Figure 1

Workflow of genetic networks construction. This workflow contains four major stages. (a) TF binding site identification. Genomic sequences of annotated genes are retrieved and aligned, and conserved TF binding sites in genomic sequences are identified. Binding probability scores are calculated using the identified binding sites. (b) TF target identification. The P value for observing a given binding probability score or higher by chance is calculated using permutation of TF binding sites. Using a P value cutoff, regulatory targets of each TF are identified. (c) Coexpressed gene cluster identification. Gene expression profiles are collected from experiments. Coherently expressed genes are identified and clustered. (d) Network construction. Genetic networks are identified for each coexpressed gene cluster using the target genes predicted for each TF within each gene cluster. The complete regulatory network is then constructed by consolidating individual networks. Hs, Homo sapiens; Mm, Mus musculus.