ArticlePloS one2011
RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 102 citations in OpenAlex.
- RNA Sequencing Analysis of Patients with Chronic Hepatitis B Treated Using PEGylated Interferon.International journal of general medicine · 2024Article
- Transcriptome profiling and analysis of patients with esophageal squamous cell carcinoma from Kazakhstan.Frontiers in genetics · 2024Article
- Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma.World journal of gastroenterology · 2023Review
- Comprehensive analysis of a TPX2-related TRHDE-AS1/PKIA ceRNA network involving prognostic signatures in Hepatitis B virus-infected hepatocellular carcinoma.Frontiers in cellular and infection microbiology · 2022Article
- Advances in Multi-Omics Applications in HBV-Associated Hepatocellular Carcinoma.Frontiers in medicine · 2021Review
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes.Microbial genomics · 2021Article
- Multiple novel hepatocellular carcinoma signature genes are commonly controlled by the master pluripotency factor OCT4.Cellular oncology (Dordrecht, Netherlands) · 2020Article
- AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species.BMC bioinformatics · 2020Article
- Screening and Identification of Potential Biomarkers in Hepatitis B Virus-Related Hepatocellular Carcinoma by Bioinformatics Analysis.Frontiers in genetics · 2020Article
- Analysis of Differentially Expressed Genes in a Chinese Cohort of Esophageal Squamous Cell Carcinoma.Journal of Cancer · 2020Article
- Tumor-infiltrating immune cells in hepatocellular carcinoma: Tregs is correlated with poor overall survival.PloS one · 2020Article
- Inflammation associated with noise-induced hearing loss.The Journal of the Acoustical Society of America · 2019Review
- Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma.Journal of translational medicine · 2019Article
- Detection of Novel Fusion Transcript VTI1A-CFAP46 in Hepatocellular Carcinoma.Gastrointestinal tumors · 2019Article
- Ancestry patterns inferred from massive RNA-seq data.RNA (New York, N.Y.) · 2019Article
- Dissecting the expression landscape of cytochromes P450 in hepatocellular carcinoma: towards novel molecular biomarkers.Genes & cancer · 2019Article
- Profiling of LINE-1-Related Genes in Hepatocellular Carcinoma.International journal of molecular sciences · 2019Review
- Article
- Integrated analysis of lncRNA-associated ceRNA network reveals potential biomarkers for the prognosis of hepatitis B virus-related hepatocellular carcinoma.Cancer management and research · 2019Article
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-seq is a powerful tool for comprehensive characterization of whole transcriptome at both gene and exon levels and with a unique ability of identifying novel splicing variants. To date, RNA-seq analysis of HBV-related hepatocellular carcinoma (HCC) has not been reported. In this study, we performed transcriptome analyses for 10 matched pairs of cancer and non-cancerous tissues from HCC patients on Solexa/Illumina GAII platform. On average, about 21.6 million sequencing reads and 10.6 million aligned reads were obtained for samples sequenced on each lane, which was able to identify >50% of all the annotated genes for each sample. Furthermore, we identified 1,378 significantly differently expressed genes (DEGs) and 24, 338 differentially expressed exons (DEEs). Comprehensive function analyses indicated that cell growth-related, metabolism-related and immune-related pathways were most significantly enriched by DEGs, pointing to a complex mechanism for HCC carcinogenesis. Positional gene enrichment analysis showed that DEGs were most significantly enriched at chromosome 8q21.3-24.3. The most interesting findings were from the analysis at exon levels where we characterized three major patterns of expression changes between gene and exon levels, implying a much complex landscape of transcript-specific differential expressions in HCC. Finally, we identified a novel highly up-regulated exon-exon junction in ATAD2 gene in HCC tissues. Overall, to our best knowledge, our study represents the most comprehensive characterization of HBV-related HCC transcriptome including exon level expression changes and novel splicing variants, which illustrated the power of RNA-seq and provided important clues for understanding the molecular mechanisms of HCC pathogenesis at system-wide levels.
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