论文信息 - Fast optimal leaf ordering for hierarchical clustering

Fast optimal leaf ordering for hierarchical clustering

We present the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering. Hierarchical clustering has been extensively used to analyze gene expression data, and we show how optimal leaf ordering can reveal biological structure that is not observed with an existing heuristic ordering method. For a tree with n leaves, there are 2(n-1) linear orderings consistent with the structure of the tree. Our optimal leaf ordering algorithm runs in time O(n(4)), and we present further improvements that make the running time of our algorithm practical.

T. Jaakkola | D. Gifford | Z. Bar-Joseph

[1] E. Lander,et al. Remodeling of yeast genome expression in response to environmental changes. , 2001, Molecular biology of the cell.

[2] Ash A. Alizadeh,et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[3] U. Alon,et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[4] J. Mesirov,et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[5] David Eppstein,et al. Fast hierarchical clustering and other applications of dynamic closest pairs , 1999, SODA '98.

[6] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[7] Michael Ruogu Zhang,et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.