Crosstalk relationship graphs of S phase. Yellow circles indicate modules from identified cooperative module pairs, and green circles indicate regulators not contained in any modules. The size of the yellow circles is proportional to the number of genes within the modules. Links indicate either relationships dependent on a significant number of protein-protein interactions (blue links) or relationships dependent on a significant number of regulatory interactions (red or purple links) (see the Methods section for details). Only relationships among correlated genes and their correlated module pairs were used to construct the relationship graphs (Figure 3). When a phase-specific transcription factor was contained in module X and regulated a significant number of genes in module Y, a red link was drawn from the circle representing X to the circle representing Y. On the contrary, if a phase specific-regulator was regulated by more than one factor in module Z, a purple link was drawn from the circle representing Z to the circle representing the module containing the regulator or the circle indicating the regulator. (a) Relationship graph of S phase-related transcription factors. Factors considered in the graph include SWI4, SWI6, MBP1, NDD1, and Skn7. SWI4 is contained in module 30 (cell morphogenesis) and module 66 (amino sugar metabolic processes). SWI6 and SKN7 are contained in module 0 (response to DNA damage stimulus). NDD1 is contained in module14 (regulation of transcription during G2/M phase interphase). (b) Relationship graph of S phase-related CDC genes. Cdc7, Cdc8, Cdc21, and Cdc24 are considered in the graph. CDC7 is contained in module 12 (DNA-dependent DNA replication initiation). CDC24 is contained in module 77 (regulation of nuclear division).