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NetConfer: a web application for comparative analysis of multiple biological networks

BACKGROUND: Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The co...

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Autores principales: Nagpal, Sunil, Baksi, Krishanu Das, Kuntal, Bhusan K., Mande, Sharmila S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236966/
https://www.ncbi.nlm.nih.gov/pubmed/32430035
http://dx.doi.org/10.1186/s12915-020-00781-9
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author Nagpal, Sunil
Baksi, Krishanu Das
Kuntal, Bhusan K.
Mande, Sharmila S.
author_facet Nagpal, Sunil
Baksi, Krishanu Das
Kuntal, Bhusan K.
Mande, Sharmila S.
author_sort Nagpal, Sunil
collection PubMed
description BACKGROUND: Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The complexity of biological systems and the interactions of their various components, such as genes, proteins, taxa, and metabolites, have been inferred, represented, and visualized via graph theory-based networks. Comparisons of multiple networks can help in identifying variations across different biological systems, thereby providing additional insights. However, while a number of online and stand-alone tools exist for generating, analyzing, and visualizing individual biological networks, the utility to batch process and comprehensively compare multiple networks is limited. RESULTS: Here, we present a graphical user interface (GUI)-based web application which implements multiple network comparison methodologies and presents them in the form of organized analysis workflows. Dedicated comparative visualization modules are provided to the end-users for obtaining easy to comprehend, insightful, and meaningful comparisons of various biological networks. We demonstrate the utility and power of our tool using publicly available microbial and gene expression data. CONCLUSION: NetConfer tool is developed keeping in mind the requirements of researchers working in the field of biological data analysis with limited programming expertise. It is also expected to be useful for advanced users from biological as well as other domains (working with association networks), benefiting from provided ready-made workflows, as they allow to focus directly on the results without worrying about the implementation. While the web version allows using this application without installation and dependency requirements, a stand-alone version has also been supplemented to accommodate the offline requirement of processing large networks.
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spelling pubmed-72369662020-05-27 NetConfer: a web application for comparative analysis of multiple biological networks Nagpal, Sunil Baksi, Krishanu Das Kuntal, Bhusan K. Mande, Sharmila S. BMC Biol Software BACKGROUND: Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The complexity of biological systems and the interactions of their various components, such as genes, proteins, taxa, and metabolites, have been inferred, represented, and visualized via graph theory-based networks. Comparisons of multiple networks can help in identifying variations across different biological systems, thereby providing additional insights. However, while a number of online and stand-alone tools exist for generating, analyzing, and visualizing individual biological networks, the utility to batch process and comprehensively compare multiple networks is limited. RESULTS: Here, we present a graphical user interface (GUI)-based web application which implements multiple network comparison methodologies and presents them in the form of organized analysis workflows. Dedicated comparative visualization modules are provided to the end-users for obtaining easy to comprehend, insightful, and meaningful comparisons of various biological networks. We demonstrate the utility and power of our tool using publicly available microbial and gene expression data. CONCLUSION: NetConfer tool is developed keeping in mind the requirements of researchers working in the field of biological data analysis with limited programming expertise. It is also expected to be useful for advanced users from biological as well as other domains (working with association networks), benefiting from provided ready-made workflows, as they allow to focus directly on the results without worrying about the implementation. While the web version allows using this application without installation and dependency requirements, a stand-alone version has also been supplemented to accommodate the offline requirement of processing large networks. BioMed Central 2020-05-19 /pmc/articles/PMC7236966/ /pubmed/32430035 http://dx.doi.org/10.1186/s12915-020-00781-9 Text en © The Author(s) 2020 Open AccessThis 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/. 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 in a credit line to the data.
spellingShingle Software
Nagpal, Sunil
Baksi, Krishanu Das
Kuntal, Bhusan K.
Mande, Sharmila S.
NetConfer: a web application for comparative analysis of multiple biological networks
title NetConfer: a web application for comparative analysis of multiple biological networks
title_full NetConfer: a web application for comparative analysis of multiple biological networks
title_fullStr NetConfer: a web application for comparative analysis of multiple biological networks
title_full_unstemmed NetConfer: a web application for comparative analysis of multiple biological networks
title_short NetConfer: a web application for comparative analysis of multiple biological networks
title_sort netconfer: a web application for comparative analysis of multiple biological networks
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236966/
https://www.ncbi.nlm.nih.gov/pubmed/32430035
http://dx.doi.org/10.1186/s12915-020-00781-9
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