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massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis

Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted...

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Detalles Bibliográficos
Autores principales: Cerulo, Luigi, Pagnotta, Stefano Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9140214/
https://www.ncbi.nlm.nih.gov/pubmed/35626622
http://dx.doi.org/10.3390/e24050739
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author Cerulo, Luigi
Pagnotta, Stefano Maria
author_facet Cerulo, Luigi
Pagnotta, Stefano Maria
author_sort Cerulo, Luigi
collection PubMed
description Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles. We analyzed the properties of the Mann–Whitney–Wilcoxon test, a competitive method, and adapted its interpretation in the context of enrichment analysis by introducing a Normalized Enrichment Score that summarize two interpretations: a probability estimate and a location index. Two implementations are presented and compared with relevant literature methods: an R package and an online web tool. Both allow for obtaining tabular and graphical results with attention to reproducible research.
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spelling pubmed-91402142022-05-28 massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis Cerulo, Luigi Pagnotta, Stefano Maria Entropy (Basel) Article Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles. We analyzed the properties of the Mann–Whitney–Wilcoxon test, a competitive method, and adapted its interpretation in the context of enrichment analysis by introducing a Normalized Enrichment Score that summarize two interpretations: a probability estimate and a location index. Two implementations are presented and compared with relevant literature methods: an R package and an online web tool. Both allow for obtaining tabular and graphical results with attention to reproducible research. MDPI 2022-05-23 /pmc/articles/PMC9140214/ /pubmed/35626622 http://dx.doi.org/10.3390/e24050739 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Cerulo, Luigi
Pagnotta, Stefano Maria
massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis
title massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis
title_full massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis
title_fullStr massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis
title_full_unstemmed massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis
title_short massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis
title_sort massivegst: a mann–whitney–wilcoxon gene-set test tool that gives meaning to gene-set enrichment analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9140214/
https://www.ncbi.nlm.nih.gov/pubmed/35626622
http://dx.doi.org/10.3390/e24050739
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