ChromHMM: automating chromatin-state discovery and characterization

To the Editor: Chromatin-state annotation using combinations of chromatin modification patterns has emerged as a powerful approach for discovering regulatory regions and their cell type–specific activity patterns and for interpreting disease-association studies1, 2, 3, 4, 5. However, the computational challenge of learning chromatin-state models from large numbers of chromatin modification datasets in multiple cell types still requires extensive bioinformatics expertise. To address this challenge, we developed ChromHMM, an automated computational system for learning chromatin states, characterizing their biological functions and correlations with large-scale functional datasets and visualizing the resulting genome-wide maps of chromatin-state annotations.Massachusetts Institute of Technology. Computational and Systems Biology InitiativeNational Science Foundation (U.S.) (postdoctoral fellowship 0905968)National Institutes of Health (U.S.) (1-RC1- HG005334)National Institutes of Health (U.S.) (1 U54 HG004570