The FASTQ files for ChIP-seq assays were downloaded from NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) with searching key word: “chip-seq transcription factor human.” Data sets were frozen by July 25, 2011. Experiments that were overlapped with the ENCODE Project were removed to avoid redundancy. All the FASTQ files were mapped to hg19 by BWA with the default setting. Only uniquely mapping reads (with q > 0) were used for the peaks calling. For ChIP-seq with replicates, the peaks were called by SPP-IDR pipeline with FDR less than 0.01 (Kharchenko et al. 2008). For ChIP-seq without replicates, peaks were called by MACS with parameter –p equal to 1 × 10−7 (Zhang et al. 2008).
