Differential expression analysis and functional enrichment

DESeq2 (v1.26.0) [14] was applied for the detection of differentially expressed genes (DEGs) and other non-coding RNAs between tumor and non-tumor samples with a P-value of ≤0.05 and fold change (FC) of ≥2. The student’s t-test was performed with a permutation-based P-value of ≤0.05 and FC ≥1.2 to identify differentially expressed proteins (DEPs) or phosphosites in a pairwise manner. Gene Set Enrichment Analysis (GSEA) [15] was applied to find enriched pathways in transcriptome and proteome. Curated gene sets (H2) and GO gene sets (C5) were used for enrichment analysis, and an FDR value of 0.05 was adjusted as a cutoff.