Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification

Irene Kouskoumvekaki, Zhiyong Yang, Svava Osk Jonsdottir, Lisbeth Olsson, Gianni Panagiotou

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    Abstract

    Background: In the present investigation, we have used an exhaustive metabolite profiling approach to search for biomarkers in recombinant Aspergillus nidulans (mutants that produce the 6- methyl salicylic acid polyketide molecule) for application in metabolic engineering. Results: More than 450 metabolites were detected and subsequently used in the analysis. Our approach consists of two analytical steps of the metabolic profiling data, an initial non-linear unsupervised analysis with Self-Organizing Maps (SOM) to identify similarities and differences among the metabolic profiles of the studied strains, followed by a second, supervised analysis for training a classifier based on the selected biomarkers. Our analysis identified seven putative biomarkers that were able to cluster the samples according to their genotype. A Support Vector Machine was subsequently employed to construct a predictive model based on the seven biomarkers, capable of distinguishing correctly 14 out of the 16 samples of the different A. nidulans strains. Conclusion: Our study demonstrates that it is possible to use metabolite profiling for the classification of filamentous fungi as well as for the identification of metabolic engineering targets and draws the attention towards the development of a common database for storage of metabolomics data.
    Original languageEnglish
    JournalBMC Bioinformatics
    Volume9
    Pages (from-to)59
    ISSN1471-2105
    DOIs
    Publication statusPublished - 2008

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