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


BACKGROUND
NET-SYNTHESIS is freely downloadable from http://www.cs.uic.edu/~dasgupta/network-synthesis/
Kachalo
Sema
S
Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA.
Zhang
Ranran
R
Sontag
Eduardo
E
Albert
Réka
R
DasGupta
Bhaskar
B
D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D020543:Proteome