Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

Table 3 Comparison of different methods for identifying functional peaks

Method	Total number of peaks	Number of genes mapped	Intersection with SRC1-dependent genes
MACS p = 1E-10	1,286	684	44
MACS p = 1E-8	1,966	996	57
MACS p = 1E-5	4,678	2,054	123
supervised-NB(th = 0.8,1:2)	11,835	3,875	238