Benjamin Hescott, assistant professor of Computer Science, published Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data in BMC Bioinformatics. This work was published with Tufts co-authors Andrew Gallant and Maxim Kachalov, undergrads in computer science, and Professor of Computer Science, Lenore Cowen. The abstract is below –
Background
New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier) the double-knockout organism will be compared to what would be expected from the sickness of the component single knockouts. Recent algorithmic work has identified graph-theoretic patterns in this data that can indicate functional modules, and even sets of genes that may occur in compensatory pathways, such as a BPM-type schema first introduced by Kelley and Ideker. However, to date, any algorithms for finding such patterns in the data were implemented internally, with no software being made publically available.Results
Genecentric is a new package that implements a parallelized version of the Leiserson et al. algorithm [1] for generating generalized BPMs from high-throughput genetic interaction data. Given a matrix of weighted epistasis values for a set of double knock-outs, Genecentric returns a list of generalized BPMs that may represent compensatory pathways. Genecentric also has an extension, GenecentricGO, to query FuncAssociate [2] to retrieve GO enrichment statistics on generated BPMs. Python is the only dependency, and our web site provides working examples and documentation.Conclusion
We find that Genecentric can be used to find coherent functional and perhaps compensatory gene sets from high throughput genetic interaction data. Genecentric is made freely available for download under the GPLv2 from http://bcb.cs.tufts.edu/genecentric.Gallant, A., Leiserson, M. D., Kachalov, M., Cowen, L. J., & Hescott, B. J. (2013). Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data. BMC bioinformatics, 14(1), 23.