Comprehensive analysis of CpG islands in human chromosomes 21 and 22

By Daiya Takai, Peter A. Jones. Proceedings of the National Academy of Sciences of the United States of America, 2002

1,618 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a5b9485f0bebfab76402f32b4dde806f56ffd840

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Citations in the corpus

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome (2007, background): “Promoters with intermediate CpG content (ICPs) contain many promoters that are close to the CpG island criteria introduced in ref”
Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context (2009, methodology): “The manufacturer recommended CpG island designation of array CpGs was used and follows the definition of CpG island in [26].”
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). (2008, methodology): “Canonical somatic DNA methylation profiles of human promoters Consistent with previous findings, we see a bimodal distribution of observed/expected CpG densities (CpGo/e) in promoter regions (Fig. 2A) ( Takai and Jones 2002; Saxonov et al. 2006; Weber et al. 2007).”
Epigenetics in cancer. (2010, neutral): “) [15,16].”
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data (2012, background): “…in SQN the normalization is performed on probe subsets defined by specific CpG characteristics (e.g. shelves, shores, CpG islands); however, multiple different definitions for say CpG islands exist (Gardiner-Garden and Frommer, 1987; Takai and Jones, 2002; Wu et al., 2010; Zhao et al., 2009).”
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules (2012, methodology): “For CpG island and non-CpG island promoters, we used the Takai-Jones definition (Takai and Jones 2002).”
DNA methylation profiling of human chromosomes 6, 20 and 22 (2006, background): “44 , except that they had to have a minimum length of 400 bp rather than 200 bp, as longer CGIs are less frequently associated with Alu repeat”
Early detection: The power and the promise of DNA methylation markers (2003, neutral): “How do we identify the DNA methylation markers that will be of greatest clinical use among the tens of millions of CpG dinucleotides and tens of thousands of gene-associated CpG island”
The mammalian epigenome. (2007, neutral): “A more reﬁned deﬁnition, the Takai-Jones criteria, provides a better association with 5 0 regions of genes and excludes most Alu repeats (Takai and Jones, 2002).”
CpG islands – ‘A rough guide’ (2009, background): “This algorithm also reduced the number of gene promoter associated islands, suggesting that bona fide CGIs were also being discarded [24].”
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. (2006, background): “CpG islands were defined as in Takai and Jones, 2002 .”
High density DNA methylation array with single CpG site resolution. (2011, methodology): “As described by Takai and Jones [35], regions of DNA of greater than 500 bp with GC composition equal to or greater than 55% and observed CpG/expected CpG of 0.65 were more likely to be associated with the 5′ regions of genes.”
DNA methylation: The nuts and bolts of repression (2007, background): “CpG islands are defined as being longer than 500 bp and having a GC content greater than 55% and an observed CpG/expected CpG ratio of 0.65 (Takai and Jones, 2002).”
The epigenomics of cancer. (2007, background): “However, it remains true that about 40% of human genes do not contain bona fide CpG islands in their promoters (Takai and Jones, 2002).”
Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. (2006, methodology): “Databases and GenBank accession number The miRNA sequences were analyzed using miRBase (http://microrna. sanger.ac.uk/), University of California at Santa Cruz Human Genome Browser (http://genome.cse.ucsc.edu/), and CpG Island Searcher Program (http://cpgislands.usc.edu/; Takai and Jones, 2002).”