Identifying Functional Annotation for Noncoding Genomic Sequences
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- Abstract
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- Literature Cited
Abstract
The recent success of genome?wide association studies has generated a trove of biologically significant variants implicated in human disease. However, many, if not most, of these variants fall in noncoding regions that have traditionally lacked much functional annotation. New data sets and tools allow for a more detailed assessment of potential importance of noncoding genetic variants. An overview of types of regulatory annotation that are currently available, and approaches to analyzing this data are provided with emphasis on usage of the UCSC genome browser. Curr. Protoc. Hum. Genet. 72:1.10.1?1.10.10 © 2012 by John Wiley & Sons, Inc.
Keywords: cis?regulatory element; epigenomics; ENCODE; conservation; ChIP?seq
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Key Concepts
- Basic Protocol 1: Identifying Candidate Noncoding Regulatory Elements Using the UCSC Genome Browser and the Encode Integrated Regulation Track
- Literature Cited
- Figures
- Tables
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Basic Protocol 1: Identifying Candidate Noncoding Regulatory Elements Using the UCSC Genome Browser and the Encode Integrated Regulation Track
Materials
|
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Figure 1.10.1 Example of data derived by browsing an intergenic region between CLEC16A and SOCS1 that spans several variants associated with altered risk for multiple sclerosis (Zuvich et al., ). Panels A, B , and C show successively “zoomed‐in” views of narrower sub‐regions. Several tracks of interest, including conservation, histone markings, DNase hypersensitivity, and TFBS are displayed. The red boxes in A and B indicate the areas shown more fully in B and C, respectively. These panels were made from PDF files downloaded directly from the UCSC browser. Note that more details come into view for some of the tracks as the smaller sub‐regions are examined; the level of detail for selected tracks were changed manually, by changing the display mode for individual tracks (see UCSC Genome Browser help page for detailed instructions on how to alter track settings). The histone modification data peaks are color‐coded by cell type; the overlapping colors may look improved on the actual screen as compared to this figure. View Image -
Figure 1.10.2 Display of the ENCODE Integrated Regulation track on the UCSC genome browser. The Integrated Regulation track is actually six separate tracks, collectively referred to as a “super‐track.” Each of the six tracks summarizes a different class of mapping experiments that were performed in a large collection of cell types by members of the ENCODE consortium. Thus, the “DNase Clusters” track summarizes DNase hypersensitivity mapping, the “Txn Factor ChIP” track summarizes transcription factor mapping, and the “Layered H3K4me1, H3K4me3, H3K27ac” tracks summarize covalent histone modification mapping. Panel A shows an example of the Integrated Regulation track data for a region spanning the human BMP2 gene. Display settings for this track can be accessed by following the appropriate hyperlink (red arrow). Settings used for this particular example are shown in panel B . View Image
Videos
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