ArticlePloS one2008
Genome-wide co-expression analysis in multiple tissues.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Integrating selective signatures and Cis-eQTLs to prioritize candidate genes potentially related to milk production traits in dual-purpose cattle.Frontiers in veterinary science · 2026Article
- The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats.Nucleic acids research · 2022Article
- RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture.Frontiers in genetics · 2021Article
- Conserved properties of genetic architecture of renal and fat transcriptomes in rat models of insulin resistance.Disease models & mechanisms · 2019Article
- Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.Molecular psychiatry · 2014Article
- Mapping eQTLs in the Norfolk Island genetic isolate identifies candidate genes for CVD risk traits.American journal of human genetics · 2013Article
- Genome-Wide Detection of Gene Coexpression Domains Showing Linkage to Regions Enriched with Polymorphic Retrotransposons in Recombinant Inbred Mouse Strains.G3 (Bethesda, Md.) · 2013Article
- Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population.BMC plant biology · 2012Article
- Identifying the genetic variation of gene expression using gene sets: application of novel gene Set eQTL approach to PharmGKB and KEGG.PloS one · 2012Article
- Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans.PLoS genetics · 2011Article
- Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.Physiological genomics · 2011Article
- Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Small RNA expression and strain specificity in the rat.BMC genomics · 2010Article
- The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution.The New phytologist · 2010Review
- Recent advances in genetics of the spontaneously hypertensive rat.Current hypertension reports · 2010Review
- A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia.PLoS genetics · 2009Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
Expression quantitative trait loci (eQTLs) represent genetic control points of gene expression, and can be categorized as cis- and trans-acting, reflecting local and distant regulation of gene expression respectively. Although there is evidence of co-regulation within clusters of trans-eQTLs, the extent of co-expression patterns and their relationship with the genotypes at eQTLs are not fully understood. We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains. Here we investigate the genome-wide correlation structure in expression levels of eQTL transcripts and underlying genotypes to elucidate the nature of co-regulation within cis- and trans-eQTL datasets. Across the four tissues, we consistently found statistically significant correlations of cis-regulated gene expression to be rare (<0.9% of all pairs tested). Most (>80%) of the observed significant correlations of cis-regulated gene expression are explained by correlation of the underlying genotypes. In comparison, co-expression of trans-regulated gene expression is more common, with significant correlation ranging from 2.9%-14.9% of all pairs of trans-eQTL transcripts. We observed a total of 81 trans-eQTL clusters (hot-spots), defined as consisting of > or =10 eQTLs linked to a common region, with very high levels of correlation between trans-regulated transcripts (77.2-90.2%). Moreover, functional analysis of large trans-eQTL clusters (> or =30 eQTLs) revealed significant functional enrichment among genes comprising 80% of the large clusters. The results of this genome-wide co-expression study show the effects of the eQTL genotypes on the observed patterns of correlation, and suggest that functional relatedness between genes underlying trans-eQTLs is reflected in the degree of co-expression observed in trans-eQTL clusters. Our results demonstrate the power of an integrative, systematic approach to the analysis of a large gene expression dataset to uncover underlying structure, and inform future eQTL studies.
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