Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification

Background: Gene expression programs depend on recognition of cis elements in promoter region of target genes by transcription factors (TFs), but how TFs regulate gene expression via recognition of cis elements is still not clear. To study this issue, we define the cis-regulatory circuit of a gene as a system that consists of its cis elements and the interactions among their recognizing TFs and develop a dynamic model to study the functional architecture and dynamics of the circuit. This is in contrast to traditional approaches where a cis-regulatory circuit is constructed by a mutagenesis or motif-deletion scheme. We estimate the regulatory functions of cis-regulatory circuits using microarray data. Results: A novel cross-gene identification scheme is proposed to infer how multiple TFs coordinate to regulate gene transcription in the yeast cell cycle and to uncover hidden regulatory functions of a cis-regulatory circuit. Some advantages of this approach over most current methods are ...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen
• Keywords: BMCBI 2005, Cis Elements, Cis-regulatory Circuits, Regulatory Functions