Figure 1

Transcriptional regulatory network. (a) A transcriptional regulatory network in the form of a bipartite graph, in which a small number of transcription factors (TFs), represented by circles, regulate a large number of genes (represented by squares) by binding to their promoter regions. The black lines in the square boxes indicate gene expression profiles, that is, gene expression values measured under different experimental conditions or for different time points. The black lines in the circles represent TF activity profiles, that is, the concentrations of the TF subpopulation capable of DNA binding. Note that these TF activity profiles are usually unobserved owing to posttranslational modifications, and should hence be included as hidden or latent variables in the statistical model. (b) A more accurate representation of transcriptional regulation that allows for the cooperation of several TFs forming functional complexes; this complex formation is particularly common in higher eukaryotes.