title: MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.
abstract: Laboratory mouse, Mus musculus, is one of the most important animal tools in biomedical research. Functional characterization of the mouse genes, hence, has been a long-standing goal in mammalian and human genetics. Although large-scale knockout phenotyping is under progress by international collaborative efforts, a large portion of mouse genome is still poorly characterized for cellular functions and associations with disease phenotypes. A genome-scale functional network of mouse genes, MouseNet, was previously developed in context of MouseFunc competition, which allowed only limited input data for network inferences. Here, we present an improved mouse co-functional network, MouseNet v2 (available at http://www.inetbio.org/mousenet), which covers 17 714 genes (>88% of coding genome) with 788 080 links, along with a companion web server for network-assisted functional hypothesis generation. The network database has been substantially improved by large expansion of genomics data. For example, MouseNet v2 database contains 183 co-expression networks inferred from 8154 public microarray samples. We demonstrated that MouseNet v2 is predictive for mammalian phenotypes as well as human diseases, which suggests its usefulness in discovery of novel disease genes and dissection of disease pathways. Furthermore, MouseNet v2 database provides functional networks for eight other vertebrate models used in various research fields.
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Eiru
authors.initials: E
authors.lastname: Kim
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.
authors.forename: Sohyun
authors.initials: S
authors.lastname: Hwang
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Hyojin
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Hongseok
authors.initials: H
authors.lastname: Shim
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Byunghee
authors.initials: B
authors.lastname: Kang
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Sunmo
authors.initials: S
authors.lastname: Yang
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Jae Ho
authors.initials: JH
authors.lastname: Shim
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Seung Yeon
authors.initials: SY
authors.lastname: Shin
authors.affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Marcotte
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea insuklee@yonsei.ac.kr.
authors.forename: Insuk
authors.initials: I
authors.lastname: Lee
mesh_terms: D000818:Animals; D002417:Cattle; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics; D004285:Dogs; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D051379:Mice / Q000235:genetics*; D010641:Phenotype; D051381:Rats