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pmid:33376723
Identification of Potential Hub Genes Related to Diagnosis and Prognosis of Hepatitis B Virus-Related Hepatocellular Carcinoma via Integrated Bioinformatics Analysis.
Yuqin Tang · Yongqiang Zhang · Xun Hu
BioMed research international · 2020 doi:10.1155/2020/4251761
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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Our study intended to identify the candidate potential hub genes associated with the carcinogenesis of HBV-related HCC (HBV-HCC), which may be helpful in developing novel tumor biomarkers for potential targeted therapies. Four transcriptome datasets (GSE84402, GSE25097, GSE94660, and GSE121248) were used to screen the 309 overlapping differentially expressed genes (DEGs), including 100 upregulated genes and 209 downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were used to explore the biological function of DEGs. A PPI network based on the STRING database was constructed and visualized by the Cytoscape software, consisting of 209 nodes and 1676 edges. Then, we recognized 17 hub genes by CytoHubba plugin, which were further validated on additional three datasets (GSE14520, TCGA-LIHC, and ICGC-LIRI-JP). The diagnostic effectiveness of hub genes was assessed with receiver operating characteristic (ROC) analysis, and all hub genes displayed good performance in discriminating TNM stage I patient samples and normal tissue ones. For prognostic analysis, two prognostic key genes (TOP2A and KIF11) out of the 17 hub genes were screened and used to develop a prognostic signature, which showed good potential for overall survival (OS) stratification of HBV-HCC patients. Gene Set Enrichment Analysis (GSEA) was performed in order to better understand the function of this prognostic gene signature. Finally, the miRNA-mRNA regulatory relationships of all hub genes in human liver were predicted using miRNet. In conclusion, the current study gives further insight on the pathogenesis and carcinogenesis of HBV-HCC, and the identified DEGs provide a promising direction for improving the diagnostic, prognostic, and therapeutic outcomes of HBV-HCC.", "claims": [{"id": "claim-method", "statement": "Meanwhile, the limma package [27] was applied to screen DEGs between HBV-HCC samples and noncancerous samples, with P value <0.05 and ∣log2 FC | ≥1 were set as the statistical cutoff criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33376723", "locator": "sections[4] \"2.2. 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Survival Analysis", "row_count": 28, "column_count": 4}, "table": {"label": "Table 2", "caption": "Clinicopathological features of HBV-HCC patients according to the two-hub gene-based signature in the cohort of GSE14520.", "rows": [["Characteristics", "Low risk (n = 107)", "High risk (n = 106)", "P value"], ["Gender"], ["Female", "17", "13", "0.447"], ["Male", "90", "93"], ["Age"], ["<50", "48", "47", "0.939"], ["≥50", "59", "59"], ["ALT level"], ["High (>50 U/L)", "41", "47", "0.518"], ["Low (≤50 U/L)", "66", "59"], ["Main tumor size†"], ["Large (>5 cm)", "35", "40", "0.412"], ["Small (≤5 cm)", "72", "65"], ["Cirrhosis"], ["Yes", "96", "100", "0.213"], ["No", "11", "6"], ["TNM stage"], ["I", "56", "33", "0.002∗"], ["II+III", "51", "73"], ["BCLC stage"], ["0-A", "90", "74", "0.013∗"], ["B-C", "17", "32"], ["CLIP stage"], ["0", "58", "36", "0.003∗"], ["≥1", "49", "70"], ["AFP level†"], ["High (≥300 ng/ml)", "37", "58", "0.007∗"], ["Low (<300 ng/ml)", "67", "49"]], "row_count": 28, "column_count": 4, "numeric_cells": 58, "header_rows": 1, "locator": "section[17]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:33376723:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8099ca2f64a122feca1c24fabe92326ad953e4f6233b55d48f084d6d8233fa58", "bytes": 1173, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#tab3", "version": null, "note": "Univariate and multivariate analyses of the cohort GSE14520.", "structure": {"pmcid": "PMC7744201", "section_index": 17, "section_title": "3.6. 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