Supplementary Information for
Leng Han and Zhongming Zhao "CpG islands or CpG
clusters: how to identify functional GC-rich regions in a genome?"
Introduction
CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers in vertebrate genomes. Methylation of promoter-associated CGIs plays an important role in the regulation of gene expression and carcinogenesis. This study performed systematic comparison between two major algorithms (Takai and Jones 2002 and CpGcluster 2006). The comparisons revealed that Takai and Jones' algorithm is overall more appropriate for identifying promoter-associated islands of CpGs in vertebrate genomes. The detailed CpG island and CpGcluster data and gene annotations are available. CpG islands (Takai and
Jones, 2002)
The
program could be downloaded from http://cpgislands.usc.edu/ .
CGIs identified by Takai and Jones' algorithm in the human and mouse
genomes:
CGIs
in the human genome (NCBI build 36)
CGIs
in the mouse genome (NCBI build 37)
Each column displays:
-Species
and chromosome
-CGI
ID
-Start
position
-End
position
-GC
content (%)
-ObsCpG/ExpCpG
-Length
CpG clusters
(Hackenberg et al. 2006)
The program could be downloaded from http://bioinfo2.ugr.es/CpGcluster.
CpG clusters identified by Hackenberg et
al.'s algorithm in the human and mouse genomes:
CpG
clusters in the human genome (NCBI build 36)
CpG clusters in the mouse genome (NCBI build 37)Each column displays:
-CpG cluster ID
-Start position
-End position
-Length
-GC content (%)
- ObsCpG/ExpCpG
-Number of CpGs
-Mean distance between CpGs
-P-value
|
|
Last updated: |