Biclustering for the comprehensive search of correlated gene expression patterns using clustered seed expansion.

BACKGROUND: In a functional analysis of gene expression data, biclustering method can give crucial information by showing correlated gene expression patterns under a subset of conditions. However, conventional biclustering algorithms still have some limitations to show comprehensive and stable outputs.

RESULTS: We propose a novel biclustering approach called "BIclustering by Correlated and Large number of Individual Clustered seeds (BICLIC)" to find comprehensive sets of correlated expression patterns in biclusters using clustered seeds and their expansion with correlation of gene expression. BICLIC outperformed competing biclustering algorithms by completely recovering implanted biclusters in simulated datasets with various types of correlated patterns: shifting, scaling, and shifting-scaling. Furthermore, in a real yeast microarray dataset and a lung cancer microarray dataset, BICLIC found more comprehensive sets of biclusters that are significantly enriched to more diverse sets of biological terms than those of other competing biclustering algorithms.

CONCLUSIONS: BICLIC provides significant benefits in finding comprehensive sets of correlated patterns and their functional implications from a gene expression dataset.