Constructing the gene regulation-level representation of microarray data for cancer classification

In this paper, we propose a regulation-level representation for microarray data and optimize it using genetic algorithms (GAs) for cancer classification. Compared with the traditional expression-level features, this representation can greatly reduce the dimensionality of microarray data and accommodate noise and variability such that many statistical machine-learning methods now become applicable and efficient for cancer classification. Experimental results on real-world microarray datasets show that the regulation-level representation can consistently converge at a solution with three regulation levels. This verifies the existence of the three regulation levels (up-regulation, down-regulation and non-significant regulation) associated with a particular biological phenotype. The ternary regulation-level representation not only improves the cancer classification capability but also facilitates the visualization of microarray data. © 2007 Elsevier Inc. All rights reserved.