About The Database

Human Chromosome Density Map of CpG Islands in the HCGI12K chip

Welcome to the UHN Microarray Centre's CpG Island Database! Here you will find all the information you need to get started with analysing your results from experiments performed on our HCGI 12K and HCGI 8.1K Microarray chip.

The HCGI12K array contains 12192 CpG Island clones derived from a set purchased from the Sanger Centre, UK. For information on the the preparation of the original library, please see Cross, S.H., et. al., Purification of CpG Islands using a methylated DNA binding column. Nature Genetics (1994) 6:236-244.

All clones were sequenced originally at Sanger, with further verification performed at the British Columbia Genome Sciences Centre and internally at the UHN Microarray Centre. Arabadopsis controls from the UHN Microarray Centre have been added. In addition, Stratagene's SpotReport™ Alien™ cDNA Array Validation System has been printed onto the arrays.

Our second human CpG island array is the single-spotted HCGI8.1K array. This array contains 8,109 CpG-island clones consolidated from UHN's HCGI12K set (3,611 clones) and an independent 8.5K set (4,498 clones) obtained from Tim Huang at Ohio State University (Columbus, OH). This library and array was described in Heisler (Heisler et. al. NAR (2005) 33:2952-1961). Both source sequence sets were sequenced at the Michael Smith Genome Sciences Centre and internally at the UHN Microarray Centre. BLAT-annotated clones with overlapping sequences over 20% of either clone were considered as duplicates and excluded. Clones consisting primarily of repeat sequence, with no or more than one BLAT hits and those mapping to chromosome M (mitochondria) were also excluded.

In addition to the initial 12K from the Wellcome Trust Sanger Institute and the 8.1K obtained from Tim Huang (Ohio State University), the UHN Microarray Centre also offers a 6.8K CpG-island set (6,814 clones). This set was developed by designing unique primer-pairs that encompass potential CpG-island regions that are not currently present in our exisiting collection. They were selected based on unique location that does not overlap more than 20% of existing CpG-island clones when annotated by BLAT as well as not mapped to chromosome M (mitochondria).


The level of redness denotes the relative number of CpG Islands that can be located on the chromosome in that region. Click on the image for an enlarged version.