Fuzzy J-Means and VNS methods for clustering genes from microarray data.
BACKGROUND
In the interpretation of gene expression data from a group of microarray experiments that include samples from either different patients or conditions, special consideration must be given to the pleiotropic and epistatic roles of genes, as observed in the variation of gene coexpression patterns. Crisp clustering methods assign each gene to one cluster, thereby omitting information about the multiple roles of genes.


RESULTS
Here, we present the application of a local search heuristic, Fuzzy J-Means, embedded into the variable neighborhood search metaheuristic for the clustering of microarray gene expression data. We show that for all the datasets studied this algorithm outperforms the standard Fuzzy C-Means heuristic. Different methods for the utilization of cluster membership information in determining gene coregulation are presented. The clustering and data analyses were performed on simulated datasets as well as experimental cDNA microarray data for breast cancer and human blood from the Stanford Microarray Database.


BACKGROUND
The source code of the clustering software (C programming language) is freely available from Nabil.Belacel@nrc-cnrc.gc.ca
Belacel
Nabil
N
National Research Council Canada, Institute for Information Technology-e-Health group, 127 Carleton Street, St-John, NB, Canada E2L2Z6. Nabil.Belacel@nrc-cnrc.gc.ca
Cuperlović-Culf
Miroslava
M
Laflamme
Mark
M
Ouellette
Rodney
R
D000465:Algorithms; D001798:Blood Proteins / Q000145:classification / Q000235:genetics*; D001943:Breast Neoplasms / Q000145:classification / Q000175:diagnosis / Q000235:genetics*; D016000:Cluster Analysis; D003198:Computer Simulation; D017143:Fuzzy Logic; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D005820:Genetic Testing / Q000379:methods; D014644:Genetic Variation; D006801:Humans; D009363:Neoplasm Proteins / Q000145:classification / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D001798:Blood Proteins; D009363:Neoplasm Proteins