We first created an integrated database, RegulomeDB, which provides a flexible platform for the addition of various data sources. We currently include all available ENCODE transcription factor (TF) ChIP-seq, histone ChIP-seq, FAIRE, and DNase I hypersensitive site data (The ENCODE Project Consortium 2012). In addition, we have included transcription factor ChIP-seq data available from the NCBI Sequence Read Archive (Hollenhorst et al. 2009; Jolma et al. 2010; Verzi et al. 2010; Wei et al. 2010; Hu et al. 2011; Lo et al. 2011; Novershtern et al. 2011; Palii et al. 2011; Yu et al. 2011). We also include a large collection of eQTL (Myers et al. 2007; Stranger et al. 2007; Schadt et al. 2008; Veyrieras et al. 2008; Dimas et al. 2009; Gibbs et al. 2010; Montgomery et al. 2010; Pickrell et al. 2010; Zeller et al. 2010), dsQTL (Degner et al. 2012), and ChIP-exo (Rhee and Pugh 2011) data. A total of 962 experimental data sets are included, covering over 100 tissues and cells lines and representing nearly 60 million annotations (Table 1).
