Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer

BMC Med Genomics. 2011 Jan 12;4:6. doi: 10.1186/1755-8794-4-6.

Abstract

Background: Expression quantitative trait loci (eQTL) studies have helped identify the genetic determinants of gene expression. Understanding the potential interacting mechanisms underlying such findings, however, is challenging.

Methods: We describe a method to identify the trans-acting drivers of multiple gene co-expression, which reflects the action of regulatory molecules. This method-termed co-regulatory expression quantitative trait locus (creQTL) mapping-allows for evaluation of a more focused set of phenotypes within a clear biological context than conventional eQTL mapping.

Results: Applying this method to a study of endometrial cancer revealed regulatory mechanisms supported by the literature: a creQTL between a locus upstream of STARD13/DLC2 and a group of seven IFNβ-induced genes. This suggests that the Rho-GTPase encoded by STARD13 regulates IFNβ-induced genes and the DNA damage response.

Conclusions: Because of the importance of IFNβ in cancer, our results suggest that creQTL may provide a finer picture of gene regulation and may reveal additional molecular targets for intervention. An open source R implementation of the method is available at http://sites.google.com/site/kenkompass/.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromosome Mapping / methods*
  • Databases, Genetic
  • Endometrial Neoplasms / genetics*
  • Female
  • Gene Expression
  • Gene Expression Regulation
  • Humans
  • Phenotype
  • Quantitative Trait Loci*