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GeCoNet-Tool: a software package for gene co-expression network construction and analysis
BACKGROUND: Network analysis is a powerful tool for studying gene regulation and identifying biological processes associated with gene function. However, constructing gene co-expression networks can be a challenging task, particularly when dealing with a large number of missing values. RESULTS: We i...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10334629/ https://www.ncbi.nlm.nih.gov/pubmed/37434115 http://dx.doi.org/10.1186/s12859-023-05382-1 |
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author | Kuang, Junyao Michel, Kristin Scoglio, Caterina |
author_facet | Kuang, Junyao Michel, Kristin Scoglio, Caterina |
author_sort | Kuang, Junyao |
collection | PubMed |
description | BACKGROUND: Network analysis is a powerful tool for studying gene regulation and identifying biological processes associated with gene function. However, constructing gene co-expression networks can be a challenging task, particularly when dealing with a large number of missing values. RESULTS: We introduce GeCoNet-Tool, an integrated gene co-expression network construction and analysis tool. The tool comprises two main parts: network construction and network analysis. In the network construction part, GeCoNet-Tool offers users various options for processing gene co-expression data derived from diverse technologies. The output of the tool is an edge list with the option of weights associated with each link. In network analysis part, the user can produce a table that includes several network properties such as communities, cores, and centrality measures. With GeCoNet-Tool, users can explore and gain insights into the complex interactions between genes. |
format | Online Article Text |
id | pubmed-10334629 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-103346292023-07-12 GeCoNet-Tool: a software package for gene co-expression network construction and analysis Kuang, Junyao Michel, Kristin Scoglio, Caterina BMC Bioinformatics Software BACKGROUND: Network analysis is a powerful tool for studying gene regulation and identifying biological processes associated with gene function. However, constructing gene co-expression networks can be a challenging task, particularly when dealing with a large number of missing values. RESULTS: We introduce GeCoNet-Tool, an integrated gene co-expression network construction and analysis tool. The tool comprises two main parts: network construction and network analysis. In the network construction part, GeCoNet-Tool offers users various options for processing gene co-expression data derived from diverse technologies. The output of the tool is an edge list with the option of weights associated with each link. In network analysis part, the user can produce a table that includes several network properties such as communities, cores, and centrality measures. With GeCoNet-Tool, users can explore and gain insights into the complex interactions between genes. BioMed Central 2023-07-11 /pmc/articles/PMC10334629/ /pubmed/37434115 http://dx.doi.org/10.1186/s12859-023-05382-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Kuang, Junyao Michel, Kristin Scoglio, Caterina GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
title | GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
title_full | GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
title_fullStr | GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
title_full_unstemmed | GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
title_short | GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
title_sort | geconet-tool: a software package for gene co-expression network construction and analysis |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10334629/ https://www.ncbi.nlm.nih.gov/pubmed/37434115 http://dx.doi.org/10.1186/s12859-023-05382-1 |
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