MethylC track

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Introduction

Methylc track overview.png

The methylC track is a novel track type of WashU EpiGenome Browser. It is designed to display single-base DNA methylation data, especially (but not limited) for whole-genome bisulfite sequencing (WGBS) experiments. Above example shows the H1ES WGBS results in a methylC track.

Color legend:

  1. blue bars for cytosine methylation level at CG context
  2. orange bars for cytosine methylation level at CHG context
  3. magenta bars for cytosine methylation level at CHH context
  4. gray background (in the place of blue bars) identifies a CG cytosine with low methylation
  5. light orange background (in the place of orange bars) identifies a CHG cytosine with low methylation
  6. light magenta background (in the place of magenta bars) identifies a CHH cytosine with low methylation
  7. gray curve is sequencing read depth

methylC track format

A methylC track is able to represent following genome-wide information on both strands of DNA, making a total of 8 types of data:

  1. methylation level for CG cytosines
  2. methylation level for CHG cytosines
  3. methylation level for CHH cytosines
  4. read depth

These 8 data types are uniformly presented as bedGraph tracks. Thus one methylC track can contain up to 8 bedGraph tracks.


The methylC track is defined using JSON in datahub:

{
type:"methylC",
name:"H1 ESC methylome",
mode:"show",
height:70,
combinestrands:false,
scalebarheight:false,
smoothwindow:11,
details:{
    Publication:"Human DNA methylomes at base resolution ...",
    Source:"http://neomorph.salk.edu/human_methylome/data.html",
    "Download date":"Feb 2014",
},
tracks:{
	forward:{
		ReadDepth:{color:'#525252',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/H1.forward.readDepth.bedGraph.gz'},
		CG:{color:'rgb(100,139,216)',
                        bg:'#d9d9d9',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.f.cg.gz'},
		CHG:{color:'rgb(255,148,77)',
                        bg:'#ffe0cc',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.f.chg.noZero.gz'},
		CHH:{color:'rgb(255,0,255)',
                        bg:'#ffe5ff',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.f.chh.noZero.gz'},
		},
	reverse:{
		ReadDepth:{color:'#525252',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/H1.reverse.readDepth.bedGraph.gz'},
		CG:{color:'rgb(100,139,216)',
                        bg:'#d9d9d9',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.r.cg.gz'},
		CHG:{color:'rgb(255,148,77)',
                        bg:'#ffe0cc',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.r.chg.noZero.gz'},
		CHH:{color:'rgb(255,0,255)',
                        bg:'#ffe5ff',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.r.chh.noZero.gz'},
		},
	}
},

Minimal methylC track

Just two bedGraph tracks (CG methylation and read depth) can be used to define a minimal methylC track, in which the CG methylation and read depth tracks should be assigned to "forward strand", despite they might be representing combined strands.

{
type:"methylC",
name:"toy example",
mode:"show",
height:70,
tracks:{
	forward:{
		ReadDepth:{color:'#525252',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/H1.combined.readDepth.bedGraph.gz'},
		CG:{color:'rgb(100,139,216)',
                        bg:'#d9d9d9',
			url:'http://vizhub.wustl.edu/public/hg18/pmid19829295/h1.combined.cg.gz'},
		},
        }
},

Displaying methylC track on browser

The methylC track can only be defined in a datahub at the moment. Example: http://vizhub.wustl.edu/public/hg18/pmid19829295/hub.h1es

A methylC track can be submitted to the browser in following ways:

  1. submitted via the datahub submission panel
  2. linked through the URL_parameter#datahub, example: http://epigenomegateway.wustl.edu/browser/?genome=hg18&datahub=http://vizhub.wustl.edu/public/hg18/pmid19829295/hub
  3. from an embedded browser, example: http://egg.wustl.edu/+/embed/methylc.html

Combining strands

When a methylC track is equipped with strand-specific data, user can choose to show this track in separate strands or have two strands combined. To do so, right click on the track and select Configure. Then check the checkbox labeled "Combine two strands".

Read depth

Read depth data at each genomic location from two strands will be added when combining strands.

Cytosines in CG context

The methylation levels from the two cytosines in a CpG dinucleotide will be recalculated into a single methylation level for the CG dinucleotide. This takes into account of methylation level and read depth of each cytosine.

Suppose the two cytosines in CG are labeled "c1" and "c2", M for "methylation", R for read depth:

M(cg) = (M(c1)*R(c1) + M(c2)*R(c2)) / (R(c1) + R(c2))

Cytosines in CHG context

By default the CHG cytosine methylation levels are NOT combined. User may choose to combine CHG cytosine data by checking a second checkbox following the "Combine two strands".

When combining CHG, only CAG/CTG contexts will be combined (in the same method as for CG).

CCG and CGG contexts are not combined since there is CG dinucleotide in the triplet. It is treated as an isolated cytosine together with a CG dinucleotide.

Cytosines in CHH context

CHH cytosines are not combined.

Scaling bar heights using read depth

Right click on a methylC track and select Configure. Check the checkbox labeled "Scale bar height by read depth". The bar plots for the cytosine methylation level will have the heights scaled by read depth of that specific position in relation to the maximum read depth of the view range. The read depth curve will not be shown.

Filtering data using read depth threshold

Right click on methylC track and select Configure. Check the checkbox labeled "Filter by read depth" and choose a cutoff value. Cytosines with read depth data below cutoff will have their methylation data become invisible.

Restriction

  1. To display two methylC tracks in the browser at same time, these two tracks cannot share member tracks, that is, the member tracks must not have identical bedGraph file URL. An easy work-around is duplicating the bedGraph file by creating soft links with separate names on the hosting server.

Reference

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

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

Bioinformatics (2014) advanced access http://bioinformatics.oxfordjournals.org/content/early/2014/04/10/bioinformatics.btu191.abstract