Regions delineated using observed DNaseI data across 53 epigenomes, annotated with both the 5-mark 15-state model based on observed data as well as the 12-mark 25-state model based on imputed data, across 127 epigenomes (Roadmap + ENCODE).
All coordinates are based on the Human hg19 genome assembly.
The resulting regions are simultaneously co-clustered for both the 15-state and 25-state model data. This makes a direct comparision between these two models possible.
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DNaseI regions selected with -log10(p) >= 2

Promoters: 56,893 putative promoter regions (1.29% of genome)

ChromHMM state calls (15-state model, RData)
ChromHMM state calls (25-state model, RData)
Clustered with k=57, for a resolution of ~1k regions per cluster
15-state model (observed) 25-state model (imputed)

Enhancers: 1,598,323 putative enhancer regions (10.48% of genome)

ChromHMM state calls (15-state model, RData)
ChromHMM state calls (25-state model, RData)
Clustered with k=160, for a resolution of ~10k regions per cluster 15-state model (observed) 25-state model (imputed)

Dyadics: 31,255 putative dyadic regions (0.3% of genome)

ChromHMM state calls (15-state model, RData)
ChromHMM state calls (25-state model, RData)
Clustered with k=63, for a resolution of ~500 regions per cluster 15-state model (observed) 25-state model (imputed)

DNaseI regions selected with -log10(p) >= 10

Promoters: 33,086 putative promoter regions (1% of genome)

ChromHMM state calls (15-state model, RData)
ChromHMM state calls (25-state model, RData)
Clustered with k=33, for a resolution of ~1k regions per cluster
15-state model (observed) 25-state model (imputed)

Enhancers: 474,004 putative enhancer regions (5.92% of genome)

ChromHMM state calls (15-state model, RData)
ChromHMM state calls (25-state model, RData)
Clustered with k=47, for a resolution of ~10k regions per cluster 15-state model (observed) 25-state model (imputed)

Dyadics: 7,974 putative dyadic regions (0.11% of genome)

ChromHMM state calls (15-state model, RData)
ChromHMM state calls (25-state model, RData)
Clustered with k=16, for a resolution of ~500 regions per cluster 15-state model (observed) 25-state model (imputed)

For questions/comments, contact Wouter Meuleman (lastname at mit edu)