HEP Data Description

The Human Epigenome Project (HEP) aims to identify, catalogue and interpret genome-wide DNA methylation patterns of all human genes in all major tissues (Bradbury, 2003). The data from HEP is tissue-specific DNA Methylation reference profiles of the human genome, but by now just contains chromosome 6, 20 and 22 data (Eckhardt et al., 2006). The chosen approach involves treatment of the genomic DNA with sodium bisulphite which converts unmethylated cytosines into uracil but does not affect methylated cytosines. Following PCR amplification and sequencing of selected amplicons from bisulphite-converted DNA, the degree of Methylation can be determined by comparison of the corresponding signal ratios at CpG dinucleotides, the predominant sites of DNA methylation.

Data from HEP were integrated into MethyCancer.

References:
Bradbury J. (2003). Human epigenome project--up and running. PLoS Biol 1: E82.

Eckhardt F., Lewin J., Cortese R., Rakyan V. K., Attwood J., Burger M., Burton J., Cox T. V., Davies R., Down T. A., Haefliger C., Horton R., Howe K., Jackson D. K., Kunde J., Koenig C., Liddle J., Niblett D., Otto T., Pettett R., Seemann S., Thompson C., West T., Rogers J., Olek A., Berlin K., and Beck S. (2006). DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378-85.