Fig. 1

Pipeline for the identification of concordant copy number loss and down-regulation of tumor suppressor genes in human cancer. This figure shows the pipeline for identifying the tumor suppressor genes (TSGs) with concordant copy number variations (CNVs) and gene expression. It involves four main steps. 1) Downloading TSGs from the TSGene 2.0 database and overlapping to the TCGA pan-cancer CNV data. 2) The resulted 1170 TSGs with CNV overlapping information were further extracted and calculated the precise copy number gain (CNG) and loss (CNL). 3) Based on the number of samples with CNGs and CNLs in the pan-cancer CNV data, we collected 207 TSGs with frequent CNLs. 4) Using the gene expression data from the matched TCGA cancer samples, we identified 81 TSGs with consistent CNLs and decreased gene expression in the same samples