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

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

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

¹The number of genes contained in a module.
²The number of links of a module in the cooperative module network (CMN).
³For each module, we only listed the most significantly enriched functional GO categories (with p-value) (complete results are listed in Additional file 3).
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).
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.

ISSN: 1471-2105