Paper by Erik D. Demaine
- Therese Biedl, Broňa Brejová, Erik D. Demaine, Angèle M. Hamel, and Tomáš Vinař, “Optimal Arrangement of Leaves in the Tree Representing Hierarchical Clustering of Gene Expression Data”, Technical Report 2001-14, Department of Computer Science, University of Waterloo, April 2001.
In this paper, we study how to present gene expression data to display
similarities by trying to find a linear ordering of genes such that genes with
similar expression profiles will be close in this ordering. In general, finding
the best possible order is intractable. Therefore we assume that hierarchical
clustering has been applied to the gene expression profiles and show that the
best order respecting the clustering can be computed efficiently. We perform
experiments comparing the optimal order to several other methods. The
implementation of the algorithm, as well as a simple program for viewing
hierarchically clustered expression array data and the complete results of our
experiments are available at
- Detailed results, source code, and running times
- The paper is 12 pages.
- The paper is available in PostScript (4386k), gzipped PostScript (640k), and PDF (556k).
- See information on file formats.
- [Google Scholar search]
- Related papers:
- GeneExpression_WABI2002 (K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data)
See also other papers by Erik Demaine.
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