Simultaneously segmenting multiple gene expression time courses by analyzing cluster dynamics

Satish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bud Mishra, Richard F. Helm

Research output: Contribution to journalArticle

Abstract

We present a new approach to segmenting multiple time series by analyzing the dynamics of cluster formation and rearrangement around putative segment boundaries. This approach finds application in distilling large numbers of gene expression profiles into temporal relationships underlying biological processes. By directly minimizing information-theoretic measures of segmentation quality derived from Kullback-Leibler (KL) divergences, our formulation reveals clusters of genes along with a segmentation such that clusters show concerted behavior within segments but exhibit significant regrouping across segmentation boundaries. The results of the segmentation algorithm can be summarized as Gantt charts revealing temporal dependencies in the ordering of key biological processes. Applications to the yeast metabolic cycle and the yeast cell cycle are described.

Original languageEnglish (US)
Pages (from-to)339-356
Number of pages18
JournalJournal of Bioinformatics and Computational Biology
Volume7
Issue number2
DOIs
StatePublished - 2009

Keywords

  • Clustering
  • KL-divergence
  • Temporal regulation
  • Time series segmentation

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

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