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Table 4 ER ChIP-Seq and chip-chip peaks in MCF-7 cell line

From: HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

ChIP-Seq Chip-chip
Library Total peaks Total peaks Overlapped peaks Unique peaks Overlap (%)
IP_1 69390 4621 4492 129 97.2
IP_2 46688 4621 4391 230 95.0
IP_3 57657 4621 4450 171 96.3
  1. A list of 4,621 highly confident (p value < =1e-5) chip-chip peaks was extracted from the file “ER_binding_p-value.xls” downloaded from http://research4.dfci.harvard.edu/brownlab//datasets/index.php?dir=ER_MCF7_whole_human_genome/. ChIP-Seq peaks were identified by MACS at the q value cutoff of 0.01. Both ChIP-Seq and chip-chip analysis used hg18 reference sequence.