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Bioinformatics Advance Access originally published online on November 22, 2007
Bioinformatics 2008 24(2):293-295; doi:10.1093/bioinformatics/btm571
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks

Sema Kachalo 1, Ranran Zhang 2, Eduardo Sontag 3, Réka Albert 4 and Bhaskar DasGupta 5,*

1Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, 2Penn State Cancer Institute and Integrative Biosciences Graduate Program, Pennsylvania State University, Hershey, PA 17033, 3Department of Mathematics, Rutgers University, New Brunswick, NJ 08903, 4Departments of Physics and Biology, Pennsylvania State University, University Park, PA 16802 and 5Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We present a software for combined synthesis, inference and simplification of signal transduction networks. The main idea of our method lies in representing observed indirect causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. We illustrate the biological usability of our software by applying it to a previously published signal transduction network and by using it to synthesize and simplify a novel network corresponding to activation-induced cell death in large granular lymphocyte leukemia.

Availability: NET-SYNTHESIS is freely downloadable from http://www.cs.uic.edu/~dasgupta/network-synthesis/

Contact: dasgupta{at}cs.uic.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on August 21, 2007; revised on November 2, 2007; accepted on November 9, 2007

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