Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data.

ABSTRACT:

Motivation

We address the issue of finding a three-way gene interaction, i.e. two interacting genes in expression under the genotypes of another gene, given a dataset in which expressions and genotypes are measured at once for each individual. This issue can be a general, switching mechanism in expression of two genes, being controlled by categories of another gene, and finding this type of interaction can be a key to elucidating complex biological systems. The most suitable method for this issue is likelihood ratio test using logistic regressions, which we call interaction test, but a serious problem of this test is computational intractability at a genome-wide level.

Results

We developed a fast method for this issue which improves the speed of interaction test by around 10

SUBMITTER: Kayano M 

PROVIDER: S-EPMC2781753 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature