Crosstalk relationship graphs of M 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 M phase-related transcription factors. Factors considered in the graph include Ace2, Swi5, and Mcm1. ACE2 and SWI5 are contained in module 14 (regulation of transcription during G2/M phase interphase). (b) The relationship graph of G2 phase-related CDC genes, cyclins, and CDC28. Ccd28, Clb1, Clb2, Clb3, and Clb4 are considered in the graph. CDC28 is contained in module 1 (regulation of cell cycle), module 30 (cell morphogenesis), module 32 (regulation of cell division), module 42 (G1/S transition of mitotic cell cycle and interphase), module 44 (regulation of mitosis), and module 79 (regulation of cyclin-dependent protein kinase activity). CLB2 is contained in module 0 (response to DNA damage stimuli). CLB3 is contained in module 3 (mitosis).