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Cytoscape: Software for Visualization and Analysis of Biological Networks

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Data Mining in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 696))

Abstract

Substantial progress has been made in the field of “omics” research (e.g., Genomics, Transcriptomics, Proteomics, and Metabolomics), leading to a vast amount of biological data. In order to represent large biological data sets in an easily interpretable manner, this information is frequently visualized as graphs, i.e., a set of nodes and edges. Nodes are representations of biological molecules and edges connect the nodes depicting some kind of relationship.

Obviously, there is a high demand for computer-based assistance for both visualization and analysis of biological data, which are often heterogeneous and retrieved from different sources. This chapter focuses on software tools that assist in visual exploration and analysis of biological networks. Global requirements for such programs are discussed. Utilization of visualization software is exemplified using the widely used Cytoscape tool. Additional information about the use of Cytoscape is provided in the Notes section. Furthermore, special features of alternative software tools are highlighted in order to assist researchers in the choice of an adequate program for their specific requirements.

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Acknowledgments

This work is funded by the Bundesministerium für Bildung und Forschung (BMBF, grant 01 GS 08143) and by the Deutsche Forschungsgemeinschaft within the SFB 642. Thanks are also due to the Agilent Laboratories and Annette Adler for the financial support for the color versions of the figures.

Author information

Authors and Affiliations

  1. Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany

    Michael Kohl, Sebastian Wiese & Bettina Warscheid

  2. Clinical & Cellular Proteomics, Medical Faculty and Center for Medical Biotechnology, Duisburg-Essen University, Essen, Germany

    Bettina Warscheid

Authors
  1. Michael Kohl
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  2. Sebastian Wiese
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  3. Bettina Warscheid
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Corresponding author

Correspondence to Michael Kohl .

Editor information

Editors and Affiliations

  1. Lead Discovery Center GmbH, Emil-Figge-Straße 76a76a, Dortmund, 44227, Germany

    Michael Hamacher

  2. Medizinisches Proteom-Center, Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, 44801, Germany

    Martin Eisenacher

  3. Medizinisches Proteom-Center, Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, 44801, Germany

    Christian Stephan

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Kohl, M., Wiese, S., Warscheid, B. (2011). Cytoscape: Software for Visualization and Analysis of Biological Networks. In: Hamacher, M., Eisenacher, M., Stephan, C. (eds) Data Mining in Proteomics. Methods in Molecular Biology, vol 696. Humana Press. https://doi.org/10.1007/978-1-60761-987-1_18

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  • DOI: https://doi.org/10.1007/978-1-60761-987-1_18

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-986-4

  • Online ISBN: 978-1-60761-987-1

  • eBook Packages: Springer Protocols

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