BIG/UHN Data Description

BIG/UHN represents the integrated CpG Island (CGI) clone sequences generated by Beijing Institute of Genomics (BIG), Chinese Academy of Sciences and downloaded from UHN Human CpG Island Microarray Database (UHN) (Heisler et al., 2005; Schumacher et al., 2006).

In order to study the global CGI distribution in human genome and alteration of DNA methylation patterns in promoter CGIs, BIG has generated approximately 20,000 CGI clone sequences by large-scale sequencing of the CGI library from the Sanger Institute (Cross et al., 1994). The number continues to increase with development of the new sequencing technologies. In addition, 17,132 CGI clone sequences downloaded from UHN Human CpG Island Microarray Database were also integrated. Taken together, currently a total of 34,738 CGI clones have been included in MethyCancer database. By mapping the clones onto human genome (NCBI Build36) using BLAT and BLAST, all clones were clustered into 18,240 genomic loci.

Cross S. H., Charlton J. A., Nan X., and Bird A. P. (1994). Purification of CpG islands using a methylated DNA binding column. Nat Genet 6: 236-44.

Heisler L. E., Torti D., Boutros P. C., Watson J., Chan C., Winegarden N., Takahashi M., Yau P., Huang T. H., Farnham P. J., Jurisica I., Woodgett J. R., Bremner R., Penn L. Z., and Der S. D. (2005). CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 33: 2952-61.

Schumacher A., Kapranov P., Kaminsky Z., Flanagan J., Assadzadeh A., Yau P., Virtanen C., Winegarden N., Cheng J., Gingeras T., and Petronis A. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res 34: 528-42.