Statecharts for gene network modeling.
State diagrams (stategraphs) are suitable for describing the behavior of dynamic systems. However, when they are used to model large and complex systems, determining the states and transitions among them can be overwhelming, due to their flat, unstratified structure. In this article, we present the use of statecharts as a novel way of modeling complex gene networks. Statecharts extend conventional state diagrams with features such as nested hierarchy, recursion, and concurrency. These features are commonly utilized in engineering for designing complex systems and can enable us to model complex gene networks in an efficient and systematic way. We modeled five key gene network motifs, simple regulation, autoregulation, feed-forward loop, single-input module, and dense overlapping regulon, using statecharts. Specifically, utilizing nested hierarchy and recursion, we were able to model a complex interlocked feed-forward loop network in a highly structured way, demonstrating the potential of our approach for modeling large and complex gene networks.
Shin
Yong-Jun
YJ
Department of Electrical Engineering, University of Texas at Dallas, Richardson, Texas, United States of America. yshin@utdallas.edu
Nourani
Mehrdad
M
D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D014176:Protein Biosynthesis / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*
D001426:Bacterial Proteins