Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma

Abstract

BackgroundHepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma.MethodsTranscriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data.ResultsThe integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs.ConclusionsBy identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.

Identifying Potential Tumor Antigens and Antigens-Related Subtypes in Hepatocellular Carcinoma for mRNA Vaccine Development

“…Only a small number of patients with HCC achieved clinical benefit from ICPI therapy [ 23 , 24 ]. As reported previously, high-throughput studies on HCC samples have identified many patients to harbor transcriptomic hallmarks of adaptive or exhausted immunity [ 9 , 25 , 26 ]. It is urgent to translate this transcription-related knowledge into clinically predictive relationships of response and survival to spare patients from potentially ineffective mRNA vaccination therapies.…”

“…Concurrently, a total of 424 LIHC samples with the information of gene expression data, CNV data, and mutation data, from TCGA database were used as validation ( Table S2 ). The cBioPortal database can provide the interactive exploration of multidimensional cancer genomics data sets [ 8 , 9 ]. Thus, the gene expression (level 3), clinical data, and mutation data for validation were downloaded from TCGA ( https://tcga-data.nci.nih.gov/ ) and cBioPortal Database ( https://www.cbioportal.org/ ) ( Table S3 ) [ 10 ].…”

Bioinformatics Analysis of the Inflammation-Associated lncRNA-mRNA Coexpression Network in Type 2 Diabetes

“…A lncRNA-miRNA-mRNA network may be constructed from the prediction results of various prediction tools to link lncRNAs with target genes [ 16 ]. It is also possible to construct lncRNA-mRNA coexpression networks [ 17 , 18 ] that predict the target genes of lncRNAs. The candidate lncRNAs were validated using RT-qPCR or Northern blotting to determine their expression differences.…”

Upregulation of lncRNA DQ679794 contributes to preventing the progression of hepatocellular carcinoma both in vitro and in vivo

“…HCC is a leading cause of cancer-related death worldwide, and the recurrence and metastasis of tumors are the main factors leading to poor prognosis of patients with HCC [17]. As a new class of ncRNAs, thousands of lncRNAs have been found to be important regulators of human gene expression.…”