| Literature DB >> 34087888 |
Yu Luo1, Hongjuan Li1, Hongli Huang1, Lian Xue1, Haiwen Li1, Li Liu2, Haiyan Fu1.
Abstract
BACKGROUND: Long noncoding RNAs (lncRNAs) can work as microRNA (miRNA) sponges through a competitive endogenous RNA (ceRNA) mechanism. LncRNAs and miRNAs are important components of competitive endogenous binding, and their expression imbalance in hepatocellular carcinoma (HCC) is closely related to tumor development, diagnosis, and prognosis. This study explored the potential impact of the ceRNA regulatory network in HCC on the prognosis of HCC patients.Entities:
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Year: 2021 PMID: 34087888 PMCID: PMC8183720 DOI: 10.1097/MD.0000000000026194
Source DB: PubMed Journal: Medicine (Baltimore) ISSN: 0025-7974 Impact factor: 1.817
Figure 1Identification of significant expression changes in RNAs in HCC. A Volcano plot for the DElncRNAs and DEmiRNAs in GSE98269 and DEmRNAs in GSE60502. The black dots represent genes that are not differentially expressed between the HCC samples and normal samples, and the green dots and red dots represent the downregulated and upregulated genes, respectively, in HCC samples. B Heatmap of the DElncRNAs and DEmiRNAs in GSE98269 and DEmRNAs in GSE60502. Genes expressed at high levels are shown in red, and genes expressed at low levels are shown in green.
Figure 2ceRNA network. The triangle represents lncRNAs, the square represents miRNAs, and the circle represents mRNAs. Red nodes represent upregulated genes, and green nodes represent downregulated genes.
Results of the top 10 GO terms and the top 10 KEGG pathway analyses.
| Category | Term | Description | Gene counts | LogP |
| Upregulated | ||||
| GO: 0051301 | BP | Cell division | 23 | −11 |
| GO: 0007059 | BP | Chromosome segregation | 17 | −10 |
| GO: 0006260 | BP | DNA replication | 15 | −9.4 |
| GO: 0000228 | CC | Nuclear chromosome | 19 | −7.8 |
| GO: 0098813 | BP | Nuclear chromosome segregation | 13 | −7.7 |
| GO: 0045786 | BP | Negative regulation of cell cycle | 19 | −7.4 |
| GO: 0000819 | BP | Sister chromatid segregation | 11 | −7.3 |
| GO: 0098687 | CC | Chromosomal region | 14 | −7.2 |
| GO: 0000280 | BP | Nuclear division | 15 | −7.1 |
| GO: 0044454 | CC | Nuclear chromosome part | 17 | −6.7 |
| hsa04110 | Cell cycle | 6 | −3.8 | |
| hsa05215 | Prostate cancer | 5 | −3.6 | |
| hsa05224 | Breast cancer | 6 | −3.5 | |
| hsa05230 | Central carbon metabolism in cancer | 4 | −3.1 | |
| hsa05216 | Thyroid cancer | 3 | −3.1 | |
| hsa05218 | Melanoma | 4 | −3 | |
| hsa05200 | Pathways in cancer | 9 | −3 | |
| hsa05219 | Bladder cancer | 3 | −2.6 | |
| hsa03440 | Homologous recombination | 3 | −2.6 | |
| hsa05161 | Hepatitis B | 5 | −2.6 | |
| Downregulated | ||||
| GO: 0046951 | BP | Ketone body biosynthetic process | 2 | −5.3 |
| GO: 0046950 | BP | Cellular ketone body metabolic process | 2 | −5.1 |
| GO: 0032230 | BP | Positive regulation of synaptic transmission, GABAergic | 2 | −5 |
| GO: 1902224 | BP | Ketone body metabolic process | 2 | −5 |
| GO: 0032228 | BP | Regulation of synaptic transmission, GABAergic | 2 | −4.1 |
| GO: 0051932 | BP | Synaptic transmission, GABAergic | 2 | −3.8 |
| GO: 0099617 | CC | Matrix side of mitochondrial inner membrane | 1 | −3.4 |
| GO: 0001985 | BP | Negative regulation of heart rate involved in baroreceptor response to increased systemic arterial b | 1 | −3.4 |
| GO: 0001983 | BP | Baroreceptor response to increased systemic arterial blood pressure | 1 | −3.4 |
| GO: 0001978 | BP | regulation of systemic arterial blood Pressure by carotid sinus baroreceptor feedback | 1 | −3.4 |
| hsa00072 | Synthesis and degradation of ketone bodies | 2 | −5.2 | |
| hsa00650 | Butanoate metabolism | 2 | −4.2 | |
| hsa04976 | Bile secretion | 2 | −3.4 | |
| hsa00910 | Nitrogen metabolism | 1 | −2.2 | |
| hsa04964 | Proximal tubule bicarbonate reclamation | 1 | −2 | |
| hsa04966 | Collecting duct acid secretion | 1 | −2 | |
| hsa05219 | Bladder cancer | 1 | −1.8 | |
| hsa05144 | Malaria | 1 | −1.7 | |
| hsa05150 | Staphylococcus aureus infection | 1 | −1.6 | |
| hsa04115 | p53 signaling pathway | 1 | −1.5 | |
Figure 3Top 20 clusters with their representative enriched terms (colored by cluster ID), where nodes that share the same cluster ID are typically close to each other.
Figure 4PPI network of DEGs.
Figure 5Hub gene analysis and GSEA. A The Highest connectivity modules according to MCODE analysis. B Top 15 hub genes according to CytoHubba. C GSEA of hub genes.
Figure 6Prognostic values and expression levels of the 4 hub genes in HCC patients. A Expression level of 6 hub genes in HCC and normal tissues. B Prognostic value of 6 hub genes in HCC.