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Bioinformatics Advance Access published online on January 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl684
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

APOPTO-CELL – A simulation tool and interactive database for analyzing cellular susceptibility to apoptosis

Heinrich J. Huber 1,2,3,*, Markus Rehm 1,2,*, Martin Plchut 3, Heiko Düssmann 2 and Jochen H.M. Prehn 1,2

1 Systems Biology Group, RCSI Research Institute, 2 Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland. 3 Siemens Medical Division, Siemens Ireland, Dublin 2, Ireland.

*both authors contributed equally. Heinrich J. Huber, Markus Rehm, E-mail: mrehm{at}rcsi.ie


  Abstract

We have developed a web service that provides a comprehensive analysis of the susceptibility of cells to undergo apoptosis in response to an activation of the mitochondrial apoptotic pathway. Based on ordinary differential equations, (pre-determined) protein concentrations and release kinetics of mitochondrial pro-apoptotic factors, a network of 52 reactions and 19 reaction partners can be employed as a tool to display temporal protein profiles, to identify key regulatory proteins, and to determine critical threshold concentrations required for the execution of apoptosis in HeLa cancer cells or other cell types. The web service also provides an interactive database function for the deposition of cell type-specific quantitative data. In addition, the web service provides an output that can be compared directly to experimental results obtained from real-time single-cell experiments, making this a widely applicable systems biology tool for apoptosis and cancer researchers.

Availability: http://systemsbiology.rcsi.ie/apopto-cell.html

Associate Editor: Olga Troyanskaya

Received on December 13, 2006; revised on December 13, 2006; accepted on January 7, 2007

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