Skip Navigation


Bioinformatics Advance Access originally published online on April 14, 2008
Bioinformatics 2008 24(11):1374-1380; doi:10.1093/bioinformatics/btn135
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
24/11/1374    most recent
btn135v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Santoni, D.
Right arrow Articles by Castiglione, F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Santoni, D.
Right arrow Articles by Castiglione, F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions

Daniele Santoni 1,2,{dagger}, Marco Pedicini 1 and Filippo Castiglione 1,*,{dagger}

1Institute for Computing Applications ‘M. Picone’, National Research Council (CNR), V.le del Policlinico, 137 – 00161 Rome, Italy and 2Department of Genetics and Molecular Biology, University of Rome ‘La Sapienza’, P. le A. Moro 5, 00185 Rome, Italy

*To whom correspondence should be addressed.


  Abstract

Motivation: An unbalanced differentiation of T helper cells from precursor type TH0 to the TH1 or TH2 phenotype in immune responses often leads to a pathological condition. In general, immune reactions biased toward TH1 responses may result in auto-immune diseases, while enhanced TH2 responses may cause allergic reactions. The aim of this work is to integrate a gene network of the TH differentiation in an agent-based model of the hyper-sensitivity reaction. The implementation of such a system introduces a second level of description beyond the mesoscopic level of the inter-cellular interaction of the agent-based model. The intra-cellular level consists in the cell internal dynamics of gene activation and transcription. The gene regulatory network includes genes-related molecules that have been found to be involved in the differentiation process in TH cells.

Results: The simulator reproduces the hallmarks of an IgE-mediated hypersensitive reaction and provides an example of how to combine the mesoscopic level description of immune cells with the microscopic gene-level dynamics.

Availability: The basic version of the simulator of the immune response can be downloaded here: http://www.iac.cnr.it/~filippo/C-ImmSim.html

Contact: f.castiglione{at}iac.cnr.it

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} These authors wish it to be known that, in their opinion, the first and third authors should be regarded as joint First Authors.

Associate Editor: Trey Ideker

Received on January 28, 2008; revised on March 14, 2008; accepted on April 9, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.