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. 2014 Aug 1;30(15):2206-7.
doi: 10.1093/bioinformatics/btu191. Epub 2014 Apr 10.

methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser

Xin Zhou  1 , Daofeng Li  1 , Rebecca F Lowdon  1 , Joseph F Costello  1 , Ting Wang  1
Affiliations

methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser

Xin Zhou et al. Bioinformatics. .

Abstract

Summary: We present methylC track, an efficient mechanism for visualizing single-base resolution DNA methylation data on a genome browser. The methylC track dynamically integrates the level of methylation, the position and context of the methylated cytosine (i.e. CG, CHG and CHH), strand and confidence level (e.g. read coverage depth in the case of whole-genome bisulfite sequencing data). Investigators can access and integrate these information visually at specific locus or at the genome-wide level on the WashU EpiGenome Browser in the context of other rich epigenomic datasets.

Availability and implementation: The methylC track is part of the WashU EpiGenome Browser, which is open source and freely available at http://epigenomegateway.wustl.edu/browser/. The most up-to-date instructions and tools for preparing methylC track are available at http://epigenomegateway.wustl.edu/+/cmtk.

Contact: twang@genetics.wustl.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Format and display of the methylC track. (a) Track definition in JSON. (b) methylC track showing various DNA methylation assays over the HOXA gene cluster in the human genome. Four tracks are displayed: Infinium 450 K assay for H1 ESC, RRBS for H1 ESC, WGBS for both H1 ESC and IMR90. WGBS data are displayed in strand-specific mode. Cytosine methylation levels and contexts are identified using combinations of foreground/background bar colors (blue/gray for CG, orange/light orange for CHG and magenta/light magenta for CHH). Read depth (smoothed over 4 kb windows) is displayed as a black curve. (c) A zoomed-in view of H1 ESC WGBS data [marked by light red box in (b)]. The left axis marks methylation level. The axis on the right marks read depth. (d) WGBS data as in (b) with two strands combined. (e) A zoomed-out view of WGBS data with two strands combined
See this image and copyright information in PMC

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