Explorative data analysis of two-dimensional electrophoresis gels

J. Schultz, D.M. Gottlieb, Marianne Kjerstine Petersen, Ljiljana Nesic, Susanne Jacobsen, Ib Søndergaard

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.
    Original languageEnglish
    JournalElectrophoresis
    Volume25
    Pages (from-to)502-511
    ISSN0173-0835
    Publication statusPublished - 2004

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