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

Duccio Cavalieri, Damariz Rivero, Luca Beltrame, Sonja I. Buschow, Enrica Calura, Lisa Rizzetto, Sandra Gessani, Maria C. Gauzzi, Walter Reith, Andreas Baur, Roberto Bonaiuti, Marco Brandizi, Carlotta De Filippo, Ugo D'Oro, Sorin Draghici, Isabelle Dunand-Sauthier, Evelina Gatti, Francesca Granucci, Michaela Gündel, Matthijs KramerMirela Kuka, Arpad Lanyi, Cornelis J M Melief, Nadine Van Montfoort, Renato Ostuni, Philippe Pierre, Razvan Popovici, Eva Rajnavolgyi, Stephan Schierer, Gerold Schuler, Vassili Soumelis, Andrea Splendiani, Irene Stefanini, Maria G. Torcia, Ivan Zanoni, Raphael Zollinger, Carl G. Figdor, Jonathan M. Austyn

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number10
JournalImmunome Research
Volume6
Issue number1
DOIs
Publication statusPublished - 2010

Fingerprint

Dissect
Dendritic Cells
Signal transduction
Systems Biology
Signal Transduction
Receptor
Pathway
Resources
Immune system
Immune System
Specificity
Cytology
Immunotherapy
Markup languages
Biological Models
Regulatory Networks
Toll-Like Receptors
Cell
Grouping
Data Model

ASJC Scopus subject areas

  • Immunology
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics
  • Computer Science Applications

Cite this

DC-ATLAS : A systems biology resource to dissect receptor specific signal transduction in dendritic cells. / Cavalieri, Duccio; Rivero, Damariz; Beltrame, Luca; Buschow, Sonja I.; Calura, Enrica; Rizzetto, Lisa; Gessani, Sandra; Gauzzi, Maria C.; Reith, Walter; Baur, Andreas; Bonaiuti, Roberto; Brandizi, Marco; De Filippo, Carlotta; D'Oro, Ugo; Draghici, Sorin; Dunand-Sauthier, Isabelle; Gatti, Evelina; Granucci, Francesca; Gündel, Michaela; Kramer, Matthijs; Kuka, Mirela; Lanyi, Arpad; Melief, Cornelis J M; Van Montfoort, Nadine; Ostuni, Renato; Pierre, Philippe; Popovici, Razvan; Rajnavolgyi, Eva; Schierer, Stephan; Schuler, Gerold; Soumelis, Vassili; Splendiani, Andrea; Stefanini, Irene; Torcia, Maria G.; Zanoni, Ivan; Zollinger, Raphael; Figdor, Carl G.; Austyn, Jonathan M.

In: Immunome Research, Vol. 6, No. 1, 10, 2010.

Research output: Contribution to journalArticle

Cavalieri, D, Rivero, D, Beltrame, L, Buschow, SI, Calura, E, Rizzetto, L, Gessani, S, Gauzzi, MC, 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, CJM, Van Montfoort, N, Ostuni, R, Pierre, P, Popovici, R, Rajnavolgyi, E, Schierer, S, Schuler, G, Soumelis, V, Splendiani, A, Stefanini, I, Torcia, MG, Zanoni, I, Zollinger, R, Figdor, CG & Austyn, JM 2010, 'DC-ATLAS: A systems biology resource to dissect receptor specific signal transduction in dendritic cells', Immunome Research, vol. 6, no. 1, 10. https://doi.org/10.1186/1745-7580-6-10
Cavalieri, Duccio ; Rivero, Damariz ; Beltrame, Luca ; Buschow, Sonja I. ; Calura, Enrica ; Rizzetto, Lisa ; Gessani, Sandra ; Gauzzi, Maria C. ; Reith, Walter ; Baur, Andreas ; Bonaiuti, Roberto ; Brandizi, Marco ; De Filippo, Carlotta ; D'Oro, Ugo ; Draghici, Sorin ; Dunand-Sauthier, Isabelle ; Gatti, Evelina ; Granucci, Francesca ; Gündel, Michaela ; Kramer, Matthijs ; Kuka, Mirela ; Lanyi, Arpad ; Melief, Cornelis J M ; Van Montfoort, Nadine ; Ostuni, Renato ; Pierre, Philippe ; Popovici, Razvan ; Rajnavolgyi, Eva ; Schierer, Stephan ; Schuler, Gerold ; Soumelis, Vassili ; Splendiani, Andrea ; Stefanini, Irene ; Torcia, Maria G. ; Zanoni, Ivan ; Zollinger, Raphael ; Figdor, Carl G. ; Austyn, Jonathan M. / DC-ATLAS : A systems biology resource to dissect receptor specific signal transduction in dendritic cells. In: Immunome Research. 2010 ; Vol. 6, No. 1.
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AU - Cavalieri, Duccio

AU - Rivero, Damariz

AU - Beltrame, Luca

AU - Buschow, Sonja I.

AU - Calura, Enrica

AU - Rizzetto, Lisa

AU - Gessani, Sandra

AU - Gauzzi, Maria C.

AU - Reith, Walter

AU - Baur, Andreas

AU - Bonaiuti, Roberto

AU - Brandizi, Marco

AU - De Filippo, Carlotta

AU - D'Oro, Ugo

AU - Draghici, Sorin

AU - Dunand-Sauthier, Isabelle

AU - Gatti, Evelina

AU - Granucci, Francesca

AU - Gündel, Michaela

AU - Kramer, Matthijs

AU - Kuka, Mirela

AU - Lanyi, Arpad

AU - Melief, Cornelis J M

AU - Van Montfoort, Nadine

AU - Ostuni, Renato

AU - Pierre, Philippe

AU - Popovici, Razvan

AU - Rajnavolgyi, Eva

AU - Schierer, Stephan

AU - Schuler, Gerold

AU - Soumelis, Vassili

AU - Splendiani, Andrea

AU - Stefanini, Irene

AU - Torcia, Maria G.

AU - Zanoni, Ivan

AU - Zollinger, Raphael

AU - Figdor, Carl G.

AU - Austyn, Jonathan M.

PY - 2010

Y1 - 2010

N2 - 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.

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