title: The long noncoding RNA expression profile of hepatocellular carcinoma identified by microarray analysis.
abstract: BACKGROUND
  Thousands of long noncoding RNAs (lncRNAs) have been reported in mammalian genomes. These RNAs represent an important subset of pervasive genes involved in a broad range of biological functions. Aberrant expression of lncRNAs is associated with many types of cancers. Here, in order to explore the potential lncRNAs involved in hepatocellular carcinoma (HCC) oncogenesis, we performed lncRNA gene expression profile analysis in 3 pairs of human HCC and adjacent non-tumor (NT) tissues by microarray.
  
  
  METHODS
  Differentially expressed lncRNAs and mRNAs were detected by human lncRNA microarray containing 33,045 lncRNAs and 30,215 coding transcripts. Bioinformatic analyses (gene ontology, pathway and network analysis) were applied for further study of these differentially expressed mRNAs. By qRT-PCR analysis in nineteen pairs of HCC and adjacent normal tissues, we found that eight lncRNAs were aberrantly expressed in HCC compared with adjacent NT tissues, which is consistent with microarray data.
  
  
  CONCLUSIONS
  We identified 214 lncRNAs and 338 mRNAs abnormally expressed in all three HCC tissues (Fold Change ≥2.0, P<0.05 and FDR <0.05) with the genome-wide lncRNAs and mRNAs expression profile analysis. The lncRNA-mRNA co-expression network was constructed, which may be used for predicting target genes of lncRNAs. Furthermore, we demonstrated for the first time that BC017743, ENST00000395084, NR_026591, NR_015378 and NR_024284 were up-regulated, whereas NR_027151, AK056988 and uc003yqb.1 were down-regulated in nineteen pairs of HCC samples compared with adjacent NT samples. Expression of seven lncRNAs was significantly correlated to their nearby coding genes. In conclusion, our results indicated that the lncRNA expression profile in HCC was significantly changed, and we identified a series of new hepatocarcinoma associated lncRNAs. These results provide important insights about the lncRNAs in HCC pathogenesis.
authors.affiliation: College of Life Sciences, Jilin University, Changchun, China; Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Zhu
authors.affiliation: College of Life Sciences, Jilin University, Changchun, China; Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Liu
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Fuqiang
authors.initials: F
authors.lastname: Ye
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Tie
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhu
authors.affiliation: College of Life Sciences, Jilin University, Changchun, China.
authors.forename: Yinghua
authors.initials: Y
authors.lastname: Jin
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Zheng
authors.affiliation: College of Life Sciences, Jilin University, Changchun, China.
authors.forename: Yongge
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, China.
authors.forename: Hanjiang
authors.initials: H
authors.lastname: Fu
mesh_terms: D000328:Adult; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D019295:Computational Biology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D062085:RNA, Long Noncoding; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D012307:Risk Factors; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger