Order preserving clustering over multiple time course experiments

Authors:
Stefan Bleuler;Eckart Zitzler
Affiliations:
Computer Engineering and Networks Laboratory (TIK), Swiss Federal Institute of Technology Zurich, Zürich, Switzerland;Computer Engineering and Networks Laboratory (TIK), Swiss Federal Institute of Technology Zurich, Zürich, Switzerland
Venue:
EC'05 Proceedings of the 3rd European conference on Applications of Evolutionary Computing
Year:
2005

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Abstract

Clustering still represents the most commonly used technique to analyze gene expression data—be it classical clustering approaches that aim at finding biologically relevant gene groups or biclustering methods that focus on identifying subset of genes that behave similarly over a subset of conditions. Usually, the measurements of different experiments are mixed together in a single gene expression matrix, where the information about which experiments belong together, e.g., in the context of a time course, is lost. This paper investigates the question of how to exploit the information about related experiments and to effectively use it in the clustering process. To this end, the idea of order preserving clusters that has been presented in [2] is extended and integrated in an evolutionary algorithm framework that allows simultaneous clustering over multiple time course experiments while keeping the distinct time series data separate.