Figures
- From genome to epigenome

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Figure 1. Potential scheme for integrated technology platforms to produce an epigenome database.

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Figure 2. The HEP database, a web-based, ENSEMBL-like genome browser for displaying HEP data which is publicly available at http://www.epigenome.org/data/. The methylation levels 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 into tissue type. The red bar indicates the genomic region analysed. Also shown are chromosome coordinates, CGI SNPs, 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) or heterogeneously methylated (fourth amplicon).

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Figure 3. Basic concept of Hepitypes: genotyping for SNPs to define haplotypes (top panel) and epigenotyping for MVPs to define epitypes (bottom panel) can be brought together to define hepitypes which could be associated with a disease phenotype and which could otherwise go undetected by genotyping or epigenotyping in isolation.