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

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

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
  1. 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).