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Table 1 Modules in the cooperative module network (CMN).

From: A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle

ID No. genes1 Deg2 Function (p-value)3 Cell cycle-related genes4
0 91 34 response to DNA damage stimulus (3.93e-33) RAD24,RAD53,RAD9,DUN1,MEC1, MAD3,MRE11, MEC3,SGS1,CLB2
2 59 13 Golgi vesicle transport (5.21e-12) CDC50,GCS1,RGP1,SEC28,KAR2
30 27 13 cell morphogenesis (3.53e-09) CDC28,CLN4,PHO85,PCL2,SWE1, SWI4,FUS1,CDC12
3 42 8 mitosis (4.92e-14) BUB3,MAD1,MAD2,MAD3,BFA1, RAD53,CLN3
13 17 6 nucleosome assembly (1.99e-18) ABF1,ABF2,HTB1,HTB2,HHT1
39 13 6 protein amino acid acetylation (9.87e-12) GCN5,TAF1,TRA1,SPT8
22 15 5 nucleosome disassembly (4.47e-40) RCS1,RCS2,RCS4,RCS6,RCS8
28 24 5 lipid biosynthetic process (6.24e-09) LAC1,GAS3
4 27 4 ubiquitin-dependent protein catabolism (2.20e-30) RAD23,RPT1,RPT6,RPN11,RPN12
14 5 4 regulation of transcription (G2/M-phase) (1.83e-08) FKH1,FKH2,NDD1,ACE2,SWI5
32 11 4 regulation of cell division (1.55e-11) CDC28,CLN2,CLN3,STB1,FUS3
54 7 4 protein folding (0.00015) HAP1
  1. 1The number of genes contained in a module.
  2. 2The number of links of a module in the cooperative module network (CMN).
  3. 3For each module, we only listed the most significantly enriched functional GO categories (with p-value) (complete results are listed in Additional file 3).
  4. 4A subset of cell cycle-related genes contained in each module is listed in the last column (complete results are listed in Additional file 5).
  5. Table 1 lists all modules that cooperate with more than four modules. For each module, we listed the most significantly enriched functional GO category (with p-value). We found that all of these modules were annotated to cell cycle-associated or specific functions. To further analyze specific functions and interactions mediated by each module, cell cycle-related genes reported in previous studies [40] were identified in each module (complete results are listed in Additional file 5). These genes include cell cycle-regulated genes and genes annotated in the functional categories of cell cycle and DNA processing. A subset of cell cycle-related genes contained in each module is listed in the last column. Cell cycle-related genes in each module that control the progression of the cell cycle, such as CDC28, cyclins, transcription factors, and checkpoint-related genes, are listed in the last column.