.uk.
Medical subject headings
- Algorithms
- Computational Biology
- Databases, Genetic
- Gene Regulatory Networks
- Metabolic Networks and Pathways
- Sequence Analysis, DNA
- Software