The cooperative module network. The cooperative module network (CMN) was constructed from the identified significantly cooperative module pairs. Modules are represented as circles and 101 identified associations between modules are represented as undirected links. The size of the circles is proportional to the number of genes within the modules. Purple circles indicate modules that appear in greater than or equal to four cooperative module pairs (Table 1). Genes contained in each module are listed in Additional file 2. Functions annotated from Gene Ontology (GO) are listed in Table 1 and Additional file 3. Most modules, especially modules presented as purple circles, were annotated as cell cycle related functions with significant p-values. Essential regulators that control cell cycle progression were also identified in functionally corresponding modules. For example, module 0 (response to DNA damage stimulus) contains RAD53; module 30 (cell morphogenesis) contains CLN4; module 3 (mitosis) contains MAD1; module 14 (regulation of transcription during G2/M-phase) contains FKH1; module 32 (regulation of cell division) contains CDC28.