Paper by Erik D. Demaine

Reference:

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.

BibTeX

@TechReport{GeneExpression_UWTR2001,
  AUTHOR        = {Therese Biedl and Bro\v{n}a Brejov\'a and Erik D. Demaine
                   and Ang\`ele M. Hamel and Tom\'a\v{s} Vina\v{r}},
  TITLE         = {Optimal Arrangement of Leaves in the Tree Representing
                   Hierarchical Clustering of Gene Expression Data},
  INSTITUTION   = {Department of Computer Science, University of Waterloo},
  NUMBER        = {2001-14},
  MONTH         = {April},
  YEAR          = 2001,

  LENGTH        = {12 pages},
  COMMENTS      = {<A HREF="http://monod.uwaterloo.ca/supplements/01expr/">Detailed results, source code, and running times</A>},
  PAPERS        = {GeneExpression_WABI2002},
}

Abstract:

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 http://monod.uwaterloo.ca/supplements/01expr/.

Comments:

Detailed results, source code, and running times

Length:

The paper is 12 pages.

Availability:

The paper is available in PostScript (4386k), gzipped PostScript (640k), and PDF (556k).

See information on file formats.

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Related papers:

GeneExpression_WABI2002 (K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data)