A Review of Integration Strategies to Support Gene Regulatory Network Construction

Figure 4

Workflow of the GRAM algorithm. Known TF binding motifs are blasted against the promoter sequences in the genome-wide scope to infer the corresponding TF binding sites. A set of synergic TFs is identified when the TFs’ binding sites are close to each other. Regulated gene sets are defined by the corresponding sets of synergic TFs through location analysis. A “seed” of a gene module is selected from the regulated gene set based on the highly correlated expression. Then GRAM revisits the genomic expression to add more genes with closely correlated expression with the “seed” into the gene module of the “seed.” The GRN construction is fostered by the established regulations between the coexpression gene modules and their corresponding sets of synergic TFs.