Proximity model for expression quantitative trait loci (eQTL) detection

Jonathan A Gelfond, Joseph G. Ibrahim, Fei Zou

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Expression quantitative trait loci (eQTL) are loci or markers on the genomes that are associated with gene expression. It is well known to biologists that some (cis) genetic influences on expression occur over short distances on the genome while some (trans) influences can operate remotely. We use a log-linear model to place structure on the prior probability for genetic control of a transcript by a marker locus so that the loci that are closest to a transcript are given a higher prior probability of controlling that transcript to reflect the important role that genomic proximity can play in the regulation of expression. This proximity model is an extension of the mixture over marker (MOM) model for the simultaneous detection of cis and trans eQTL of Kendziorski (Kendziorski et al., 2006, Biometrics 62(1), 19-27). The genomic locations of the transcripts are used to improve the accuracy of the posterior distribution for the location of the eQTL. We compare the MOM method to our extension with both simulated data and data sets of recombinant inbred mouse lines. We also discuss an extension of the MOM method to model multiple eQTLs, and find that many transcripts are likely associated with more than one eQTL.

Original languageEnglish (US)
Pages (from-to)1108-1116
Number of pages9
JournalBiometrics
Volume63
Issue number4
DOIs
StatePublished - Dec 2007
Externally publishedYes

Fingerprint

Quantitative Trait Loci
Proximity
quantitative trait loci
loci
Locus
Prior Probability
Genes
Genome
genomics
genome
Genomics
Biometrics
biometry
Gene expression
Model
biologists
Linear Models
Log-linear Models
linear models
Multiple Models

Keywords

  • DNA
  • Empirical Bayes
  • Gene expression
  • Microarray
  • Mixture model
  • Quantitative trait loci

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Public Health, Environmental and Occupational Health
  • Agricultural and Biological Sciences (miscellaneous)
  • Applied Mathematics
  • Statistics and Probability

Cite this

Proximity model for expression quantitative trait loci (eQTL) detection. / Gelfond, Jonathan A; Ibrahim, Joseph G.; Zou, Fei.

In: Biometrics, Vol. 63, No. 4, 12.2007, p. 1108-1116.

Research output: Contribution to journalArticle

Gelfond, Jonathan A ; Ibrahim, Joseph G. ; Zou, Fei. / Proximity model for expression quantitative trait loci (eQTL) detection. In: Biometrics. 2007 ; Vol. 63, No. 4. pp. 1108-1116.
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