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Tools for protein-protein interaction network analysis in cancer research

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  • Advances in Translational Oncology
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Abstract

As cancer is a complex disease, the representation of a malignant cell as a protein-protein interaction network (PPIN) and its subsequent analysis can provide insight into the behaviour of cancer cells and lead to the discovery of new biomarkers. The aim of this review is to help life-science researchers without previous computer programming skills to extract meaningful biological information from such networks, taking advantage of easyto-use, public bioinformatics tools. It is structured in four parts: the first section describes the pipeline of consecutive steps from network construction to biological hypothesis generation. The second part provides a repository of public, user-friendly tools for network construction, visualisation and analysis. Two different and complementary approaches of network analysis are presented: the topological approach studies the network as a whole by means of structural graph theory, whereas the global approach divides the PPIN into sub-graphs, or modules. In section three, some concepts and tools regarding heterogeneous molecular data integration through a PPIN are described. Finally, the fourth part is an example of how to extract meaningful biological information from a colorectal cancer PPIN using some of the described tools.

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Authors and Affiliations

  1. Unit of Biomarkers and Susceptibility Catalan Institute of Oncology (ICO) Bellvitge Institute for Biomedical Research (IDIBELL) Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), L’Hospitalet de Llobregat, Av. Gran Vía, 199, ES-08908, Barcelona, Spain

    Rebeca Sanz-Pamplona, Antoni Berenguer, Xavier Sole, David Cordero, Marta Crous-Bou, Jordi Serra-Musach, Elisabet Guinó, Miguel Ángel Pujana & Víctor Moreno

  2. Department of Clinical Sciences Faculty of Medicine, University of Barcelona, Barcelona, Spain

    Víctor Moreno

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  1. Rebeca Sanz-Pamplona
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  2. Antoni Berenguer
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  3. Xavier Sole
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  4. David Cordero
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  8. Miguel Ángel Pujana
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  9. Víctor Moreno
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Correspondence to Víctor Moreno.

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Sanz-Pamplona, R., Berenguer, A., Sole, X. et al. Tools for protein-protein interaction network analysis in cancer research. Clin Transl Oncol 14, 3–14 (2012). https://doi.org/10.1007/s12094-012-0755-9

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  • DOI: https://doi.org/10.1007/s12094-012-0755-9

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