High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae

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.

ISSN: 1474-760X