title: Multiscale characterization of signaling network dynamics through features.
abstract: Inference methods applied to biological networks suffer from a main criticism: as the latter reflect associations measured under static conditions, an evaluation of the underlying modular organization can be biologically meaningful only if the dynamics can also be taken into consideration. The same limitation is present in protein interactome networks. Given the substantial uncertainty characterizing protein interactions, we identify at least three aspects that must be considered for inference purposes: 1. Coverage, which for most organisms is only partial; 2. Stochasticity, affecting both the high-throughput experimental and the computational settings from which the interactions are determined, and leading to suboptimal measurement accuracy; 3. Information variety, due to the heterogeneity of technological and biological sources generating the data. Consequently, advances in inference methods require adequate treatment of both system uncertainty and dynamical aspects. Feasible solutions are often made possible by data (omic) integration procedures that complement the experimental design and the computational approaches for network modeling. We present a multiscale stochastic approach to deal with protein interactions involved in a well-known signaling network, and show that based on some topological network features, it is possible to identify timescales (or resolutions) that characterize complex pathways.
authors.affiliation: CRS4 Bioinformatics.
authors.forename: Enrico
authors.initials: E
authors.lastname: Capobianco
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Marras
authors.forename: Antonella
authors.initials: A
authors.lastname: Travaglione
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D020930:MAP Kinase Kinase Kinases / Q000235:genetics / Q000378:metabolism; D020935:MAP Kinase Signaling System; D010675:Pheromones / Q000378:metabolism; D010766:Phosphorylation; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D012680:Sensitivity and Specificity; D015398:Signal Transduction; D013269:Stochastic Processes; D014158:Transcription, Genetic
chemical_list: D010675:Pheromones; D029701:Saccharomyces cerevisiae Proteins; D020930:MAP Kinase Kinase Kinases; C078754:STE20 protein, S cerevisiae