Figure 1 : The updated Registry of candidate cis-Regulatory elements

Figure 1 | The updated Registry of candidate cis-Regulatory elements. 

a, Schematic of the pipeline used to make Version 4 of the Registry of cCREs. We defined element anchors by generating representative DHSs (rDHSs) and representative transcription factor clusters (rClusters). Element anchors are scored with H3K4me3, H3K27ac, and CTCF ChIP-seq and ATAC-seq signals (yellow box) and classified according to the scheme in b. This results in 2.37 million cCREs in the human genome and 967 thousand in the mouse genome. We supplement the Registry with additional ENCODE Encyclopedia annotations including transcription quantifications, 3D chromatin contacts, functional characterization measurements, sequence features, and genetic variation (blue box). The Registry of cCREs and all layered annotations are housed in our web portal SCREEN. New components of the pipeline are denoted by stars. b, Overview of our cCRE classification scheme. cCREs are classified based on their patterns of biochemical signals (chromatin accessibility in green, H3K4me3 in red, H3K27ac in yellow, CTCF in blue, transcription factor in purple) and distance from annotated TSSs. High signals are denoted by peaks. The +/- symbols indicate the corresponding signal may or may not be present and its presence does not impact classification. New categories of elements are denoted by stars. c, Bar graphs depicting the number of cCREs annotated in each class for human (left) and mouse (right).