Fig. (1).

The general framework of reverse engineering transcriptional regulatory networks. (A) The framework of inferring regulatory network from gene expression profiles. There are various sample types of gene expression data, such as condition-specific, perturbation and time series data. A reverse engineering algorithm takes the input of the gene expression profiles and outputs the inferred gene regulatory relationships in form of a network. (B) The interrelated four levels of regulatory parameter information should be determined in the reverse engineering. The algorithm addresses the gene regulatory questions at one or several combined levels. (C) The regulatory pair and system in the modeling. The decision-making of regulatory relationship of an individual pair is in an isolated manner. However, the regulatory system consists of complicated regula-tions of combination and cooperation, such as the indirect regulation from gene G1 to gene G2 conditioned upon gene G3, which needs to be modeled in a systematic manner.