WormNet v3: A network-assisted hypothesis-generating server for Caenorhabditis elegans

Ara Cho, Junha Shin, Sohyun Hwang, Chanyoung Kim, Hongseok Shim, Hyojin Kim, Hanhae Kim, Insuk Lee

Research output: Contribution to journalArticle

23 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)W76-W82
JournalNucleic acids research
Volume42
Issue numberW1
DOIs
Publication statusPublished - 2014 Jul 1

All Science Journal Classification (ASJC) codes

  • Genetics

Fingerprint Dive into the research topics of 'WormNet v3: A network-assisted hypothesis-generating server for Caenorhabditis elegans'. Together they form a unique fingerprint.

  • Cite this