Nonlinear Dynamic Trans/Cis Regulatory Circuit for Gene Transcription via Microarray Data

The trans-regulatory circuit is considered as the regulatory interactions between upstream regulatory genes and transcription factor binding site motifs or cis elements. And the cis-regulatory circuit is viewed as a dynamic interactive circuit among binding site motifs with their effective action on the expression scheme of target gene. In brief, gene transcription depends on the trans/cis regulatory circuits. In this study, nonlinear trans/cis regulatory circuits for gene transcription in yeast are constructed using microarray data, translation time delay, and information of transcription factors (TFs) binding sites. We provide a useful nonlinear dynamic modeling and develop a parameter estimating method for the construction of trans/cis regulatory circuits, which is powerful for understanding gene transcription. We apply our method to construct trans/cis regulatory circuits of yeast cell cycle-related genes and successfully quantify their regulatory abilities and find possible cis-element interactions. Not only could the data of yeast be applied by our method, but those of other species also could. The proposed method can provide a quantitative basis for system analysis of gene circuits, which is potential for gene regulatory circuit design with a desired gene expression.