Efficiently mining time-delayed gene expression patterns

IEEE Trans Syst Man Cybern B Cybern. 2010 Apr;40(2):400-11. doi: 10.1109/TSMCB.2009.2025564. Epub 2009 Oct 30.

Abstract

Unlike pattern-based biclustering methods that focus on grouping objects in the same subset of dimensions, in this paper, we propose a novel model of coherent clustering for time-series gene expression data, i.e., time-delayed cluster (td-cluster). Under this model, objects can be coherent in different subsets of dimensions if these objects follow a certain time-delayed relationship. Such a cluster can discover the cycle time of gene expression, which is essential in revealing gene regulatory networks. This paper is the first attempt to mine time-delayed gene expression patterns from microarray data. A novel algorithm is also presented and implemented to mine all significant td-clusters. Our experimental results show following two results: 1) the td-cluster algorithm can detect a significant amount of clusters that were missed by previous models, and these clusters are potentially of high biological significance and 2) the td-cluster model and algorithm can easily be extended to 3-D gene x sample x time data sets to identify 3-D td-clusters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Cluster Analysis*
  • Computational Biology / methods
  • Data Mining / methods*
  • Gene Expression Profiling / methods*
  • Oligonucleotide Array Sequence Analysis
  • Pattern Recognition, Automated / methods*