Finding multiple coherent biclusters in microarray data using variable string length multiobjective genetic algorithm

IEEE Trans Inf Technol Biomed. 2009 Nov;13(6):969-75. doi: 10.1109/TITB.2009.2017527. Epub 2009 Mar 16.

Abstract

Microarray technology enables the simultaneous monitoring of the expression pattern of a huge number of genes across different experimental conditions. Biclustering in microarray data is an important technique that discovers a group of genes that are coregulated in a subset of conditions. Biclustering algorithms require to identify coherent and nontrivial biclusters, i.e., the biclusters should have low mean squared residue and high row variance. A multiobjective genetic biclustering technique is proposed here that optimizes these objectives simultaneously. A novel encoding scheme that uses variable chromosome length is developed. Moreover, a new quantitative measure to evaluate the goodness of the biclusters is proposed. The performance of the proposed algorithm has been evaluated on both simulated and real-life gene expression datasets, and compared with some other well-known biclustering techniques.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Cluster Analysis*
  • Computational Biology / methods*
  • Computer Simulation
  • Databases, Genetic
  • Gene Expression Profiling
  • Humans
  • Leukemia
  • Models, Genetic*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Yeasts