Multiple gene expression profile alignment for microarray time-series data clustering

Numanul Subhani, Luis Rueda*, Alioune Ngom, Conrad J. Burden

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    18 Citations (Scopus)

    Abstract

    Motivation: Clustering gene expression data given in terms of time-series is a challenging problem that imposes its own particular constraints. Traditional clustering methods based on conventional similarity measures are not always suitable for clustering time-series data. A few methods have been proposed recently for clustering microarray time-series, which take the temporal dimension of the data into account. The inherent principle behind these methods is to either dene a similaritymeasure appropriate for temporal expression data, or pre-process the data in such a way that the temporal relationships between and within the time-series are considered during the subsequent clustering phase. Results: We introduce pairwise gene expression prole alignment, which vertically shifts two proles in such a way that the area between their corresponding curves is minimal. Based on the pairwise alignment operation, we dene a new distance function that is appropriate for time-series proles. We also introduce a new clustering method that involves multiple expression prole alignment, which generalizes pairwise alignment to a set of proles. Extensive experiments on well-known datasets yield encouraging results of at least 80% classication accuracy.

    Original languageEnglish
    Article numberbtq422
    Pages (from-to)2281-2288
    Number of pages8
    JournalBioinformatics
    Volume26
    Issue number18
    DOIs
    Publication statusPublished - 16 Jul 2010

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