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K-ary clustering with optimal leaf ordering for gene expression data.

Ziv Bar-Joseph1, Erik D Demaine, David K Gifford

  • 1Laboratory for Computer Science, MIT, 545 Technology Square, Cambridge, MA 02139, USA. zivbj@mit.edu

Bioinformatics (Oxford, England)
|June 13, 2003
PubMed
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This study introduces a novel k-ary hierarchical clustering algorithm that is more robust to noise and missing data in gene expression analysis. The new method improves cluster identification and data visualization compared to traditional binary approaches.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Gene expression analysis requires effective data organization and visualization.
  • Hierarchical clustering is a popular tool but is sensitive to noise and lacks distinct cluster identification.
  • Existing methods produce numerous possible orderings for hierarchical clustering trees.

Purpose of the Study:

  • To develop a new hierarchical clustering algorithm to address limitations of existing methods.
  • To reduce susceptibility to noise and improve cluster identification in gene expression data.
  • To provide a single optimal ordering for the hierarchical clustering tree.

Main Methods:

  • An efficient algorithm constructs a k-ary tree, allowing up to k children per node.

Related Experiment Videos

  • The algorithm optimally orders the leaves of the constructed k-ary tree.
  • Combining k clusters at each step enhances robustness against noise and missing values.

    • Main Results:

    • The k-ary construction algorithm runs in O(n^3) regardless of k.
    • The leaf ordering algorithm runs in O(4^k * n^3).
    • Examples demonstrate superior global presentation and cluster identification compared to binary tree methods.

    Conclusions:

    • The proposed k-ary hierarchical clustering algorithm offers improved robustness and visualization for gene expression data.
    • Optimal leaf ordering maintains pairwise relationships without sacrificing robustness.
    • The implementation is available in C++ on Linux.