MethylomeDB

Browse DNA methylomes

We use UCSC Genome Browser Mirror Site as our MethylomeDB Browser (with the permission of UCSC Genome Bioinformatics group). The methylomes of human and mouse brains have been configured into a few track groups, such as Methylation Profile in dlPFC (Microarray Format) and Methylation Profile in dlPFC (Wiggle Format), depending on the organism, the brain region, and the display format. We employ two display formats: Microarray and Wiggle, to show methylation profiles.

Search DNA methylomes

  • Search by gene name
    1. Step 1: Type gene name in the gene search box and hit enter or click the "jump" buttom
    2. Gene search step 1

    3. Step 2: Display methylation profile of the gene
    4. Gene search step 2

  • Search by genomic region
  • Type genomic region in the position search box and hit enter.

  • Search by other markers
  • In the homepage of Genome Browser Gateway, UCSC Genome Browser suggests many types of search terms, such as mRNA GenBank accession numbers, RefSeq identifiers, key words, and author names.

Download methylation profiles

  • Download compiled methylation data from the MethylomeDB website
  • The download page provides compiled methylation data for each sample. The data file includes information of genomic coordinates at single-CpG resolution, methylation probabilities, and read coverage.

  • Download regional methylation data from UCSC custom tracks
  • Given a genomic region, the methylation profile can be downloaded using Table Browser. Follow the steps below to download methylation patterns for a genomic region.

    1. Select the genome and assembly in the Table Browser.
    2. Select a table under a methylation group. For example, schizophreniaSdbRawDef3 table under the group of Methylation Profile in dlPFC (Wiggle Format).
    3. Input genomic position.
    4. Click get output to download methylation profile of the given genomic region.

    For example, the methylation profile of chr12:57795963-57815592 for the mouse genome is partly shown below:

          track type=wiggle_0 name="Control1" description="Methylation Profile in dlPFC - Control1"
          #	output date: ...
          #	chrom specified: chr11
          #	position specified: 27484975-27676294
          #	This data has been compressed with a minor loss in resolution.
          #	(Worst case: 0.0078125)  The original source data
          #	(before querying and compression) is available at 
          #		http://hgdownload.cse.ucsc.edu/downloads.html
          variableStep chrom=chr11 span=1
          27484977	0
          27484978	0
          .
          .
          27676217	0.98
          27676218	0.98