Table C1.

Data portals and the date of downloads of the used datasets.

Dataset	Date of download	Source
GE	November 16, 2016	TCGA project (GDC data portal: https://portal.gdc.cancer.gov)
SV	January 20, 2017	TCGA project (GDC data portal: https://portal.gdc.cancer.gov)
METH	May 18, 2018	http://firebrowse.org/ provided by TCGA project; filenames: *.meth.by_mean.data.txt
COSMIC	January 12, 2017	Catalog of the Somatic Mutations in Cancer: https://cancer.sanger.ac.uk/cosmic
GTEx	December 2016	dbGaP (The Database of Genotypes and Phenotypes: https://www.ncbi.nlm.nih.gov/gap)
MET500	January 4, 2018	dbGaP (The Database of Genotypes and Phenotypes: https://www.ncbi.nlm.nih.gov/gap)

Abbreviations: COSMIC, Catalogue of Somatic Mutations in Cancer; GE, gene expression; METH, methylation; NPV, negative predictive value; SV, somatic variant; TCGA, The Cancer Genome Atlas.