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lüll Genome-wide analysis of long noncoding RNA (lncRNA) expression in hepatoblastoma tissues Dong R; Jia D; Xue P; Cui X; Li K; Zheng S; He X; Dong KPLoS One 2014[]; 9 (1): e85599Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma. Hepatoblastoma and normal liver tissue samples were obtained from hepatoblastoma patients. The genome-wide analysis of lncRNA expression in these tissues was performed using a 4x180 K lncRNA microarray and Sureprint G3 Human lncRNA Chips. Quantitative RT-PCR (qRT-PCR) was performed to confirm these results. The differential expressions of lncRNAs and mRNAs were identified through fold-change filtering. Gene Ontology (GO) and pathway analyses were performed using the standard enrichment computation method. Associations between lncRNAs and adjacent protein-coding genes were determined through complex transcriptional loci analysis. We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues. Among these, 1757 lncRNAs were upregulated more than two-fold relative to normal tissues and 979 lncRNAs were downregulated. Moreover, in hepatoblastoma there were 420 matched lncRNA-mRNA pairs for 120 differentially expressed lncRNAs, and 167 differentially expressed mRNAs. The co-expression network analysis predicted 252 network nodes and 420 connections between 120 lncRNAs and 132 coding genes. Within this co-expression network, 369 pairs were positive, and 51 pairs were negative. Lastly, qRT-PCR data verified six upregulated and downregulated lncRNAs in hepatoblastoma, plus endothelial cell-specific molecule 1 (ESM1) mRNA. Our results demonstrated that expression of these aberrant lncRNAs could respond to hepatoblastoma development. Further study of these lncRNAs could provide useful insight into hepatoblastoma biology.|*Gene Expression Profiling[MESH]|*Gene Expression Regulation, Neoplastic[MESH]|Child[MESH]|Female[MESH]|Gene Ontology[MESH]|Gene Regulatory Networks[MESH]|Genome, Human/*genetics[MESH]|Hepatoblastoma/blood/*genetics[MESH]|Humans[MESH]|Liver Neoplasms/blood/*genetics[MESH]|Male[MESH]|RNA, Long Noncoding/*genetics/metabolism[MESH]|RNA, Messenger/genetics/metabolism[MESH]|Reproducibility of Results[MESH]|Reverse Transcriptase Polymerase Chain Reaction[MESH]|Signal Transduction/genetics[MESH]|Young Adult[MESH]|alpha-Fetoproteins/metabolism[MESH] |