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

Ghislain Rocheleau; Iain S. Forrest; Áine Duffy; Shantanu Bafna; Amanda Dobbyn; Marie Verbanck; Hong Hee Won; Daniel M. Jordan; Ron Do

doi:10.1038/s42003-022-03820-z

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

Ghislain Rocheleau, Iain S. Forrest, Áine Duffy, Shantanu Bafna, Amanda Dobbyn, Marie Verbanck, Hong Hee Won, Daniel M. Jordan, Ron Do

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English
Article number	849
Journal	Communications Biology
Volume	5
Issue number	1
DOIs	https://doi.org/10.1038/s42003-022-03820-z
State	Published - Dec 2022

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

abstract = "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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AU - Rocheleau, Ghislain

AU - Forrest, Iain S.

AU - Duffy, Áine

AU - Bafna, Shantanu

AU - Dobbyn, Amanda

AU - Verbanck, Marie

AU - Won, Hong Hee

AU - Jordan, Daniel M.

AU - Do, Ron

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

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