Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

Abstract Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis — the ontology and the annotations — evolve rapidly....

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Autores principales:	Aurelie Tomczak, Jonathan M. Mortensen, Rainer Winnenburg, Charles Liu, Dominique T. Alessi, Varsha Swamy, Francesco Vallania, Shane Lofgren, Winston Haynes, Nigam H. Shah, Mark A. Musen, Purvesh Khatri
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/22ec44186f434485be70d5c0e2be2183
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spelling	oai:doaj.org-article:22ec44186f434485be70d5c0e2be21832021-12-02T15:07:57ZInterpretation of biological experiments changes with evolution of the Gene Ontology and its annotations10.1038/s41598-018-23395-22045-2322https://doaj.org/article/22ec44186f434485be70d5c0e2be21832018-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-23395-2https://doaj.org/toc/2045-2322Abstract Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis — the ontology and the annotations — evolve rapidly. We used gene signatures derived from 104 disease analyses to systematically evaluate how enrichment analysis results were affected by evolution of the GO over a decade. We found low consistency between enrichment analyses results obtained with early and more recent GO versions. Furthermore, there continues to be a strong annotation bias in the GO annotations where 58% of the annotations are for 16% of the human genes. Our analysis suggests that GO evolution may have affected the interpretation and possibly reproducibility of experiments over time. Hence, researchers must exercise caution when interpreting GO enrichment analyses and should reexamine previous analyses with the most recent GO version.Aurelie TomczakJonathan M. MortensenRainer WinnenburgCharles LiuDominique T. AlessiVarsha SwamyFrancesco VallaniaShane LofgrenWinston HaynesNigam H. ShahMark A. MusenPurvesh KhatriNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-10 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aurelie Tomczak Jonathan M. Mortensen Rainer Winnenburg Charles Liu Dominique T. Alessi Varsha Swamy Francesco Vallania Shane Lofgren Winston Haynes Nigam H. Shah Mark A. Musen Purvesh Khatri Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
description	Abstract Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis — the ontology and the annotations — evolve rapidly. We used gene signatures derived from 104 disease analyses to systematically evaluate how enrichment analysis results were affected by evolution of the GO over a decade. We found low consistency between enrichment analyses results obtained with early and more recent GO versions. Furthermore, there continues to be a strong annotation bias in the GO annotations where 58% of the annotations are for 16% of the human genes. Our analysis suggests that GO evolution may have affected the interpretation and possibly reproducibility of experiments over time. Hence, researchers must exercise caution when interpreting GO enrichment analyses and should reexamine previous analyses with the most recent GO version.
format	article
author	Aurelie Tomczak Jonathan M. Mortensen Rainer Winnenburg Charles Liu Dominique T. Alessi Varsha Swamy Francesco Vallania Shane Lofgren Winston Haynes Nigam H. Shah Mark A. Musen Purvesh Khatri
author_facet	Aurelie Tomczak Jonathan M. Mortensen Rainer Winnenburg Charles Liu Dominique T. Alessi Varsha Swamy Francesco Vallania Shane Lofgren Winston Haynes Nigam H. Shah Mark A. Musen Purvesh Khatri
author_sort	Aurelie Tomczak
title	Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
title_short	Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
title_full	Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
title_fullStr	Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
title_full_unstemmed	Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
title_sort	interpretation of biological experiments changes with evolution of the gene ontology and its annotations
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/22ec44186f434485be70d5c0e2be2183
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Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

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