An integrative modeling framework reveals plasticity of TGF-β signaling. - Inserm - Institut national de la santé et de la recherche médicale
Article Dans Une Revue BMC Systems Biology Année : 2014

An integrative modeling framework reveals plasticity of TGF-β signaling.

Résumé

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.

Domaines

Génomique, Transcriptomique et Protéomique [q-bio.GN] Bio-Informatique, Biologie Systémique [q-bio.QM] Bio-informatique [q-bio.QM]
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https://inserm.hal.science/inserm-00978313

Soumis le : lundi 14 avril 2014-09:49:43

Dernière modification le : jeudi 7 novembre 2024-13:34:02

Archivage à long terme le : lundi 14 juillet 2014-10:51:39

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Dates et versions

inserm-00978313 , version 1 (14-04-2014)

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Geoffroy Andrieux, Michel Le Borgne, Nathalie Théret. An integrative modeling framework reveals plasticity of TGF-β signaling.. BMC Systems Biology, 2014, 8 (1), pp.30. ⟨10.1186/1752-0509-8-30⟩. ⟨inserm-00978313⟩

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