title: OrthoClust: an orthology-based network framework for clustering data across multiple species.
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.
authors.forename: Koon-Kiu
authors.initials: KK
authors.lastname: Yan
authors.forename: Daifeng
authors.initials: D
authors.lastname: Wang
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Henry
authors.initials: H
authors.lastname: Zheng
authors.forename: Chao
authors.initials: C
authors.lastname: Cheng
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D020869:Gene Expression Profiling; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity