Using the Wash U Epigenome Browser to Examine Genome‐Wide Sequencing Data

Xin Zhou1, Ting Wang1

1 Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 10.10
DOI:  10.1002/0471250953.bi1010s40
Online Posting Date:  December, 2012
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This unit describes the Wash U Epigenome Browser, a next‐generation genomic data visualization system. The Browser currently hosts ENCODE and Roadmap Epigenomics data for human and model organisms. The Browser displays many sequencing‐based data sets across all or part of the genome, on specific gene sets or pathways, and in the context of their metadata. Investigators can order, filter, aggregate, classify, and display data interactively based on given feature sets including metadata features, annotated biological pathways, and user‐defined collections of genes or genomic coordinates. Further, statistical tests can be performed on selected data. Individual labs can upload their sequencing or array‐based data as custom tracks and display them in the context of consortium data, allowing for direct comparisons. The Browser is an increasingly important and widely accessible tool for deriving biological insights from unprecedented amounts of high‐quality genomic, epigenomic, and expression data. Curr. Protoc. Bioinform. 40:10.10.1‐10.10.14. © 2012 by John Wiley & Sons, Inc.

Keywords: genome browser; DNA sequencing data sets; high‐throughput genomics epigenomics

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Table of Contents

  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Dreszer, T.R., Karolchik, D., Zweig, A.S., Hinrichs, A.S., Raney, B.J., Kuhn, R.M., Meyer, L.R., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B., Pohl, A., Malladi, V.S., Li, C.H., Learned, K., Kirkup, V., Hsu, F., Harte, R.A., Guruvadoo, L., Goldman, M., Giardine, B.M., Fujita, P.A., Diekhans, M., Cline, M.S., Clawson, H., Barber, G.P., Haussler, D., and Kent, W.J. 2012. The UCSC Genome Browser Database: Extensions and updates 2011. Nucleic Acids Res. 40:D918‐D923.
   Kent, W.J., Zweig, A.S., Barber, G., Hinrichs, A.S., and Karolchik, D., 2010. BigWig and BigBed: Enabling browsing of large distributed datasets. 26:2204‐2207.
   Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment Map (SAM) format and SAMtools. Bioinformatics 25:2078‐2079.
   Sanborn, J.Z., Benz, S.C., Craft, B., Szeto, C., Kober, K.M., Meyer, L., Vaske, C.J., Goldman, M., Smith, K.E., Kuhn, R.M., Karolchik, D., Kent, W.J., Stuart, J.M., Haussler, D., and Zhu, J. 2011. The UCSC cancer genomics browser database: Update 2011. Nucleic Acids Res. 39:D951‐D959.
Key Reference
   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., and Wang, T. 2011. The human epigenome browser at Washington University. Nat. Methods 8:989‐990.
  The original publication describing Wash U Epigenome Browser's innovative designs and critical applications.
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