Discover gene specific local co-regulations using progressive genetic algorithm

Abstract

[Abstract]: The problem of gene specific co-regulation discovery is that, for a particular gene of interest, identify its closely co-regulated genes and the associated subsets of experimental conditions in which such co-regulations occur. The co-regulations are local in the sense that they occur in some subsets of full experimental conditions. In this paper, we propose an innovative method for finding gene specific co-regulations using genetic algorithm (GA). Two novel ad hoc GAs, the single-stage and two-stage progressive GA, are proposed. They are called progressive because the initial population for the GA in a window position inherits the top-ranked individuals obtained in the preceding window position, enabling them to achieve better accuracy than the non-progressive algorithm. Experimental results with real-life gene expression data demonstrate the efficiency and effectiveness of our technique in discovering gene specific co-regulations.