We used open source data generated by TCGA genome data analysis centers [19 (link)]. Data on methylation 450K were downloaded from the TCGA Data Portal (https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Data on CNV and RNA expression were downloaded from the Broad genome data analysis center Firehose website (http://gdac.broadinstitute.org/). Data on RNA expression of XIST and clinical data were gathered using the CGDS-R package, which is a package of R for querying the Cancer Genomics Data Server and is hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center [21 ]. The beta values for DNA methylation status were estimated using the Illumina Infinium Human Methylation 450K arrays. The beta value was calculated as an estimate of the ratio of intensities between methylated and unmethylated alleles. Segmented copy number was estimated by log2 of the ratio of total intensity of the tumor and the normal tissue using Affymetrix SNP6.0. Normalized RNA-Seq by expectation maximization (RSEM) were used as an estimate for mRNA expression [22 (link)]. Detailed information about the patients and experiment methods have been described elsewhere [19 (link)].
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