Figure 3

Module scores of the valid modules versus equally ranked random modules. Plot of the scores of the 70 best ranked modules versus a baseline for a) a random set and b) the true sets. The baseline consists of the average scores of the 70 best ranked modules in 10 different randomizations. For the "true sets" we used as input a set of 10 TFs amongst which OCT4, SOX2 and NANOG were present, while the random sets use as an input a set of TFs without the OCT4, SOX2 and NANOG. The random sets are thus not expected to contain any true modules. Panel a) all selected modules are random and reflect scores of false positives. They are distributed on the diagonal of the first quadrant. Panel b) the scores of the highly ranked modules in the true dataset score consistently higher than the equally ranked modules in the random sets.