Similarly, on the MCF7 sample, the StringTie-HISAT2 approach predicted important breast cancer-related genes including TFF1, AGR2, TFF3, SERPINA3, SLC7A2, DSCAM-AS1, SEMA3C, KRT19, and KRT8 among its top 10 upregulated genes (Supplementary Table 16). Here, SEMA3C is linked to breast cancer.