Download Bin Discovery Plus Txt
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Download Bin Discovery Plus Txt
This track displays a chromatin state segmentation for each ofnine human cell types.A common set of states across the cell types were learned bycomputationally integrating ChIP-seq data fornine factors plus inputusing a Hidden Markov Model (HMM). In total, fifteen states were used tosegment the genome, and these states were then grouped and colored tohighlight predicted functional elements. Display Conventions and Configuration This track is a composite track that contains multiple subtracks. Each subtrack represents datafor a different cell type and displays individually on the browser. Instructions for configuring trackswith multiple subtracks arehere.The fifteen states of the HMM, their associated segment color, and thecandidate annotations are as follows:State 1 - Bright Red - Active PromoterState 2 - Light Red -Weak PromoterState 3 - Purple - Inactive/poised PromoterState 4 - Orange - Strong enhancerState 5 - Orange - Strong enhancerState 6 - Yellow - Weak/poised enhancerState 7 - Yellow - Weak/poised enhancerState 8 - Blue - InsulatorState 9 - Dark Green - Transcriptional transitionState 10 - Dark Green - Transcriptional elongationState 11 - Light Green - Weak transcribedState 12 - Gray - Polycomb-repressedState 13 - Light Gray - Heterochromatin; low signalState 14 - Light Gray - Repetitive/Copy Number VariationState 15 - Light Gray - Repetitive/Copy Number VariationMetadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.
ChIP-seq data from the Broad Histonetrack was used to generate this track. Data fornine factors plus inputand nine cell typeswas binarized separately at a 200 base pair resolution based on a Poissonbackground model. The chromatin states were learned from this binarized datausing a multivariate Hidden Markov Model (HMM) that explicitly models thecombinatorial patterns of observed modifications (Ernst and Kellis, 2010).To learn a common set of states across the nine cell types, first the genomes were concatenatedacross the cell types. For each of the nine cell types, each 200 base pair intervalwas then assigned to its most likely state under the model. Detailed information about the modelparameters and state enrichments can be found in (Ernst et al, accepted).Release NotesThis is release 1 (Jun 2011) of this track. It was lifted over from theNCBI36/hg18 version of the track, and is therefore based on the NCBI36/hg18release of the Broad Histonetrack. It is anticipated that the HMM methods will be run on the newerdatasets in the GRCh37/hg19 version of theBroad Histone track, and, once thathappens, the new data will replace this liftOver.CreditsThe 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 users may freely use ENCODE data, but may not, without priorconsent, submit publications that use an unpublished ENCODE dataset untilnine months following the release of the dataset. This date is listed inthe Restricted Until column on the track configuration page andthe download page. The full data release policy for ENCODE is availablehere.
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Programs used in the GISTEMP analysis and documentation on