Table 2

Overall comparison with other methods

GO functional enrichment level

Overall modules

Method

No. of modules

No. of distinct genes

No. of distinct TFs

BP

MF

CC

Target genes of common 38 TFs

EPM

47

2,099

109

14.36 (8.63)

12.94 (8.53)

15.32 (7.80)

17.86 (21.49)

RM

289

2,099

109

7.56 (3.43)

6.51 (3.24)

7.23 (4.95)

GRAM

106

655

69

8.54 (1.05)

7.77 (4.64)

8.73 (2.18)

12.28 (19.47)

COGRIM (B-/C+)

39

841

39

8.67 (2.97)

6.81 (4.24)

7.43 (2.72)

8.81 (13.43)

COGRIM (B+/C+)

39

936

39

5.3 (0.68)

4.55 (0.18)

4.86 (0.68)

5.19 (4.81)

The number of modules obtained from each method and the number of distinct genes and transcription factors (TFs) that constitute modules identified by each method are shown. In addition, GO functional enrichment levels are shown. The GO (BP, biological process; MF, molecular function; CC, cellular process) enrichment p values were transformed to negative log values and averaged over all modules. We also performed a functional enrichment test for the target genes of 38 transcriptional factors that were commonly predicted in all the three methods. The standard deviations are shown in parentheses.

Lee et al. Genome Biology 2008 9:R2   doi:10.1186/gb-2008-9-1-r2