Research Paper Volume 11, Issue 22 pp 10316—10337

Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma

Figure 1. The flowchart of strategy to identify EMT-related biomarkers in ccRCC. Firstly, text-mining of abstract of literatures associated with EMT from PubMed database identified 756 EMT-related genes and 42 ccRCC-related key pathways. Secondly, expression pattern analysis of EMT-related gene identified two main tumor clusters differ in tumor malignancy and survival. A total of 504 dynamic expression changed genes among normal controls and the two tumor clusters were identified as key genes, which may be critical in ccRCC. Further analysis identified 229 eQTMs located in 90 gene promoters and 256 gene with eQTCNs by integrating transcriptome, DNA methylation and copy number alteration (CNA) data. Finally, ccRCC-related CNAs calling analysis and survival analysis revealed FOXM1 was a driver gene, which could be a biomarker for early diagnosis and overall prognosis in ccRCC.