OrthoClust: an orthology-based network framework for clustering data across multiple species |
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| Authors: | Koon-Kiu Yan Daifeng Wang Joel Rozowsky Henry Zheng Chao Cheng Mark Gerstein |
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| Affiliation: | .Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520 USA ;.Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA ;.Department of Computer Science, Yale University, New Haven, CT 06520 USA ;.Department of Genetics, Dartmouth School of Medicine, Hanover, NH 03755 USA |
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| Abstract: | Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.Electronic supplementary materialThe online version of this article (doi:10.1186/gb-2014-15-8-r100) contains supplementary material, which is available to authorized users. |
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