A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae

Coherence of target gene expression profiles. (A) Distinctness of target gene expression profiles. The cube represents a three-dimensional expression space. Each dot represents a gene from functional module 1 (blue) or functional module 2 (red), and the location of the gene on an axis represents the expression level of the gene at the time point or condition represented by the axis. The distance that separates two genes is inversely proportional to the “coherence” of their expression profiles. Target genes are shown as regulated by the TF (arrow). This distribution of genes represents a hypothetical scenario in which the intermodule coherence between target genes is higher than that between non-target genes. (B) Notation as in A. This distribution of genes represents a hypothetical scenario in which target genes and non-target genes have very different expression profiles, even though the intermodule coherence between target genes is similar to that of non-target genes. (C) Triplet scoring notation. M₁ = genes in module 1; T = genes in genome containing binding site for TF T; m₁ = genes in M containing binding site for T (“target genes”); M₁′ = genes in M₁ that do not contain a binding site for T (“non-target genes”); r_x (M₁′) = x randomly selected genes from M₁′; M₂, m₂, M₂′ r _|x| (M₂′) defined analogously. Aggregate target genes = (m₁ ∪m₂) or (m₁∪m₂∪I_T) ; aggregate non-target genes =(M₁′ ∪ M₂′) or (M₁′ ∪ I ∪ M₂′); I and I_T represent non-target and target genes, respectively, that are present in both modules. (D) Quartet scoring notation. Variables are analogous to those in C, but here there are two TFs, X and Y. T_x = genes in genome containing binding site for X; T_y = genes in genome containing binding site for Y. B, X, Y, and N represent module components that are targets of both X and Y, X only, Y only, or neither TF, respectively: .