A vast resource of allelic expression data spanning human tissues

Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153...

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Autores: Castel, Stephane E., Aguet, François, Mohammadi, Pejman, GTEx Consortium, Ardlie, Kristin G., Lappalainen, Tuuli
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/45398
Acceso en línea:http://hdl.handle.net/10230/45398
http://dx.doi.org/10.1186/s13059-020-02122-z
Access Level:acceso abierto
Palabra clave:ASE
Allelic expression
Functional genomics
GTEx
Genomics
Regulatory variation
eQTL
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spelling A vast resource of allelic expression data spanning human tissuesCastel, Stephane E.Aguet, FrançoisMohammadi, PejmanGTEx ConsortiumArdlie, Kristin G.Lappalainen, TuuliASEAllelic expressionFunctional genomicsGTExGenomicsRegulatory variationeQTLAllele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.BioMed Central202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/45398http://dx.doi.org/10.1186/s13059-020-02122-zreponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGenome Biol. 2020; 21(1):234© The Author(s). 2020 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data mahttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/453982026-05-29T05:05:01Z
dc.title.none.fl_str_mv A vast resource of allelic expression data spanning human tissues
title A vast resource of allelic expression data spanning human tissues
spellingShingle A vast resource of allelic expression data spanning human tissues
Castel, Stephane E.
ASE
Allelic expression
Functional genomics
GTEx
Genomics
Regulatory variation
eQTL
title_short A vast resource of allelic expression data spanning human tissues
title_full A vast resource of allelic expression data spanning human tissues
title_fullStr A vast resource of allelic expression data spanning human tissues
title_full_unstemmed A vast resource of allelic expression data spanning human tissues
title_sort A vast resource of allelic expression data spanning human tissues
dc.creator.none.fl_str_mv Castel, Stephane E.
Aguet, François
Mohammadi, Pejman
GTEx Consortium
Ardlie, Kristin G.
Lappalainen, Tuuli
author Castel, Stephane E.
author_facet Castel, Stephane E.
Aguet, François
Mohammadi, Pejman
GTEx Consortium
Ardlie, Kristin G.
Lappalainen, Tuuli
author_role author
author2 Aguet, François
Mohammadi, Pejman
GTEx Consortium
Ardlie, Kristin G.
Lappalainen, Tuuli
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv ASE
Allelic expression
Functional genomics
GTEx
Genomics
Regulatory variation
eQTL
topic ASE
Allelic expression
Functional genomics
GTEx
Genomics
Regulatory variation
eQTL
description Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/45398
http://dx.doi.org/10.1186/s13059-020-02122-z
url http://hdl.handle.net/10230/45398
http://dx.doi.org/10.1186/s13059-020-02122-z
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Genome Biol. 2020; 21(1):234
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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