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https://hdl.handle.net/10356/80431
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. | URI: | https://hdl.handle.net/10356/80431 http://hdl.handle.net/10220/46551 |
DOI: | 10.1186/s12918-016-0365-1 | DOI (Related Dataset): | https://doi.org/10.21979/N9/SO9VRB | 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 (http://creativecommons.org/licenses/by/4.0/), 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 (http://creativecommons.org/publicdomain/zero/1.0/) 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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Sig2GRN- a software tool linking signaling pathway with gene regulatory network for dynamic simulation.pdf | 1.22 MB | Adobe PDF | View/Open |
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