title: Refining regulatory networks through phylogenetic transfer of information.
abstract: The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and timeconsuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed partly to the limitations of a single-organism approach. Computational biology has long used comparative and evolutionary approaches to extend the reach and accuracy of its analyses. In this paper, we describe ProPhyC, a probabilistic phylogenetic model and associated inference algorithms, designed to improve the inference of regulatory networks for a family of organisms by using known evolutionary relationships among these organisms. ProPhyC can be used with various network evolutionary models and any existing inference method. Extensive experimental results on both biological and synthetic data confirm that our model (through its associated refinement algorithms) yields substantial improvement in the quality of inferred networks over all current methods. We also compare ProPhyC with a transfer learning approach we design. This approach also uses phylogenetic relationships while inferring regulatory networks for a family of organisms. Using similar input information but designed in a very different framework, this transfer learning approach does not perform better than ProPhyC, which indicates that ProPhyC makes good use of the evolutionary information.
authors.affiliation: Laboratory for Computational Biology and Bioinformatics, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, EPFL IC IIF LCBB INJ211, Lausanne CH-1015, Switzerland. xiuwei.zhang@epfl.ch
authors.forename: Xiuwei
authors.initials: X
authors.lastname: Zhang
authors.forename: Bernard M E
authors.initials: BM
authors.lastname: Moret
mesh_terms: D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004330:Drosophila; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D010802:Phylogeny; D012372:ROC Curve; D014157:Transcription Factors
chemical_list: D014157:Transcription Factors