{"longTitle":"TCGA ovarian serous cystadenocarcinoma (OV) DNA methylation (HumanMethylation450)","cohort":"TCGA Ovarian Cancer (OV)","min":"0.00000","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ov/cgcc/jhu-usc.edu/humanmethylation450/methylation/","probeMap":"probeMap/illuminaMethyl450_hg19_GPL16304_TCGAlegacy","dataSubType":"DNA methylation","security":"public","label":"Methylation450k","max":"1.00000","tags":["cancer"],"anatomical_origin":["Ovary"],"name":"TCGA.OV.sampleMap/HumanMethylation450","dataproducer":"Johns Hopkins University and University of Southern California TCGA cancer genomic characterization center","wrangling_procedure":"Level_3 data download from TCGA DCC, processed at UCSC into Xena repository","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","groupTitle":"TCGA ovarian serous cystadenocarcinoma","type":"genomicMatrix","wrangler":"xena TCGAscript Methylation450 processed on 2017-09-08","version":"2017-09-08","unit":"beta value","primary_disease":"ovarian serous cystadenocarcinoma","platform":"Illumina Infinium HumanMethylation450","description":"TCGA ovarian serous cystadenocarcinoma (OV) DNA methylation data.<br><br> DNA methylation profile was measured experimentally using the Illumina Infinium HumanMethylation450 platform. Beta values were derived at the Johns Hopkins University and University of Southern California TCGA genome characterization center. DNA methylation values, described as beta values, are recorded for each array probe in each sample via BeadStudio software. DNA methylation beta values are continuous variables between 0 and 1, representing the ratio of the intensity of the methylated bead type to the combined locus intensity. Thus higher beta values represent higher level of DNA methylation, i.e. hypermethylation and lower beta values represent lower level of DNA methylation, i.e. hypomethylation.\n\n We observed a bimodal distribution of the beta values from both methylation27 and methylation450 platforms, with two peaks around 0.1 and 0.9 and a relatively flat valley around 0.2-0.8.  The bimodal distribution is far more pronounced and balanced in methylation450 than methylation27 platform. In the methylation27 platform, the lower beta peak is much stronger than the higher beta peak, while the two peaks are of similar height in the methylation450 platform. Microarray probes are mapped onto the human genome coordinates using xena probeMap derived from GEO GPL13534 record. Here is a <a href=\"http://www.illumina.com/documents/products/appnotes/appnote_dna_methylation_analysis_infinium.pdf\" target=\"_blank\"><u>reference</u></a> to Illumina Infinium BeadChip DNA methylation platform beta value.<br><br>"}