title: An integrative modeling framework reveals plasticity of TGF-β signaling.
abstract: BACKGROUND
  The TGF-β transforming growth factor is the most pleiotropic cytokine controlling a broad range of cellular responses that include proliferation, differentiation and apoptosis. The context-dependent multifunctional nature of TGF-β is associated with complex signaling pathways. Differential models describe the dynamics of the TGF-β canonical pathway, but modeling the non-canonical networks constitutes a major challenge. Here, we propose a qualitative approach to explore all TGF-β-dependent signaling pathways.
  
  
  RESULTS
  Using a new formalism, CADBIOM, which is based on guarded transitions and includes temporal parameters, we have built the first discrete model of TGF-β signaling networks by automatically integrating the 137 human signaling maps from the Pathway Interaction Database into a single unified dynamic model. Temporal property-checking analyses of 15934 trajectories that regulate 145 TGF-β target genes reveal the association of specific pathways with distinct biological processes. We identify 31 different combinations of TGF-β with other extracellular stimuli involved in non-canonical TGF-β pathways that regulate specific gene networks. Extensive analysis of gene expression data further demonstrates that genes sharing CADBIOM trajectories tend to be co-regulated.
  
  
  CONCLUSIONS
  As applied here to TGF-β signaling, CADBIOM allows, for the first time, a full integration of highly complex signaling pathways into dynamic models that permit to explore cell responses to complex microenvironment stimuli.
authors.forename: Geoffroy
authors.initials: G
authors.lastname: Andrieux
authors.forename: Michel
authors.initials: M
authors.lastname: Le Borgne
authors.affiliation: INSERM U1085, IRSET, Université de Rennes 1, 2 avenue Pr Léon Bernard, 35043 Rennes, France. nathalie.theret@univ-rennes1.fr.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Théret
mesh_terms: D019295:Computational Biology; D006801:Humans; D008954:Models, Biological; D015398:Signal Transduction; D051785:Smad Proteins / Q000378:metabolism; D059467:Transcriptome; D016212:Transforming Growth Factor beta / Q000378:metabolism*
chemical_list: D051785:Smad Proteins; D016212:Transforming Growth Factor beta