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Title: Sig2GRN : a software tool linking signaling pathway with gene regulatory network for dynamic simulation
Authors: Zhang, Fan
Liu, Runsheng
Zheng, Jie
Keywords: Transcription Factor Activity
Gene Regulatory Network
DRNTU::Engineering::Computer science and engineering
Issue Date: 2016
Source: Zhang, F., Liu, R., & Zheng, J. (2016). Sig2GRN : a software tool linking signaling pathway with gene regulatory network for dynamic simulation. BMC Systems Biology, 10(S4), 123-. doi:10.1186/s12918-016-0365-1
Series/Report no.: BMC Systems Biology
Abstract: Background: Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a Cytoscape plugin that is able to simulate time-course gene expression data given the user-defined external stimuli to the signaling pathways. Methods: A generalized logical model is used in modeling the upstream signaling pathways. Then a Boolean model and a thermodynamics-based model are employed to predict the downstream changes in gene expression based on the simulated dynamics of transcription factors in signaling pathways. Results: Our empirical case studies show that the simulation of Sig2GRN can predict changes in gene expression patterns induced by DNA damage signals and drug treatments. Conclusions: As a software tool for modeling cellular dynamics, Sig2GRN can facilitate studies in systems biology by hypotheses generation and wet-lab experimental design.
DOI: 10.1186/s12918-016-0365-1
DOI (Related Dataset):
Schools: School of Computer Science and Engineering 
Rights: © 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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