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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.