2015/10/10 by Jianan Tian, Tian, Jianan, Mark P. Keller +11
Biochemistry, Genetics and Molecular Biology · #Applications (stat.AP) #FOS: Biological sciences #FOS: Computer and information sciences #Gene expression and cancer classification #Genetic Mapping and Diversity in Plants and Animals #Genetic and phenotypic traits in livestock #Genomics (q-bio.GN)
paper · pdf · doi:10.48550/arxiv.1510.02863
openalex publication_date 2015/10/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effect on gene expression: expression quantitative trait locus (eQTL) hotspots. We describe a set of exploratory graphical methods as well as a formal likelihood-based test for assessing whether a given hotspot is due to one or multiple polymorphisms. We first look at the pattern of effects of the locus on the expression traits that map to the locus: the direction of the effects, as well as the degree of dominance. A second technique is to focus on the individuals that exhibit no recombination event in the region, apply dimensionality reduction (such as with linear discriminant analysis) and compare the phenotype distribution in the non-recombinants to that in the recombinant individuals: If the recombinant individuals display a different expression pattern than the non-recombinants, this indicates the presence of multiple causal polymorphisms. In the formal likelihood-based test, we compare a two-locus model, with each expression trait affected by one or the other locus, to a single-locus model. We apply our methods to a large mouse intercross with gene expression microarray data on six tissues.