Schema for Broad ChromHMM - Chromatin State Segmentation by HMM from ENCODE/Broad
  Database: hg19    Primary Table: wgEncodeBroadHmmGm12878HMM    Row Count: 571,339   Data last updated: 2011-03-22
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 10000int(10) unsigned Start position in chromosome
chromEnd 10600int(10) unsigned End position in chromosome
name 15_Repetitive/CNVvarchar(255) Name of item
score 0int(10) unsigned Optional score, nominal range 0-1000
strand .char(1) + or -
thickStart 10000int(10) unsigned Start of where display should be thick (start codon)
thickEnd 10600int(10) unsigned End of where display should be thick (stop codon)
itemRgb 16119285int(10) unsigned Used as itemRgb as of 2004-11-22

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
585chr1100001060015_Repetitive/CNV0.1000010600245,245,245
585chr1106001113713_Heterochrom/lo0.1060011137245,245,245
585chr111137117378_Insulator0.111371173710,190,254
585chr1117371193711_Weak_Txn0.1173711937153,255,102
585chr111937121377_Weak_Enhancer0.1193712137255,252,4
585chr1121371453711_Weak_Txn0.1213714537153,255,102
585chr1145372033710_Txn_Elongation0.14537203370,176,80
585chr1203372213711_Weak_Txn0.2033722137153,255,102
585chr122137229379_Txn_Transition0.22137229370,176,80
585chr1229372693710_Txn_Elongation0.22937269370,176,80

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Broad ChromHMM (wgEncodeBroadHmm) Track Description
 

 Note: these data have been converted via liftOver from the Mar. 2006 (NCBI36/hg18) version of the track.

Description

This track displays a chromatin state segmentation for each of nine human cell types. A common set of states across the cell types were learned by computationally integrating ChIP-seq data for nine factors plus input using a Hidden Markov Model (HMM). In total, fifteen states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements.

Display Conventions and Configuration

This track is a composite track that contains multiple subtracks. Each subtrack represents data for a different cell type and displays individually on the browser. Instructions for configuring tracks with multiple subtracks are here. The fifteen states of the HMM, their associated segment color, and the candidate annotations are as follows:

  • State 1 -  Bright Red  - Active Promoter
  • State 2 -  Light Red  -Weak Promoter
  • State 3 -  Purple  - Inactive/poised Promoter
  • State 4 -  Orange  - Strong enhancer
  • State 5 -  Orange  - Strong enhancer
  • State 6 -  Yellow  - Weak/poised enhancer
  • State 7 -  Yellow  - Weak/poised enhancer
  • State 8 -  Blue  - Insulator
  • State 9 -  Dark Green  - Transcriptional transition
  • State 10 -  Dark Green  - Transcriptional elongation
  • State 11 -  Light Green  - Weak transcribed
  • State 12 -  Gray  - Polycomb-repressed
  • State 13 -  Light Gray  - Heterochromatin; low signal
  • State 14 -  Light Gray  - Repetitive/Copy Number Variation
  • State 15 -  Light Gray  - Repetitive/Copy Number Variation

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Methods

ChIP-seq data from the Broad Histone track was used to generate this track. Data for nine factors plus input and nine cell types was binarized separately at a 200 base pair resolution based on a Poisson background model. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the nine cell types, first the genomes were concatenated across the cell types. For each of the nine cell types, each 200 base pair interval was then assigned to its most likely state under the model. Detailed information about the model parameters and state enrichments can be found in (Ernst et al, accepted).

Release Notes

This is release 1 (Jun 2011) of this track. It was lifted over from the NCBI36/hg18 version of the track, and is therefore based on the NCBI36/hg18 release of the Broad Histone track. It is anticipated that the HMM methods will be run on the newer datasets in the GRCh37/hg19 version of the Broad Histone track, and, once that happens, the new data will replace this liftOver.

Credits

The ChIP-seq data were generated at the Broad Institute and in the Bradley E. Bernstein lab at the Massachusetts General Hospital/Harvard Medical School, and the chromatin state segmentation was produced in Manolis Kellis's Computational Biology group at the Massachusetts Institute of Technology. Contact: Jason Ernst.

Data generation and analysis was supported by funds from the NHGRI (ENCODE), the Burroughs Wellcome Fund, Howard Hughes Medical Institute, NSF, Sloan Foundation, Massachusetts General Hospital and the Broad Institute.

References

Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.

There is no restriction on the use of segmentation data.