Cancer stem cells (CSCs) represent an important field in translational medicine for generating novel cancer treatments. To identify important stemness markers in liver CSCs that potentially explain their resistance to treatment, we analyzed 10865 single-cell RNA-seq samples across 42684 coding and non-coding genes. Our results show that CSCs have significantly increased expression of two Yamanaka factors (Oct4, 2.14X and SOX2, 1.13X) and three stemness factors (CD44, 3.25X; KRT7, 2.2X; SOX9, 1.71X), relative to liver progenitor cells. Our study demonstrates the potential power of harnessing shared big data for driving translational medicine for novel hypothesis generation.