UALCAN, cBio cancer genomics portal (cBioPortal) and CPTAC analyses

Then we obtained and downloaded the clinical and FPKM-standardized RNA-seq data and the clinical information of 531 KIRC patients from the TCGA database. The clinical data were preprocessed by removal of samples without survival status and patients with survival time less than 30 days were also excluded because they might die of non-cancer-related diseases. Furthermore, we performed univariate and multivariate Cox regression analysis to demonstrate the correlations between OS and clinical variables.

After the pan-cancer analysis, we explored the relationship between promoter methylation status and its mRNA expression of RUNX1 gene, using UALCAN and cBioPortal database. UALCAN (http://ualcan.path.uab.edu/index.html) is an interactive web resource for analyzing cancer data and providing gene expression analysis by using TCGA datasets (https://www.cancer.gov) ²². The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation (Beta value: 0.7–0.5) or hypo-methylation (Beta-value: 0.3–0.25)^23,24. The cBioPortal (http://www.cbioportal.org/) is an open access for interactive exploration of multiple cancer genomics data sets, currently covering 282 cancer researches²⁵. The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC, https://proteomics.cancer.gov/) is a public data portal of proteomic sequence and corresponding genomic sequence datasets. Using CPTAC, we mined the protein expression of RUNX genes.