Figure 1. Sample Outputs of ChromHMM.

(a) Example of state annotation tracks produced from ChromHMM and visualized in the UCSC genome browser⁶, including a dense view of the segmentation as a single track (top), and an expanded view of the segmentation showing each state as a separate track (bottom). (b) Heat maps automatically produced by ChromHMM show emission (left) and transition (right) parameters. (c) Example heat map for state functional enrichments automatically generated by ChromHMM. The columns indicate the relative percentage of the genome represented by each state (first column) and relative fold enrichment for: RefSeq transcription start sites (TSS); CpG Islands; 2000 base pair intervals around the TSS; exons; genes; transcript end sites (TES); evolutionary conservation; and nuclear lamina associated regions (Supplementary Note). a-c. Example shown corresponds to a previous model learned across nine cell types³.