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WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans
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 demonstr...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086142/ https://www.ncbi.nlm.nih.gov/pubmed/24813450 http://dx.doi.org/10.1093/nar/gku367 |
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author | Cho, Ara Shin, Junha Hwang, Sohyun Kim, Chanyoung Shim, Hongseok Kim, Hyojin Kim, Hanhae Lee, Insuk |
author_facet | Cho, Ara Shin, Junha Hwang, Sohyun Kim, Chanyoung Shim, Hongseok Kim, Hyojin Kim, Hanhae Lee, Insuk |
author_sort | Cho, Ara |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4086142 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40861422014-12-02 WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans Cho, Ara Shin, Junha Hwang, Sohyun Kim, Chanyoung Shim, Hongseok Kim, Hyojin Kim, Hanhae Lee, Insuk Nucleic Acids Res Article 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. Oxford University Press 2014-07-01 2014-05-09 /pmc/articles/PMC4086142/ /pubmed/24813450 http://dx.doi.org/10.1093/nar/gku367 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Article Cho, Ara Shin, Junha Hwang, Sohyun Kim, Chanyoung Shim, Hongseok Kim, Hyojin Kim, Hanhae Lee, Insuk WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans |
title | WormNet v3: a network-assisted hypothesis-generating server for
Caenorhabditis elegans |
title_full | WormNet v3: a network-assisted hypothesis-generating server for
Caenorhabditis elegans |
title_fullStr | WormNet v3: a network-assisted hypothesis-generating server for
Caenorhabditis elegans |
title_full_unstemmed | WormNet v3: a network-assisted hypothesis-generating server for
Caenorhabditis elegans |
title_short | WormNet v3: a network-assisted hypothesis-generating server for
Caenorhabditis elegans |
title_sort | wormnet v3: a network-assisted hypothesis-generating server for
caenorhabditis elegans |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086142/ https://www.ncbi.nlm.nih.gov/pubmed/24813450 http://dx.doi.org/10.1093/nar/gku367 |
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