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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Cho A,Shin J,Hwang S,Kim C,Shim H,Kim H,Kim H,Lee Idoi
10.1093/nar/gku367subject
Has Abstractpub_date
2014-07-01 00:00:00pages
W76-82issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gku367journal_volume
42pub_type
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