title: A Network of Splice Isoforms for the Mouse.
abstract: The laboratory mouse is the primary mammalian species used for studying alternative splicing events. Recent studies have generated computational models to predict functions for splice isoforms in the mouse. However, the functional relationship network, describing the probability of splice isoforms participating in the same biological process or pathway, has not yet been studied in the mouse. Here we describe a rich genome-wide resource of mouse networks at the isoform level, which was generated using a unique framework that was originally developed to infer isoform functions. This network was built through integrating heterogeneous genomic and protein data, including RNA-seq, exon array, protein docking and pseudo-amino acid composition. Through simulation and cross-validation studies, we demonstrated the accuracy of the algorithm in predicting isoform-level functional relationships. We showed that this network enables the users to reveal functional differences of the isoforms of the same gene, as illustrated by literature evidence with Anxa6 (annexin a6) as an example. We expect this work will become a useful resource for the mouse genetics community to understand gene functions. The network is publicly available at: http://guanlab.ccmb.med.umich.edu/isoformnetwork.
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.|Institute for Systems Biology, Seattle, Washington, United States.
authors.forename: Hong-Dong
authors.initials: HD
authors.lastname: Li
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.
authors.forename: Rajasree
authors.initials: R
authors.lastname: Menon
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.
authors.forename: Ridvan
authors.initials: R
authors.lastname: Eksi
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.
authors.forename: Aysam
authors.initials: A
authors.lastname: Guerler
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.|Institute for Systems Biology, Seattle, Washington, United States.|Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States.
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States.|Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States.|Department of Electrical Engineering and Computer Science, Ann Arbor, Michigan, United States.
authors.forename: Yuanfang
authors.initials: Y
authors.lastname: Guan
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D000069550:Machine Learning; D051379:Mice; D025941:Protein Interaction Mapping; D059368:RNA Isoforms; D015203:Reproducibility of Results
chemical_list: D059368:RNA Isoforms