Temporal clustering of gene expression patterns using short-time segments

Nguyen Nguyen, Yufang Jin, Yufei Huang, Ying Ann Chiao, Shou Jiang Gao, Merry Lindsey, Yidong Chen

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations

    Abstract

    Temporal clustering of time series data is a powerful tool to delaminate the dynamics of transcription and interactions among genes on a large scale. Different algorithms have been proposed to organize experimental data with meaningful biological clusters; however, these approaches often fail to generate well-defined temporal clusters, especially when genes exert their functions or response to stimulation coordinately only in a short time span. In this study, we propose an algorithm using sliding windows to identify different temporal patterns based on fold changes of gene expression. The algorithm was applied to simulated data and real experimental data. Furthermore, a comparison study has been carried out with the clusters obtained from commercial software packages. The identified clusters using our algorithm demonstrated better temporal matching and consistency.

    Original languageEnglish (US)
    Title of host publication2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
    Pages173-178
    Number of pages6
    DOIs
    StatePublished - 2010
    Event2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010 - HongKong, China
    Duration: Dec 18 2010Dec 21 2010

    Publication series

    Name2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010

    Other

    Other2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
    Country/TerritoryChina
    CityHongKong
    Period12/18/1012/21/10

    Keywords

    • Gene expression patterns
    • Short-time segments
    • Sliding window
    • Temporal clustering

    ASJC Scopus subject areas

    • Biomedical Engineering
    • Health Informatics

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