Long Non-coding RNAs (lncRNAs) refer to all non-protein coding transcripts longer than 200 nucleotides. Their critical roles in different biological pathways have been already well established. Altered expression of lncRNAs can be involved in the cancer initiation and/or progression. Since patients with hepatocellular carcinoma (HCC) are usually diagnosed in late stages, developing diagnostic methods seems to be essential. In this study, researchers at the Ahvaz Jundishapur University of Medical Sciences systematically analysed the expression levels of different lncRNAs in different genomic and transcriptome datasets. The analyses showed that SNHG6 is among the lncRNAs with distinctive dysregulation of expression and copy number variation in HCC tumors compared with normal tissues. The results also suggest that the dysregulation of SNHG6 is highly cancer type specific. Through co-occurrence analyses, they found that SNHG6 and its related co-expressed genes on 8q are involved in the structural integrity of ribosome and translation. This comprehensive in silico analysis, provides a resource for investigating SNHG6 in hepatocellular carcinoma and lays the groundwork for design of next researches.
TCGA hepatocellular carcinoma (LIHC) gene expression by RNA seq
TCGA hepatocellular carcinoma (LIHC) gene expression by RNA seq (IlluminaHiseq N = 423) and the differential expression of SNHG6, PVT1, and GAS5betweenthe primary tumor and the solid normal tissue. The statistical track displayed under the genomic heatmap shows the logarithmic plot of p-values for each genomic position, where the center line indicates a p-value of 1. The primary tumor tissue and the solid normal tissue subgroups were illustrated in red and green respectively. The student t-Test was performed to analyze the differentially expressed genes between the tumor cells and the normal ones, and P < 0.05 was considered statistically significant. The red bar indicates that the expression levels of genes are significantly higher in cancerous cells than normal ones. The data was extracted from Cancer Genome Browser