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Table 1 Overview of cancer cohorts used in the study

From: MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples

Cohort Cancer type Number of samples Available datatypes Number of MethCORR genes
UCSC XENA TCGA BRCA Breast invasive carcinoma 873 RNA seq
450K DNA meth
13,018
UCSC XENA TCGA PRAD Prostate adenocarcinoma 533 RNA seq
450K DNA meth
11,348
UCSC XENA TCGA LUAD Lung adenocarcinoma 477 RNA seq
450K DNA meth
11,935
UCSC XENA TCGA LUSC Lung squamous cell carcinoma 379 RNA seq
450K DNA meth
10,911
UCSC XENA TCGA STAD Stomach adenocarcinoma 372 RNA seq
450K DNA meth
11,259
UCSC XENA TCGA BLCA Bladder urothelial carcinoma 424 RNA seq
450K DNA meth
11,238
UCSC XENA TCGA SKCM Skin cutaneous melanoma 474 RNA seq
450K DNA meth
9473
UCSC XENA TCGA KIRC Kidney renal clear cell carcinoma 343 RNA seq
450K DNA meth
10,725
UCSC XENA TCGA UCEC Uterine corpus
endometrial carcinoma
197 RNA seq
450K DNA meth
9313
UCSC XENA TCGA ESCA Esophageal carcinoma 182 RNA seq
450K DNA meth
10,786
GSE117439 Breast cancer 52 450K DNA meth
GSE84207 Breast cancer 279 450K DNA meth
GSE73549 Prostate cancer 57 450K DNA meth
GSE66836 Lung adenocarcinoma 164 450K DNA meth
  1. The number of samples with matched RNA sequencing and 450K DNA methylation for each cancer type is given. The number of MethCORR genes for each cancer reflects the number of genes with R2 > 0.16 between observed and inferred RNA expression (iRNA) in both the discovery and the validation set, as previously defined for colorectal cancer [12]
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