Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study

@article{citeulike:2824834, abstract = {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 genetic variations with higher order biological modules via gene expression profiles.}, author = {Sun, Wei and Yuan, Shinsheng and Li, Ker C. }, citeulike-article-id = {2824834}, doi = {http://dx.doi.org/10.1186/1471-2164-9-242}, journal = {BMC Genomics}, keywords = {eqtl, methods, qtl, quantitative\_genetics}, number = {1}, posted-at = {2008-07-21 05:55:46}, priority = {2}, title = {Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study}, url = {http://dx.doi.org/10.1186/1471-2164-9-242}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2824834 L3 - citeulike-article-id:2824834 TI - Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study JF - BMC Genomics VL - 9 IS - 1 N2 - 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 genetic variations with higher order biological modules via gene expression profiles. KW - eqtl KW - methods KW - qtl KW - quantitative_genetics AU - Sun, Wei AU - Yuan, Shinsheng AU - Li, Ker PY - 2008/// UR - http://dx.doi.org/10.1186/1471-2164-9-242 ER -