Table I. Number of peaks called over 100 subsamplings of the complete data sets.

Method	Total No. of Peaks (All Samples)	Average No. of Peaks (per Sample)	No. of Majority Genes	Median Peak Score of Majority Genes (Top 200 Peaks)
ChIP	4,161	624	415	229 (408)
ChAP	2,221	997	918	126 (391)
TChAP	8,365	2,975	2,596	313 (2,263)