title: Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data.
abstract: The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of protein-protein interactions (PPI) with proteomics data using functional similarity measurements of interacting proteins. This integrated network analysis exactly identifies network modules with a maximal consistent functional similarity reflecting biological processes of the investigated cells. We validated our approach on small (H9N2 virus-infected gastric cells) and large (blood constituents) proteomic data sets. Using this novel algorithm, we identified characteristic functional modules in virus-infected cells, comprising key signaling proteins (e.g. the stress-related kinase RAF1) and demonstrate that this method allows a module-based functional characterization of cell types. Analysis of a large proteome data set of blood constituents resulted in clear separation of blood cells according to their developmental origin. A detailed investigation of the T-cell proteome further illustrates how the algorithm partitions large networks into functional subnetworks each representing specific cellular functions. These results demonstrate that the integrated network approach not only allows a detailed analysis of proteome networks but also yields a functional decomposition of complex proteomic data sets and thereby provides deeper insights into the underlying cellular processes of the investigated system.
authors.affiliation: From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
authors.forename: Desislava
authors.initials: D
authors.lastname: Boyanova
authors.affiliation: From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
authors.forename: Santosh
authors.initials: S
authors.lastname: Nilla
authors.affiliation: §Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG Amsterdam, The Netherlands.
authors.forename: Gunnar W
authors.initials: GW
authors.lastname: Klau
authors.affiliation: From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.affiliation: From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.affiliation: From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany; marcus.dittrich@biozentrum.uni-wuerzburg.de.
authors.forename: Marcus
authors.initials: M
authors.lastname: Dittrich
mesh_terms: D000465:Algorithms; D002478:Cells, Cultured; D003198:Computer Simulation; D006801:Humans; D053127:Influenza A Virus, H9N2 Subtype; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D011506:Proteins / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism; D040901:Proteomics; D019908:Proto-Oncogene Proteins c-raf / Q000378:metabolism; D013270:Stomach / Q000166:cytology / Q000821:virology; D049490:Systems Biology; D013601:T-Lymphocytes / Q000378:metabolism*
chemical_list: D011506:Proteins; D020543:Proteome; D019908:Proto-Oncogene Proteins c-raf