DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study for the Human Epigenome Project (original) (raw)
Figure 3
The HEP Database
(A) We have created a Web-based, ENSEMBL-like genome browser for displaying HEP data that is publicly available at http://www.epigenome.org. The methylation levels calculated by the ESME software are displayed in the form of a matrix. Each matrix contains the data obtained from all the samples of one amplicon. Each colour-coded square (yellow represents 0% methylation, blue represents 100% methylation, and green represents intermediate levels) within the matrix represents one CpG site. Clicking on a square reveals the tissue source of the sample and the level of methylation observed at that particular CpG site. Grey squares indicate CpG sites for which methylation levels could not be determined. Each row of squares represents all the CpG sites for one sample of a particular amplicon, and the samples are grouped by tissue type. The red bar indicates the genomic region analysed. Also shown are chromosome coordinates, CpG islands, SNPs, and ENSEMBL and high-quality, manually curated VEGA transcript information. The HEP database links to the Ensembl genome browser, providing additional information about the region of interest. The example shows amplicons within the SynGAP 1 gene that correspond to regions that were determined to be hypomethylated (second amplicon from the left), hypermethylated (first and fifth amplicons), and heterogeneously methylated (fourth amplicon). Insufficient data were obtained for the third amplicon.
(B) By using the zoom function, the user can view the complete DNA sequence for the analysed amplicon.