Fuzzy clustering with biological knowledge for gene selection

• An application of FCLARANS for attribute clustering and dimensionality reduction in gene expression data has been demonstrated.
• Domain knowledge based on gene ontology and differential gene expressions are employed in the process.
• Important representative features are extracted from each enriched gene partition to form the reduced gene space.
• External validation using various well-known classifiers, establishes the effectiveness of the proposed methodology.

This paper presents an application of Fuzzy Clustering of Large Applications based on Randomized Search (FCLARANS) for attribute clustering and dimensionality reduction in gene expression data. Domain knowledge based on gene ontology and differential gene expressions are employed in the process. The use of domain knowledge helps in the automated selection of biologically meaningful partitions. Gene ontology (GO) study helps in detecting biologically enriched and statistically significant clusters. Fold-change is measured to select the differentially expressed genes as the representatives of these clusters. Tools like Eisen plot and cluster profiles of these clusters help establish their coherence. Important representative features (or genes) are extracted from each enriched gene partition to form the reduced gene space. While the reduced gene set forms a biologically meaningful attribute space, it simultaneously leads to a decrease in computational burden. External validation of the reduced subspace, using various well-known classifiers, establishes the effectiveness of the proposed methodology on four sets of publicly available microarray gene expression data.