Dataset Information

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

ABSTRACT: BACKGROUND:The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs). RESULTS:Pathways are annotated using a novel data model, the Biological Connection Markup Language (BCML), a SBGN-compliant data format developed to store the large amount of information collected. The application of DC-ATLAS to pathway-based analysis of the transcriptional program of DCs stimulated with agonists of the toll-like receptor family allows an integrated description of the flow of information from the cellular sensors to the functional outcome, capturing the temporal series of activation events by grouping sets of reactions that occur at different time points in well-defined functional modules. CONCLUSIONS:The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies.

SUBMITTER: Cavalieri D

PROVIDER: S-EPMC3000836 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature

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DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

Cavalieri Duccio D Rivero Damariz D Beltrame Luca L Buschow Sonja I SI Calura Enrica E Rizzetto Lisa L Gessani Sandra S Gauzzi Maria C MC Reith Walter W Baur Andreas A Bonaiuti Roberto R Brandizi Marco M De Filippo Carlotta C D'Oro Ugo U Draghici Sorin S Dunand-Sauthier Isabelle I Gatti Evelina E Granucci Francesca F Gündel Michaela M Kramer Matthijs M Kuka Mirela M Lanyi Arpad A Melief Cornelis Jm CJ van Montfoort Nadine N Ostuni Renato R Pierre Philippe P Popovici Razvan R Rajnavolgyi Eva E Schierer Stephan S Schuler Gerold G Soumelis Vassili V Splendiani Andrea A Stefanini Irene I Torcia Maria G MG Zanoni Ivan I Zollinger Raphael R Figdor Carl G CG Austyn Jonathan M JM

Immunome research 20101119

<h4>Background</h4>The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resourc ...[more]

PMID: 21092113

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Dataset Information

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

Publications

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

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