Fig. 1

Study workflow: The workflow describes the method of pathway-based analysis to identify the pathway perturbations, the potential upstream regulators and prognostic pathways of various RCC subtypes. Based on re-evaluated RCC subtype samples, differential gene expression analysis was performed for each subtype against normal tissue; Differentially expressed genes (DEGs) within pathways (KEGG) were selected for further analysis for each subtype; Wald t-values for promiscuous-genes associating with multiple pathways was corrected; Enrichment analysis was performed based on corrected t-value of DEGs within pathways, and significantly altered pathways were identified for each subtype; Upstream regulators analysis was performed to explore the potential drivers of each subtype-specific pathway; survival analysis was carried out to evaluate the relationship between subtype-specific pathway and patient clinical outcome for each subtype