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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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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. |
format | Online Article Text |
id | pubmed-9140214 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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