Abstract Cancer stem cells (CSCs) are a small group of cancer cells with stem cell-like properties and have been revealed to be the drive force of tumorigenesis, metastasis and drug resistance in many cancers. Current CSC surface biomarkers, such as CD133, CD44 and CD166, have been used to isolate CSC population. However, they are often not specific and unassociated with tumor outcome. Here, we applied a data-driven approach to identify new and functional biomarkers of CSC. We systematically screened for genes whose expressions are statistically correlated with CSC surface biomarkers. Normalized DNA microarray data of 160 cases of squamous carcinoma and 33 cases of adenocarcinoma and 8 cases of normal lung were analyzed for association with CD133, CD44 and CD166 respectively. Multiple hypothesis testing was corrected with the false discovery rate (FDR) less than 1%. We find CD133, CD44 and CD166 each has a different set of statistically associated genes in either adeno or squamous subtypes. Moreover, correlated genes with each of the surface marker are different between adeno and squamous subtypes. Among the highly correlated receptor genes with CD133 in squamous subtype is a hormone receptor of the reproduction regulator oxytocin (OXTR, r=0.4276, p=1.699e-8). We experimentally validated the correlation between OXTR and CD133 in human lung cancer tissues and cell lines. Further with functional assays, we discovered a new role of OXTR in promoting the self-renewal and differentiation of lung CSC. Our study suggests highly heterogeneous molecular features of CSC in different lung cancer types and demonstrates that association studies of CSC surface markers can be applied to identify new CSC biomarkers, which can be potentially used for development of probes for CSC imaging and targeting. Citation Format: Hua Fan-Minogue, Atul Butte. Targeting the root of cancer: a data-driven approach for identification of lung cancer stem cell biomarkers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3880. doi:10.1158/1538-7445.AM2014-3880