Additionally, we performed the LASSO-Cox regression algorithm to construct a malignant cell index (MCI) based on five genes (BGN, SDC1, IMPDH2, SPINT1, and UQCRFS1) from the differentially expressed genes in the malignant tumor cells and validated its clinical significance in four independent TNBC cohorts (GSE58812, TCGA-TNBC, METABRIC, and GSE21653), unveiling that the TNBC patients with a lower MCI had a favorable prognosis. This evidence concerns the gene UQCRFS1 and neoplasm.