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

Table 1 Overview of cancer cohorts used in the study

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	–

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]

ISSN: 1868-7083