Inferring transcriptional modules from ChIP-chip, motif and microarray data

Table 2 Summary of the significantly cell cycle enriched modules, identified by the GRAM, SAMBA and ReMoDiscovery module discovery methods

Method	No.	Genes			Regulatory program
		Mean	Min	Max	Mean	Min	Max	No. cell cycle R/all R	No. non cell cycle R/all R	No. cell cycle R
ReMoDiscovery (seed modules)	2	2	2	2	4	3	5	0.80	0.20	6
ReMoDiscovery (extended modules)	8	97.38	12	200	3.50	2	6	0.92	0.08	10
GRAM	33	6;47	5	11	2.66	1	6	0.74	0.26	17
SAMBA	14	58,;29	17	155	2.57	0	12	0.29	0.71	5

The number of cell cycle modules (No.) and the mean (Mean), minimum (Min) and maximum (Max) number of genes and regulators in these modules are displayed. Additionally, the ratio of the number of cell cycle regulators over the total number of regulators in a module, averaged over all cell cycle modules (No. cell cycle R/all R) is shown, as well as the ratio of the number of non-cell cycle regulators over the total number of regulators in a module, averaged over all cell cycle modules (No. non-cell cycle R/all R). The last column contains the number of regulators from the compiled list of 19 known cell cycle regulators (see Materials and methods) that were present in the regulatory program of at least one of the cell cycle modules (No. cell cycle R).

ISSN: 1474-760X