ENCODE Regulation DNase Signal Track Settings
 
DNase I Hypersensitivity Signal Colored by Similarity from ENCODE

Track collection:
Integrated Regulation from ENCODE

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  Similarity↓1 Cell Type↓2 Tissue↓3   Track Name↓4  
     K562  bone marrow  K562 lymphoblast chronic myeloid leukemia cell line DNaseI Signal from ENCODE   Schema 
     NHLF  lung  NHLF lung fibroblast DNaseI Signal from ENCODE   Schema 
     HSMM  muscle  HSMM skeletal muscle myoblast DNaseI Signal from ENCODE   Schema 
     HUVEC  blood vessel  HUVEC umbilical vein endothelial cell DNaseI Signal from ENCODE   Schema 
     NHEK  skin  NHEK epidermal keratinocyte DNaseI Signal from ENCODE   Schema 
     HepG2  liver  HepG2 hepatocellular carcinoma cell line DNaseI Signal from ENCODE   Schema 
     GM12878  blood  GM12878 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE   Schema 
     H7-hESC  embryo  H7-hESC embryonic stem cell DNaseI Signal from ENCODE   Schema 
     HeLa-S3  cervix  HeLa-S3 cervical epithelial adenocarcinoma cell line DNaseI Signal from ENCODE   Schema 
    


p12 Note: includes annotations on GRCh38.p12 patch sequences

Description

This track provides an integrated display of DNase hypersensitivity in multiple cell types using overlapping colored graphs of signal density with graph colors assigned to cell types based on similarity of signal. The track is based on results of experiments performed by the John Stamatoyannapoulos lab at the University of Washington from September 2007 to January 2011 as part of the ENCODE project first production phase.

The signal graphs displayed here are also included in the comprehensive DNaseI HS track, which also provides peak and region calls and uses the same coloring based on similiarity of cell types (please note there is different coloring on the ENCODE hg38 Transcription track, Layered H3K4Me1 track, Layered H3K4Me3 track, and Layered H3K27Ac track, which match the coloring used in their previous versions lifted from the hg19 assembly).

Methods

Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline described in the DNaseI HS track description. Signal graphs were normalized so the average value genome-wide is 1. Colors for the signal graphs were assigned by the UCSC BigWigCluster tool.

The cell types were clustered into a binary tree, a rainbow was cast to the leaf nodes providing coloring based on similarity.

ENCODE cell clustering by similarity Credit: Chris Eisenhart, J. Kent lab

Credits

The processed data for this track were generated at UCSC. Credits for the primary data underlying this track are included in the DNaseI HS track description.

References

Miga KH, Eisenhart C, Kent WJ. Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res. 2015 Nov 16;43(20):e133. PMID: 26163063

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. PMID: 22955617; PMC: PMC3721348

See also the references in the DNaseI HS track.