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Identification of markers associated with global changes in DNA methylation regulation in cancers | BMC Bioinformatics | Full Text
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DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancers using data of 2434 patient samples collected by The Cancer Genome Atlas project. We developed an exploratory method to characterize CCRs in the methylation data and identified the 200 gene markers whose on-and-off statuses in DNA methylation are most significantly associated with drastic changes in CCRs throughout the genome. Clustering analysis of the methylation data of the 200 markers showed that they are tightly associated with cancer subtypes. We also generated a library of the significant CCRs that may be of interest to future studies of the regulation network of DNA methylation in cancer.
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springer nature references ballestar state privacy rights conditional mutual information results genomic patterns /~pqiu/projects/tcgamethdata/index efficiently finding genome-wide genome-wide methylation measurements author correspondence high-dimensional cytometry data cluster diagram generated uncover context-dependent relationships introduction cancer-dependent methylation correlation rights results appeared bmc bioinformatics 13 article qiu privacy choices/manage cookies authors scientific editing cancer genome atlas tmem173 expression gene expression data null entries merge results gene-expression signatures protein-dna/rna interactions [6 underlying regulatory network full size image module-module correlation matrices method seeks markers 1186/1471-2105-13-s13-s7 share content information clustering diagram dynamic nature genome-wide identification dna methylation data cell cycle progression downloaded methylation data dna methylation epigenotypes genomic network studies biomed central method data profiling epigenetic alterations genome methylation pattern li zhang van den berg cancer-induced methylation previous research found
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headline:Identification of markers associated with global changes in DNA methylation regulation in cancers
description:DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancers using data of 2434 patient samples collected by The Cancer Genome Atlas project. We developed an exploratory method to characterize CCRs in the methylation data and identified the 200 gene markers whose on-and-off statuses in DNA methylation are most significantly associated with drastic changes in CCRs throughout the genome. Clustering analysis of the methylation data of the 200 markers showed that they are tightly associated with cancer subtypes. We also generated a library of the significant CCRs that may be of interest to future studies of the regulation network of DNA methylation in cancer.
datePublished:2012-08-24T00:00:00Z
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Bioinformatics
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headline:Identification of markers associated with global changes in DNA methylation regulation in cancers
description:DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancers using data of 2434 patient samples collected by The Cancer Genome Atlas project. We developed an exploratory method to characterize CCRs in the methylation data and identified the 200 gene markers whose on-and-off statuses in DNA methylation are most significantly associated with drastic changes in CCRs throughout the genome. Clustering analysis of the methylation data of the 200 markers showed that they are tightly associated with cancer subtypes. We also generated a library of the significant CCRs that may be of interest to future studies of the regulation network of DNA methylation in cancer.
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Bioinformatics
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Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Algorithms
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