Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation.
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.


BACKGROUND
http://histone.scse.ntu.edu.sg/Sig2GRN/.
School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
Fan
F
Zhang
School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
Runsheng
R
Liu
School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore. zhengjie@ntu.edu.sg.|Complexity Institute, Nanyang Technological University, Singapore, 637723, Singapore. zhengjie@ntu.edu.sg.|Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore. zhengjie@ntu.edu.sg.
Jie
J
Zheng
D017209:Apoptosis / Q000235:genetics; D045744:Cell Line, Tumor; D004249:DNA Damage; D004347:Drug Interactions; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000187:drug effects; D006801:Humans; D008954:Models, Biological; D015398:Signal Transduction / Q000187:drug effects; D012984:Software; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism
D014157:Transcription Factors