The aim of the present study was to determine if the bone marrow (BM) beta(2)m(-)/Thy-1(+) stem cells isolated from common bile duct ligated (CBDL) rats possess hepatocyte-like characteristics in their global gene expression profiles. The Affymetrix RG U34A arrays were used to conduct transcriptomic profiling on BM beta(2)m(-)/Thy-1(+) stem cells isolated from CBDL and control rats as well as primary hepatocytes. Forty-one probe sets were up-regulated more than 2-fold in CBSL-derived beta(2)m(-)/Thy-1(+) BM stem cells compared to control BM stem cells. Twenty-seven probe sets were present in both CBDL-derived beta(2)(m)-/Thy-1(+) BM stem cells and control hepatocytes but absent in control beta(2)m(-)/Thy-1(+) BM stem cells, including Tcf1 and Dbp. Compared to the control beta(2)m(-)/ Thy-1(+) BM stem cells, CBDL-derived beta(2)m(-)/Thy-1(+) BM stem cells shared more commonly expressed genes with hepatocytes. Overall, CBDL-derived beta(2)m(-)/Thy-1(+) stem cells displayed a different transcriptomic fingerprint compared with beta(2)m(-)/Thy-1(+) BM stem cells isolated from control rats; and CBDL-derived beta(2)m(-)/Thy-1(+) stem cells started to express some hepatocyte-like genes. (C) 2004 Elsevier Inc. All rights reserved.