title: Tools for protein-protein interaction network analysis in cancer research.
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 easy-to-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.
authors.affiliation: Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Biomedical Research Centre Network for Epidemiology and Public Health, L'Hospitalet de Llobregat, Barcelona, Spain.
authors.forename: Rebeca
authors.initials: R
authors.lastname: Sanz-Pamplona
authors.forename: Antoni
authors.initials: A
authors.lastname: Berenguer
authors.forename: Xavier
authors.initials: X
authors.lastname: Sole
authors.forename: David
authors.initials: D
authors.lastname: Cordero
authors.forename: Marta
authors.initials: M
authors.lastname: Crous-Bou
authors.forename: Jordi
authors.initials: J
authors.lastname: Serra-Musach
authors.forename: Elisabet
authors.initials: E
authors.lastname: Guinó
authors.forename: Miguel Ángel
authors.initials: MÁ
authors.lastname: Pujana
authors.forename: Víctor
authors.initials: V
authors.lastname: Moreno
mesh_terms: D000818:Animals; D019295:Computational Biology; D006801:Humans; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D011506:Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D011506:Proteins