EGAD: Ultra-fast functional analysis of gene networks

Abstract

SummaryEvaluating gene networks with respect to known biology is a common task but often a computationally costly one. Many computational experiments are difficult to apply exhaustively in network analysis due to run-times. To permit high-throughput analysis of gene networks, we have implemented a set of very efficient tools to calculate functional properties in networks based on guilt-by-association methods. EGAD (Extending Guilt-by-Association by Degree) allows gene networks to be evaluated with respect to hundreds or thousands of gene sets. The methods predict novel members of gene groups, assess how well a gene network groups known sets of genes, and determines the degree to which generic predictions drive performance. By allowing fast evaluations, whether of random sets or real functional ones, EGAD provides the user with an assessment of performance which can easily be used in controlled evaluations across many parameters.\n\nAvailability and ImplementationThe software package is freely available at https://github.com/sarbal/EGAD and implemented for use in R and Matlab. The package is also freely available under the LGPL license from the Bioconductor web site (http://bioconductor.org).\n\nContactJGillis@cshl.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online and the full manual at http://gillislab.labsites.cshl.edu/software/egad-extending-guilt-by-association-by-degree/.