A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank

Phenome-wide association studies identified numerous loci associated with traits and diseases. To help interpret these associations, we constructed a phenome-wide network map of colocalized genes and phenotypes. We generated colocalized signals using the Genotype-Tissue Expression data and genome-wi...

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Autores principales: Rocheleau, Ghislain, Forrest, Iain S., Duffy, Áine, Bafna, Shantanu, Dobbyn, Amanda, Verbanck, Marie, Won, Hong-Hee, Jordan, Daniel M., Do, Ron
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9392744/
https://www.ncbi.nlm.nih.gov/pubmed/35987940
http://dx.doi.org/10.1038/s42003-022-03820-z
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author Rocheleau, Ghislain
Forrest, Iain S.
Duffy, Áine
Bafna, Shantanu
Dobbyn, Amanda
Verbanck, Marie
Won, Hong-Hee
Jordan, Daniel M.
Do, Ron
author_facet Rocheleau, Ghislain
Forrest, Iain S.
Duffy, Áine
Bafna, Shantanu
Dobbyn, Amanda
Verbanck, Marie
Won, Hong-Hee
Jordan, Daniel M.
Do, Ron
author_sort Rocheleau, Ghislain
collection PubMed
description Phenome-wide association studies identified numerous loci associated with traits and diseases. To help interpret these associations, we constructed a phenome-wide network map of colocalized genes and phenotypes. We generated colocalized signals using the Genotype-Tissue Expression data and genome-wide association results in UK Biobank. We identified 9151 colocalized genes for 1411 phenotypes across 48 tissues. Then, we constructed bipartite networks using the colocalized signals in each tissue, and showed that the majority of links were observed in a single tissue. We applied the biLouvain clustering algorithm in each tissue-specific network to identify co-clusters of genes and phenotypes. We observed significant enrichments of these co-clusters with known biological and functional gene classes. Overall, the phenome-wide map provides links between genes, phenotypes and tissues, and can yield biological and clinical discoveries.
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spelling pubmed-93927442022-08-22 A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank Rocheleau, Ghislain Forrest, Iain S. Duffy, Áine Bafna, Shantanu Dobbyn, Amanda Verbanck, Marie Won, Hong-Hee Jordan, Daniel M. Do, Ron Commun Biol Article Phenome-wide association studies identified numerous loci associated with traits and diseases. To help interpret these associations, we constructed a phenome-wide network map of colocalized genes and phenotypes. We generated colocalized signals using the Genotype-Tissue Expression data and genome-wide association results in UK Biobank. We identified 9151 colocalized genes for 1411 phenotypes across 48 tissues. Then, we constructed bipartite networks using the colocalized signals in each tissue, and showed that the majority of links were observed in a single tissue. We applied the biLouvain clustering algorithm in each tissue-specific network to identify co-clusters of genes and phenotypes. We observed significant enrichments of these co-clusters with known biological and functional gene classes. Overall, the phenome-wide map provides links between genes, phenotypes and tissues, and can yield biological and clinical discoveries. Nature Publishing Group UK 2022-08-20 /pmc/articles/PMC9392744/ /pubmed/35987940 http://dx.doi.org/10.1038/s42003-022-03820-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Rocheleau, Ghislain
Forrest, Iain S.
Duffy, Áine
Bafna, Shantanu
Dobbyn, Amanda
Verbanck, Marie
Won, Hong-Hee
Jordan, Daniel M.
Do, Ron
A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank
title A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank
title_full A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank
title_fullStr A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank
title_full_unstemmed A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank
title_short A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank
title_sort tissue-level phenome-wide network map of colocalized genes and phenotypes in the uk biobank
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9392744/
https://www.ncbi.nlm.nih.gov/pubmed/35987940
http://dx.doi.org/10.1038/s42003-022-03820-z
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