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BMC Bioinformatics. 2012 May 8;13 Suppl 7:S11. doi: 10.1186/1471-2105-13-S7-S11.

Pattern-driven neighborhood search for biclustering of microarray data.

Author information

  • 1LERIA, Université d'Angers, 2 Boulevard Lavoisier, 49045 Angers Cedex 01, France.

Abstract

BACKGROUND:

Biclustering aims at finding subgroups of genes that show highly correlated behaviors across a subgroup of conditions. Biclustering is a very useful tool for mining microarray data and has various practical applications. From a computational point of view, biclustering is a highly combinatorial search problem and can be solved with optimization methods.

RESULTS:

We describe a stochastic pattern-driven neighborhood search algorithm for the biclustering problem. Starting from an initial bicluster, the proposed method improves progressively the quality of the bicluster by adjusting some genes and conditions. The adjustments are based on the quality of each gene and condition with respect to the bicluster and the initial data matrix. The performance of the method was evaluated on two well-known microarray datasets (Yeast cell cycle and Saccharomyces cerevisiae), showing that it is able to obtain statistically and biologically significant biclusters. The proposed method was also compared with six reference methods from the literature.

CONCLUSIONS:

The proposed method is computationally fast and can be applied to discover significant biclusters. It can also used to effectively improve the quality of existing biclusters provided by other biclustering methods.

PMID:
22594997
[PubMed - indexed for MEDLINE]
PMCID:
PMC3348021
Free PMC Article
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