Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study.
BACKGROUND
Many studies have shown that the abundance level of gene expression is heritable. Analogous to the traditional genetic study, most researchers treat the expression of one gene as a quantitative trait and map it to expression quantitative trait loci (eQTL). This is 1D-trait mapping. 1D-trait mapping ignores the trait-trait interaction completely, which is a major shortcoming.


RESULTS
To overcome this limitation, we study the expression of a pair of genes and treat the variation in their co-expression pattern as a two dimensional quantitative trait. We develop a method to find gene pairs, whose co-expression patterns, including both signs and strengths, are mediated by genetic variations and map these 2D-traits to the corresponding genetic loci. We report several applications by combining 1D-trait mapping with 2D-trait mapping, including the contribution of genetic variations to the perturbations in the regulatory mechanisms of yeast metabolic pathways.


CONCLUSIONS
Our approach of 2D-trait mapping provides a novel and effective way to connect the genetic variation with higher order biological modules via gene expression profiles.
Sun
Wei
W
Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA. sunwei@ucla.edu
Yuan
Shinsheng
S
Li
Ker-Chau
KC
D014644:Genetic Variation / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics; D023281:Genomics; D006639:Histidine / Q000096:biosynthesis; D007168:IMP Dehydrogenase / Q000235:genetics / Q000378:metabolism; D007930:Leucine / Q000096:biosynthesis; D020412:Multifactorial Inheritance / Q000235:genetics*; D011687:Purines / Q000096:biosynthesis; D040641:Quantitative Trait Loci / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism
D011687:Purines; D014157:Transcription Factors; D006639:Histidine; D007168:IMP Dehydrogenase; D007930:Leucine; C030985:purine