Population differences in transregulator expression quantitative traits loci

Tuesday, October 25, 2011 — Poster Session II
Noon – 2:00 p.m.	Natcher Conference Center	NIEHS	GEN/GENOM-3

Authors

• P Bushel
• R McGovern
• L Liu
• O Hofmann
• A Huda
• J Lu
• W Hide
• X Lin

Abstract

Gene expression quantitative trait loci (eQTL) are a useful tool for identifying single nucleotide polymorphisms (SNPs) associated with genetic diseases. Often times the genetic variants associated with a disease are controlled by a master regulator. The downstream targets of the master regulator are typically co-expressed and share biological function. It is practical to screen for eQTLs by identifying SNPs that are associated with the targets of a transregulator (TR). We used a multivariate regression with the gene expression of known targets of TRs as the response and individual SNPs as predictors to identify TReQTLs in European (CEU) and African (YRI) populations revealing 234 and 154 SNPs as TReQTLs, respectively. To infer molecular pathways that regulate expression variants, we ranked TReQTLs by connectivity within the structure of biological process subtrees that TReQTL SNPs, TRs and targets represent. The structure of the subtree and a gene interaction network of the Foxp3 X-linked breast cancer suppressor TReQTL in CEU revealed that tumor necrosis factor, NF-kappaB and variants in G-protein coupled receptors signaling may play a role as communicators in the transfactor’s functional regulation. Genomic information about the potential pleiotropic effect of Foxp3 TReQTLs was gleaned from integrating mRNA-Seq data and SNP-set enrichment.

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