title: WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans.
abstract: High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types of large-scale experimental data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogeneous genomics data can be integrated into a single genome-scale gene network with high prediction power for ribonucleic acid interference (RNAi) phenotypes in Caenorhabditis elegans, a popular metazoan model in the study of developmental biology, neurobiology and genetics. Here, we present WormNet version 3 (v3), which is a new network-assisted hypothesis-generating server for C. elegans. WormNet v3 includes major updates to the base gene network, which substantially improved predictions of RNAi phenotypes. The server generates various gene network-based hypotheses using three complementary network methods: (i) a phenotype-centric approach to 'find new members for a pathway'; (ii) a gene-centric approach to 'infer functions from network neighbors' and (iii) a context-centric approach to 'find context-associated hub genes', which is a new method to identify key genes that mediate physiology within a specific context. For example, we demonstrated that the context-centric approach can be used to identify potential molecular targets of toxic chemicals. WormNet v3 is freely accessible at http://www.inetbio.org/wormnet.
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Ara
authors.initials: A
authors.lastname: Cho
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Junha
authors.initials: J
authors.lastname: Shin
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 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: Chanyoung
authors.initials: C
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: Hyojin
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
authors.forename: Hanhae
authors.initials: H
authors.lastname: Kim
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; D017173:Caenorhabditis elegans / Q000187:drug effects / Q000235:genetics*; D004006:Dichlorvos / Q000633:toxicity; D053263:Gene Regulatory Networks; D017238:Genes, Helminth; D007306:Insecticides / Q000633:toxicity; D020407:Internet; D010641:Phenotype; D034622:RNA Interference; D012984:Software
chemical_list: D007306:Insecticides; D004006:Dichlorvos