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GeNeCK: a web server for gene network construction and visualization

BACKGROUND: Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorithms have been proposed, development of computational tools to integrate results...

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Detalles Bibliográficos
Autores principales: Zhang, Minzhe, Li, Qiwei, Yu, Donghyeon, Yao, Bo, Guo, Wei, Xie, Yang, Xiao, Guanghua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323745/
https://www.ncbi.nlm.nih.gov/pubmed/30616521
http://dx.doi.org/10.1186/s12859-018-2560-0
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author Zhang, Minzhe
Li, Qiwei
Yu, Donghyeon
Yao, Bo
Guo, Wei
Xie, Yang
Xiao, Guanghua
author_facet Zhang, Minzhe
Li, Qiwei
Yu, Donghyeon
Yao, Bo
Guo, Wei
Xie, Yang
Xiao, Guanghua
author_sort Zhang, Minzhe
collection PubMed
description BACKGROUND: Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorithms have been proposed, development of computational tools to integrate results from different methods and user-friendly online tools is still lagging. RESULTS: We developed a web server that efficiently constructs gene networks from expression data. It allows the user to use ten different network construction methods (such as partial correlation-, likelihood-, Bayesian- and mutual information-based methods) and integrates the resulting networks from multiple methods. Hub gene information, if available, can be incorporated to enhance performance. CONCLUSIONS: GeNeCK is an efficient and easy-to-use web application for gene regulatory network construction. It can be accessed at http://lce.biohpc.swmed.edu/geneck. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2560-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-63237452019-01-10 GeNeCK: a web server for gene network construction and visualization Zhang, Minzhe Li, Qiwei Yu, Donghyeon Yao, Bo Guo, Wei Xie, Yang Xiao, Guanghua BMC Bioinformatics Software BACKGROUND: Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorithms have been proposed, development of computational tools to integrate results from different methods and user-friendly online tools is still lagging. RESULTS: We developed a web server that efficiently constructs gene networks from expression data. It allows the user to use ten different network construction methods (such as partial correlation-, likelihood-, Bayesian- and mutual information-based methods) and integrates the resulting networks from multiple methods. Hub gene information, if available, can be incorporated to enhance performance. CONCLUSIONS: GeNeCK is an efficient and easy-to-use web application for gene regulatory network construction. It can be accessed at http://lce.biohpc.swmed.edu/geneck. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2560-0) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-07 /pmc/articles/PMC6323745/ /pubmed/30616521 http://dx.doi.org/10.1186/s12859-018-2560-0 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Zhang, Minzhe
Li, Qiwei
Yu, Donghyeon
Yao, Bo
Guo, Wei
Xie, Yang
Xiao, Guanghua
GeNeCK: a web server for gene network construction and visualization
title GeNeCK: a web server for gene network construction and visualization
title_full GeNeCK: a web server for gene network construction and visualization
title_fullStr GeNeCK: a web server for gene network construction and visualization
title_full_unstemmed GeNeCK: a web server for gene network construction and visualization
title_short GeNeCK: a web server for gene network construction and visualization
title_sort geneck: a web server for gene network construction and visualization
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323745/
https://www.ncbi.nlm.nih.gov/pubmed/30616521
http://dx.doi.org/10.1186/s12859-018-2560-0
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