Cargando…
GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data
Intermediate phenotypes such as gene expression values can be used to elucidate the mechanisms by which genetic variation causes phenotypic variation, but jointly analyzing such heterogeneous data are far from trivial. Here we extend a so-called mediation model to handle the confounding effects of g...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118313/ https://www.ncbi.nlm.nih.gov/pubmed/30068524 http://dx.doi.org/10.1534/g3.118.200571 |
_version_ | 1783351908545593344 |
---|---|
author | Sasaki, Eriko Frommlet, Florian Nordborg, Magnus |
author_facet | Sasaki, Eriko Frommlet, Florian Nordborg, Magnus |
author_sort | Sasaki, Eriko |
collection | PubMed |
description | Intermediate phenotypes such as gene expression values can be used to elucidate the mechanisms by which genetic variation causes phenotypic variation, but jointly analyzing such heterogeneous data are far from trivial. Here we extend a so-called mediation model to handle the confounding effects of genetic background, and use it to analyze flowering time variation in Arabidopsis thaliana, focusing in particular on the central role played by the key regulator FLOWERING TIME LOCUS C (FLC). FLC polymorphism and FLC expression are both strongly correlated with flowering time variation, but the effect of the former is only partly mediated through the latter. Furthermore, the latter also reflects genetic background effects. We demonstrate that it is possible to partition these effects, shedding light on the complex regulatory network that underlies flowering time variation. |
format | Online Article Text |
id | pubmed-6118313 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-61183132018-09-04 GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data Sasaki, Eriko Frommlet, Florian Nordborg, Magnus G3 (Bethesda) Investigations Intermediate phenotypes such as gene expression values can be used to elucidate the mechanisms by which genetic variation causes phenotypic variation, but jointly analyzing such heterogeneous data are far from trivial. Here we extend a so-called mediation model to handle the confounding effects of genetic background, and use it to analyze flowering time variation in Arabidopsis thaliana, focusing in particular on the central role played by the key regulator FLOWERING TIME LOCUS C (FLC). FLC polymorphism and FLC expression are both strongly correlated with flowering time variation, but the effect of the former is only partly mediated through the latter. Furthermore, the latter also reflects genetic background effects. We demonstrate that it is possible to partition these effects, shedding light on the complex regulatory network that underlies flowering time variation. Genetics Society of America 2018-08-01 /pmc/articles/PMC6118313/ /pubmed/30068524 http://dx.doi.org/10.1534/g3.118.200571 Text en Copyright © 2018 Sasaki et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Sasaki, Eriko Frommlet, Florian Nordborg, Magnus GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data |
title | GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data |
title_full | GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data |
title_fullStr | GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data |
title_full_unstemmed | GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data |
title_short | GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data |
title_sort | gwas with heterogeneous data: estimating the fraction of phenotypic variation mediated by gene expression data |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118313/ https://www.ncbi.nlm.nih.gov/pubmed/30068524 http://dx.doi.org/10.1534/g3.118.200571 |
work_keys_str_mv | AT sasakieriko gwaswithheterogeneousdataestimatingthefractionofphenotypicvariationmediatedbygeneexpressiondata AT frommletflorian gwaswithheterogeneousdataestimatingthefractionofphenotypicvariationmediatedbygeneexpressiondata AT nordborgmagnus gwaswithheterogeneousdataestimatingthefractionofphenotypicvariationmediatedbygeneexpressiondata |