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

Autor: Matthijs Kramer, Roberto Bonaiuti, Ivan Zanoni, Gerold Schuler, Walter Reith, Sorin Draghici, Damariz Rivero, Vassili Soumelis, Jonathan M. Austyn, Ugo D'Oro, Cornelis J. M. Melief, Andrea Splendiani, Carl G. Figdor, Maria Torcia, Enrica Calura, Marco Brandizi, Renato Ostuni, Sandra Gessani, Duccio Cavalieri, Francesca Granucci, Sonja I. Buschow, Maria Cristina Gauzzi, Arpad Lanyi, Stephan Schierer, Nadine van Montfoort, Éva Rajnavölgyi, Michaela Gündel, Philippe Pierre, Raphaël Zollinger, Luca Beltrame, Lisa Rizzetto, Andreas Baur, Isabelle Dunand-Sauthier, Carlotta De Filippo, Mirela Kuka, Evelina Gatti, Irene Stefanini, Razvan Popovici
Přispěvatelé: Reith, Walter, Dunand-Sauthier, Isabelle, Pierre, Philippe, Università degli Studi di Firenze [Firenze], Radboud University Medical Center [Nijmegen], Istituto Superiore di Sanità, Rome (ISS), Department of Therapeutic Research and Medicines Evaluation, University of Geneva Medical School, Department of Pathology and Immunology, University of Erlangen, Department of Dermatology, Leaf Bioscience, Novartis Vaccines, Siena, Italy, Novartis Vaccines, Wayne State University [Detroit], Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), University of Milano-Bicocca (UNIMIB), Department of Biotechnology and Biosciences, University of Debrecen Egyetem [Debrecen], Leiden University Medical Center (LUMC), Miravtech Corporation, Immunité et cancer (U932), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie-Université Paris Descartes - Paris 5 (UPD5), University of Oxford [Oxford], Cavalieri, D, Rivero, D, Beltrame, L, Buschow, S, Calura, E, Rizzetto, L, Gessani, S, Gauzzi, M, Reith, W, Baur, A, Bonaiuti, R, Brandizi, M, De Filippo, C, D'Oro, U, Draghici, S, Dunand Sauthier, I, Gatti, E, Granucci, F, Gündel, M, Kramer, M, Kuka, M, Lanyi, A, Melief, C, Van Montfoort, N, Ostuni, R, Pierre, P, Popovici, R, Rajnavolgyi, E, Schierer, S, Schuler, G, Soumelis, V, Splendiani, A, Stefanini, I, Torcia, M, Zanoni, I, Zollinger, R, Figdor, C, Austyn, J, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Biotecnologie e Bioscienze = Department of Biotechnology and Biosciences [Milano-Bicocca] (BTBS), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Buschow, Si, Gauzzi, Mc, Kuka, Mirela, Melief, Cj, van Montfoort, N, Torcia, Mg, Figdor, Cg, Austyn, J. M., Istituto Superiore di Sanità, Rome ( ISS ), Centre d'Immunologie de Marseille - Luminy ( CIML ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), University of Milano-Bicocca ( UNIMIB ), Immunité et cancer ( U932 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut Curie, Università degli Studi di Firenze = University of Florence (UniFI), Istituto Superiore di Sanità (ISS), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Universiteit Leiden, University of Oxford
Jazyk: angličtina
Rok vydání: 2010
Předmět:
Cell type
Markup language
Computer science
Systems biology
medicine.medical_treatment
Immunology
Computational biology
ddc:616.07
computer.software_genre
03 medical and health sciences
0302 clinical medicine
Immune system
Immune Regulation [NCMLS 2]
medicine
[ SDV.IMM ] Life Sciences [q-bio]/Immunology
Elméleti orvostudományok
Molecular gastro-enterology and hepatology [IGMD 2]
Molecular Biology
030304 developmental biology
0303 health sciences
Applied Mathematics
Research
Dendritic cells
toll like receptors
pattern recognition receptors
systems biology
Pattern recognition receptor
Immunotherapy
Orvostudományok
dendritic cells
toll-like receptors
TLR
TLR pathways
systems biology
pathway analysis
Computer Science Applications
Computational Theory and Mathematics
DECIPHER
[SDV.IMM]Life Sciences [q-bio]/Immunology
Data mining
Signal transduction
computer
030215 immunology
Zdroj: Immunome Research, Vol. 6 (2010) P. 10
Immunome Research
Immunome Research, BioMed Central, 2010, 6, pp.10. ⟨10.1186/1745-7580-6-10⟩
Immunome Research; Vol 6
Immunome Research, 6, 10-10
Immunome Research, 6, pp. 10-10
Immunome Research, BioMed Central, 2010, 6, pp.10. 〈10.1186/1745-7580-6-10〉
Immunome Research, 2010, 6, pp.10. ⟨10.1186/1745-7580-6-10⟩
ISSN: 1745-7580
DOI: 10.1186/1745-7580-6-10⟩
Popis: Contains fulltext : 88001.pdf (Publisher’s version ) (Closed access) 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.
Databáze: OpenAIRE
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