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Table 3 Comparison of different methods for identifying functional peaks

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

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