ArticlePLoS computational biology2010
New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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38 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches.PLoS genetics · 2013Pooled it
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- Controlled experiments to explore the use of a multi-tissue approach to characterizing stress in wild-caught Pacific halibut (Conservation physiology · 2021Article
- A Global-Local Approach for Detecting Hotspots in Multiple-Response Regression.The annals of applied statistics · 2020Article
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- Genomic approaches for the elucidation of genes and gene networks underlying cardiovascular traits.Biophysical reviews · 2018Review
- An empirical Bayes approach for multiple tissue eQTL analysis.Biostatistics (Oxford, England) · 2018Article
- A new method to study the change of miRNA-mRNA interactions due to environmental exposures.Bioinformatics (Oxford, England) · 2017Article
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- From integrative genomics to systems genetics in the rat to link genotypes to phenotypes.Disease models & mechanisms · 2016Review
- HDTD: analyzing multi-tissue gene expression data.Bioinformatics (Oxford, England) · 2016Article
- Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci.Clinical and translational gastroenterology · 2016Article
- MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.Bioinformatics (Oxford, England) · 2016Article
- R2GUESS: A Graphics Processing Unit-Based R Package for Bayesian Variable Selection Regression of Multivariate Responses.Journal of statistical software · 2016Article
- Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci.BMC genomics · 2015Article
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Abstract
The majority of expression quantitative trait locus (eQTL) studies have been carried out in single tissues or cell types, using methods that ignore information shared across tissues. Although global analysis of RNA expression in multiple tissues is now feasible, few integrated statistical frameworks for joint analysis of gene expression across tissues combined with simultaneous analysis of multiple genetic variants have been developed to date. Here, we propose Sparse Bayesian Regression models for mapping eQTLs within individual tissues and simultaneously across tissues. Testing these on a set of 2,000 genes in four tissues, we demonstrate that our methods are more powerful than traditional approaches in revealing the true complexity of the eQTL landscape at the systems-level. Highlighting the power of our method, we identified a two-eQTL model (cis/trans) for the Hopx gene that was experimentally validated and was not detected by conventional approaches. We showed common genetic regulation of gene expression across four tissues for approximately 27% of transcripts, providing >5 fold increase in eQTLs detection when compared with single tissue analyses at 5% FDR level. These findings provide a new opportunity to uncover complex genetic regulatory mechanisms controlling global gene expression while the generality of our modelling approach makes it adaptable to other model systems and humans, with broad application to analysis of multiple intermediate and whole-body phenotypes.
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