Our observations demonstrated that lncRNAs expression profiles are likely to provide important insights into pathogenesis of HCC. HCC is the fifth most common malignancy in human beings, accounting for approximately 90% of primary liver cancers. Hepatocarcinogenesis is a complicated biological process characterized by a AS-136A myriad spectrum of molecular abnormalities. Over the past decades, the molecular mechanism of HCC has been extensively investigated. However, the exact pathogenesis of this disease is still vague. Increasing evidence indicates that lncRNAs may play a significant role in regulating gene expression. LncRNA expression is de-regulated in many types of cancers, such as HOTAIR in breast tumours and metastases, BACE1-AS in Alzheimer��s disease and Gas5 in breast cancer. Dysregulation of lncRNAs, including H19, HEIH, MVIH, HULC and MEG3, has been identified in HCC. Some of these lncRNAs were also identified in our microarry data. For example, H19 was downregulated in H1 and H2 tissues. Therefore, it is a critical step to figure out the expression profile of lncRNAs and related mRNAs in HCC in understanding its pathogenesis of HCC. In this study, we investigated gene expression profiles of HCC by using lncRNA microarray. Compared with previous report, which showed hierarchical clustering analysis of 254 mRNAs and 174 lncRNAs that were differentially expressed between five pairs of HCC samples and nontumor samples, we analyzed three pairs of HCC and adjacent non-tumor samples and identified 214 lncRNAs and 338 mRNAs abnormally expressed in all three HCC tissues which is partly different from previous results. This is due to differences in cancerous tissues. Moreover, the microarray which we used is human lncRNA microarray version 2.0, whereas the microarray which was used in the above report is human lncRNA microarray version 1.0. Compared with version 1.0, version 2.0 contains more comprehensive and reliable array content, most extensive and updated coverage available, specific exon or BMS-191095 hydrochloride splice junction probes, efficient and robust labeling system and systematic lncRNA classification. According to the absolute expression profile in three pairs of sample, the numbers of significantly differentially expressed lncRNAs and mRNAs are 624 and 1050 separately. After statistical analysis, this number decreased to only 214 and 338.