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

Sig2GRN is a software tool which links the models of signaling pathway with gene regulatory networks (GRNs). A generalized logical model, Sign2GRN 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. Sign2GRN is a Java plugin for Cytoscape (version 2.8.3) which is able to simulate the dynamics of the signaling pathways and the subsequent time-series gene expression data.