Net-synthesis
TL;DR: The biological usability of the software is illustrated 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.
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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@cs.uic.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
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References
Clonal Diseases of Large Granular Lymphocytes
TL;DR: Three distinct clinical syndromes occur in patients with increased numbers of circulating LGL, and X-linked gene analyses have supported a polyclonal LGL lymphocytosis in this syndrome.
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Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling
TL;DR: A dynamic model of ABA-induced stomatal closure is developed and it is revealed that the disruption of membrane depolarizability, anion efflux, actin cytoskeleton reorganization, cytosolic pH increase, the phosphatidic acid pathway, or K+ efflux through slowly activating K+ channels at the plasma membrane lead to the strongest reduction in ABA responsiveness.
ERK couples chronic survival of NK cells to constitutively activated Ras in lymphoproliferative disease of granular lymphocytes (LDGL)
Pearlie K. Epling-Burnette,Fanqi Bai,Sheng Wei,Pratima Chaurasia,Jeffrey S. Painter,Nancy Olashaw,Andrew D. Hamilton,Said M. Sebti,Julie Y. Djeu,Thomas P. Loughran +9 more
TL;DR: It is concluded that a constitutively active Ras/MEK/ERK pathway contributes to the accumulation of NK cells in patients with NK-LDGL, and strategies to inhibit this signaling pathway may be useful for the treatment of the NK type of LDGL.
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A novel method for signal transduction network inference from indirect experimental evidence.
Réka Albert,Bhaskar DasGupta,Riccardo Dondi,Sema Kachalo,Eduardo D. Sontag,Alexander Zelikovsky,Kelly Westbrooks +6 more
TL;DR: A new method of combined synthesis and inference of biological signal transduction networks by representing observed causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations is introduced.
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Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs
TL;DR: In this paper, the p-ary transitive reduction (TR p ) problem is considered and a polynomial-time algorithm with an approximation ratio of 1.78 is proposed.
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