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...to this type of data, methylation linear discriminant analysis (mlda). results: mlda was programmed in r (version...have been independently validated by methylation specific pcr and/or bisulphite pyrosequencing. conclusion: mlda has advantages for analyzing methylation data from cpg island microarrays, since there is a...
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...to identify cpg islands differentially methylated in pancreatic adeno- carcinoma, we used methylated cpg island amplification (mca) coupled with representational difference analysis. of 42 cpg islands identified by mca/representational difference analysis, 7 cpg islands (methylated in carcinoma of the pancreas...
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...a hypermethylator pheno- type termed cpg island methylator phenotype (cimp), which includes methylation of such genes as p16...present in gastric cancer, the methylation status of five newly cloned cpg islands was examined in 56 gastric cancers using bisulfite-pcr. simulta- neous methylation of three loci or more...
Published in 1999.
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...a computational epigenetics approach can discriminate between cpg islands that are prone to methylation from those that remain unmethylated...suggest that dna composition of cpg islands (sequence, repeats, and structure) plays a significant role in predisposing cpg islands for dna methylation. this finding may have a...
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Christine Ladd-Acosta, Bo Wen, Zhijin Wu, Carolina Montano, Patrick Onyango, Hengmi Cui, Kevin Gabo, Michael Rongione, Maree Webster, Hong Ji, James B Potash, Sarven Sabunciyanhttp://academic.research.microsoft.com/io.ashx?type=5&id=37053654&selfId1=-1&selfId2=-1&maxNumber=12&query=Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands
...promoters, and also not in cpg islands, but in sequences up to 2 kb distant, which we term 'cpg island shores'. cpg island shore methylation was strongly related to gene...enriched closer to the associated cpg islands, and hypomethylation enriched further from the associated cpg island and resembling that of noncolon normal tissues. thus, methylation changes in cancer are at...
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...a computational epigenetics approach can discriminate between cpg islands that are prone to methylation from those that remain unmethylated...suggest that dna composition of cpg islands (sequence, repeats, and structure) plays a significant role in predisposing cpg islands for dna methylation. this finding may have a...
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Zhifu Sun, Yan W. Asmann, Krishna R. Kalari, Brian Bot, Jeanette E. Eckel-Passow, Tiffany R. Baker, Jennifer M. Carr, Irina Khrebtukova, Shujun Luo, Lu Zhang, Gary P. Schroth, Edith A. Perezhttp://academic.research.microsoft.com/io.ashx?type=5&id=57398270&selfId1=-1&selfId2=-1&maxNumber=12&query=Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands
...tumor cell line (mcf10a), and methylation status of 21,570 cpg islands to identify differentially expressed genes that were correlated with methylation or copy number changes. these...overexpressed in er+ tumors. we identified 149 differentially expressed genes that exhibited differential methylation of one or more cpg islands within 5 kb of the...
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...describe an optimized microarray method for identifying genome-wide cpg island methylation called microarray-based methylation assessment of single samples (mmass) which directly compares methylated to unmethylated sequences within a...previous methods we used bioinformatic analysis to predict an optimized combination of methylation-sensitive enzymes that had the highest utility for cpg-island probes and different methods to...
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cpg island (cpgi) methylation is an epigenetic modification that...sequence patterns that distinguished between methylated and unmethylated cpgis. analysis of these characteristics offers certain insight into the conditions that permit or prevent methylation....
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Srinivasan Yegnasubramanian, Michael C. Haffner, Yonggang Zhang, Bora Gurel, Zhijin Wu, Rafael A. Irizarry, James Morgan, Jessica Hicks, Theodore L. DeWeese, William B. Isaacs, G. Steven Bova
...genomic sequencing-based approach to identify genes that are silenced by cpg island methylation in normal prostate cells but...cells as a result of cpg island hypomethylation. through this analysis, we show that a class of cancer testis antigen genes undergoes cpg island hypomethylation and over- expression in...
Published in 2008.