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Keywords {🔍}

tlr, pathway, pathways, dcatlas, data, dcs, article, google, scholar, signaling, cells, analysis, pubmed, specific, cell, figure, module, dendritic, cas, modules, signal, additional, transduction, bcml, human, file, elements, genes, biology, sbgn, receptor, lps, biological, information, immune, receptors, systems, outcome, format, gene, representation, hours, type, network, expression, map, curation, results, tolllike, modular,

Topics {✒️}

granulocyte/macrophage colony-stimulating factor receptor-induced interleukin-12p70 secretion nadine van montfoort robust multi-array average monocyte-derived dendritic cells high-throughput data coming signed p-values derived cornelis jm melief conventional dendritic cells ugo d'oro isabelle dunand-sauthier adapter-inducing interferon-beta article download pdf resulting signed p-values accession number e-mtab-448 community-input supported knowledgebase carlotta de filippo dendritic cell maturation systems biology approach dc-atlas manually annotated trif-related adapter molecule van deutekom hw privacy choices/manage cookies dc-atlas dc-atlas c-type lectin receptors initiative significantly improves dc-atlas pathways allowed systems-level approach low density pbmcs cell-type specific pathways dc-atlas tlr pathways common regulatory unit lipopolysaccharide-induced signaling dendritic cells independently dc-based vaccines controlled vocabulary built immune systems biology dendritic cell subsets human dendritic cells structured pathway definitions dc maturation process wellcome trust centre signal transduction module specifically mark genes signal transduction maps pathways specifically curated absolute-scale values immunological genome project gene expression omnibus systems biology resource

Questions {❓}

• Hennessy EJ, Parker AE, O'Neill LA: Targeting Toll-like receptors: emerging therapeutics?

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         headline:DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells
         description: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). 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. 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.
         datePublished:2010-11-19T00:00:00Z
         dateModified:2010-11-19T00:00:00Z
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            Modular Structure
            Pathway Database
            System Biology Approach
            Outcome Module
            Signal Transduction Module
            Immunology
            Bioinformatics
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      headline:DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells
      description: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). 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. 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.
      datePublished:2010-11-19T00:00:00Z
      dateModified:2010-11-19T00:00:00Z
      pageStart:1
      pageEnd:12
      license:http://creativecommons.org/licenses/by/2.0
      sameAs:https://doi.org/10.1186/1745-7580-6-10
      keywords:
         Modular Structure
         Pathway Database
         System Biology Approach
         Outcome Module
         Signal Transduction Module
         Immunology
         Bioinformatics
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            name:Sonja I Buschow
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            name:Andreas Baur
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            name:Isabelle Dunand-Sauthier
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            name:Evelina Gatti
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            name:Francesca Granucci
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      name:Department of Immunology, Institute Curie, Paris, France
      name:Department of Tumor Immunology, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
      name:Nuffield Department of Surgery, University of Oxford, Oxford, UK

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