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The Human Epigenome Browser at Washington University
Open accessAbstract
To the Editor: Advances in next-generation sequencing have reshaped the landscape of genomic and epigenomic research. Large consortia such as the Encyclopedia of DNA Elements, the Roadmap Epigenomics Mapping Consortium and The Cancer Genome Atlas have generated tens of thousands of sequencingbased genome-wide datasets, creating a reference and resource for the scientific community. Small groups of researchers now can rapidly obtain huge volumes of genomic data, which need to be placed in the context of the consortium data for comparison. These data are often accompanied by rich metadata describing the sample and experiment, which is critical for their interpretation. Visualizing, navigating and interpreting such data in a meaningful way is a daunting challenge1. We developed the Human Epigenome Browser to host Human Epigenome Atlas data produced by the Roadmap Epigenomics Project2 and to support navigation of the Atlas and its interactive visualization, integration, comparison and analysis (http://epigenomegateway.wustl.edu/; see Supplementary Note and Supplementary Protocol for main components and use). The Browser is web-based, and it extends the seminal concept introduced by the University of California Santa Cruz Cancer Genomics Browser3 to support large, sequencing-based datasets. Epigenome measurements are displayed as genome heatmaps in which color gradients reflect signal strength (Fig. 1 and Supplementary Fig. 1). Metadata such as cell type, assay type, epigenetic mark and phenotype of the sample are encoded numerically and displayed in different colors by a metadata heatmap next to the genome heatmap (Fig. 1 and Supplementary Figs. 2–4). Investigators can zoom and pan in a ‘Google Maps’–like style to examine dozens to
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Cites
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The NIH Roadmap Epigenomics Mapping Consortium
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Self-citation
Cited by
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Self-citationhTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets
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“7, EUR, with the GWAS index SNP rs12779790, 1000G Phase 1 release), two SNPs showed evidence of open chromatin [6,9,20,47], histone modifications [21,22,48] or transcription factor binding and were tested for evidence of differential transcriptional activity.”
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Metadata
- Authors
- Zhou, X., Maricque, B., Xie, M., Li, D., Sundaram, V., Martin, E. A., Koebbe, B. C., Nielsen, C., Hirst, M., Farnham, P., Kuhn, R. M., Zhu, J., Smirnov, I., Kent, W. J., Haussler, D., Madden, P. A. F., Costello, J. F., & Wang, T.
- Venue
- Nature Methods
- Published
- 2011-11-29
- Volume
- 8
- Issue
- 12
- Pages
- 989-990
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2125263315
- Cited by
- 307
- References
- 2
- FWCI
- 4.94
- Type
- journal article
- Language
- en
- Open access
- green
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