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DecoPath: a web application for decoding pathway enrichment analysis

The past decades have brought a steady growth of pathway databases and enrichment methods. However, the advent of pathway data has not been accompanied by an improvement in interoperability across databases, hampering the use of pathway knowledge from multiple databases for enrichment analysis. Whil...

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Autores principales: Mubeen, Sarah, Bharadhwaj, Vinay S, Gadiya, Yojana, Hofmann-Apitius, Martin, Kodamullil, Alpha T, Domingo-Fernández, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459727/
https://www.ncbi.nlm.nih.gov/pubmed/34568823
http://dx.doi.org/10.1093/nargab/lqab087
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author Mubeen, Sarah
Bharadhwaj, Vinay S
Gadiya, Yojana
Hofmann-Apitius, Martin
Kodamullil, Alpha T
Domingo-Fernández, Daniel
author_facet Mubeen, Sarah
Bharadhwaj, Vinay S
Gadiya, Yojana
Hofmann-Apitius, Martin
Kodamullil, Alpha T
Domingo-Fernández, Daniel
author_sort Mubeen, Sarah
collection PubMed
description The past decades have brought a steady growth of pathway databases and enrichment methods. However, the advent of pathway data has not been accompanied by an improvement in interoperability across databases, hampering the use of pathway knowledge from multiple databases for enrichment analysis. While integrative databases have attempted to address this issue, they often do not account for redundant information across resources. Furthermore, the majority of studies that employ pathway enrichment analysis still rely upon a single database or enrichment method, though the use of another could yield differing results. These shortcomings call for approaches that investigate the differences and agreements across databases and methods as their selection in the design of a pathway analysis can be a crucial step in ensuring the results of such an analysis are meaningful. Here we present DecoPath, a web application to assist in the interpretation of the results of pathway enrichment analysis. DecoPath provides an ecosystem to run enrichment analysis or directly upload results and facilitate the interpretation of results with custom visualizations that highlight the consensus and/or discrepancies at the pathway- and gene-levels. DecoPath is available at https://decopath.scai.fraunhofer.de, and its source code and documentation can be found on GitHub at https://github.com/DecoPath/DecoPath.
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spelling pubmed-84597272021-09-23 DecoPath: a web application for decoding pathway enrichment analysis Mubeen, Sarah Bharadhwaj, Vinay S Gadiya, Yojana Hofmann-Apitius, Martin Kodamullil, Alpha T Domingo-Fernández, Daniel NAR Genom Bioinform Standard Article The past decades have brought a steady growth of pathway databases and enrichment methods. However, the advent of pathway data has not been accompanied by an improvement in interoperability across databases, hampering the use of pathway knowledge from multiple databases for enrichment analysis. While integrative databases have attempted to address this issue, they often do not account for redundant information across resources. Furthermore, the majority of studies that employ pathway enrichment analysis still rely upon a single database or enrichment method, though the use of another could yield differing results. These shortcomings call for approaches that investigate the differences and agreements across databases and methods as their selection in the design of a pathway analysis can be a crucial step in ensuring the results of such an analysis are meaningful. Here we present DecoPath, a web application to assist in the interpretation of the results of pathway enrichment analysis. DecoPath provides an ecosystem to run enrichment analysis or directly upload results and facilitate the interpretation of results with custom visualizations that highlight the consensus and/or discrepancies at the pathway- and gene-levels. DecoPath is available at https://decopath.scai.fraunhofer.de, and its source code and documentation can be found on GitHub at https://github.com/DecoPath/DecoPath. Oxford University Press 2021-09-23 /pmc/articles/PMC8459727/ /pubmed/34568823 http://dx.doi.org/10.1093/nargab/lqab087 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Article
Mubeen, Sarah
Bharadhwaj, Vinay S
Gadiya, Yojana
Hofmann-Apitius, Martin
Kodamullil, Alpha T
Domingo-Fernández, Daniel
DecoPath: a web application for decoding pathway enrichment analysis
title DecoPath: a web application for decoding pathway enrichment analysis
title_full DecoPath: a web application for decoding pathway enrichment analysis
title_fullStr DecoPath: a web application for decoding pathway enrichment analysis
title_full_unstemmed DecoPath: a web application for decoding pathway enrichment analysis
title_short DecoPath: a web application for decoding pathway enrichment analysis
title_sort decopath: a web application for decoding pathway enrichment analysis
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459727/
https://www.ncbi.nlm.nih.gov/pubmed/34568823
http://dx.doi.org/10.1093/nargab/lqab087
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