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Network-Assisted Disease Classification and Biomarker Discovery

  • Protocol
Book cover Systems Medicine

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1386))

Abstract

Developing improved approaches for diagnosis, treatment, and prevention of diseases is a major goal of biomedical research. Therefore, the discovery of biomarker signatures from high-throughput “omics” data is an active research topic in the field of bioinformatics and systems medicine. A major issue is the low reproducibility and the limited biological interpretability of candidate biomarker signatures identified from high-throughput data. This impedes the use of discovered biomarker signatures into clinical applications. Currently, much focus is placed on developing strategies to improve reproducibility and interpretability. Researchers have fruitfully started to incorporate prior knowledge derived from pathways and molecular networks into the process of biomarker identification. In this chapter, after giving a general introduction to the problem of disease classification and biomarker discovery, we will review two types of network-assisted approaches: (1) approaches inferring activity scores for specific pathways which are subsequently used for classification and (2) approaches identifying subnetworks or modules of molecular networks by differential network analysis which can serve as biomarker signatures.

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Authors and Affiliations

  1. Biomathematics and Bioinformatics Unit, Leibniz-Institute for Farm Animal Biology (FBN), Institute of Genetics and Biometry, Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany

    Sonja Strunz & Alberto de la Fuente

  2. Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

    Olaf Wolkenhauer

  3. Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa

    Olaf Wolkenhauer

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  1. Sonja Strunz
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  2. Olaf Wolkenhauer
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  3. Alberto de la Fuente
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Correspondence to Alberto de la Fuente .

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Editors and Affiliations

  1. Dept of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany

    Ulf Schmitz

  2. Dept of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany

    Olaf Wolkenhauer

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Strunz, S., Wolkenhauer, O., de la Fuente, A. (2016). Network-Assisted Disease Classification and Biomarker Discovery. In: Schmitz, U., Wolkenhauer, O. (eds) Systems Medicine. Methods in Molecular Biology, vol 1386. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3283-2_16

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  • DOI: https://doi.org/10.1007/978-1-4939-3283-2_16

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