Identification of genes predicting unfavorable prognosis in hepatitis B virus-associated hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34277775", "kind": "science-record", "revision": 8, "content_hash": "sha256:90092f912c5e9bd02b6c1b9445bcc8be1b6105d9b644291bde2f2d5ecf2c2a7a", "created_at": "2026-11-01T15:41:44Z", "updated_at": "2026-11-01T22:04:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of genes predicting unfavorable prognosis in hepatitis B virus-associated hepatocellular carcinoma.", "doi": "10.21037/atm-21-2085", "pmid": "34277775", "authors": ["Meng Sha", "Jie Cao", "Zhi-Peng Zong", "Ning Xu", "Jian-Jun Zhang", "Ying Tong", "Qiang Xia"], "journal": "Annals of translational medicine", "year": 2021, "abstract": "BACKGROUND: To identify potential key genes predicting unfavorable prognosis in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC).\nMETHODS: Gene expression profiles of GSE121248, GSE62232, and GSE55092 from the GEO database were obtained and analyzed. Differentially expressed genes (DEGs) between HBV-associated HCC tissues and adjacent normal tissues were screened by the limma package and Venn diagram software. Functional assessment of DEGs was performed by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Hub genes were selected by the protein-protein interaction (PPI) network and further validated by GSE14520 clinical data.\nRESULTS: A total of 26 up-regulated genes and 76 down-regulated genes were identified by analyzing three databases. GO and KEGG analysis demonstrated that these genes were involved in cell division, metabolism-related biological processes, the p53 pathway, and the cell cycle, among others. PPI network suggested that 14 hub DEGs (TOP2A, HMMR, DTL, CCNB1, NEK2, PBK, RACGAP1, PRC1, CDK1, RRM2, ECT2, BUB1B, ANLN, and ASPM) were most dysregulated and had potential to distinguish between HBV-associated HCC and noncancerous tissues. Further survival analysis of hub genes demonstrated that high expression of TOP2A was significantly associated with poor clinical outcomes of HBV-associated HCC.\nCONCLUSIONS: TOP2A might serve as a key gene for prognosis and as a therapeutic target for HBV-associated HCC.", "claims": [{"id": "claim-data-access", "statement": "Eligible gene expression profiles of GSE 121248, GSE 62232, and GSE 55092 containing HBV-associated HCC and adjacent normal liver tissues were obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34277775", "locator": "sections[3] \"Gene datasets\" paragraph 2", "quote": "Eligible gene expression profiles of GSE 121248, GSE 62232, and GSE 55092 containing HBV-associated HCC and adjacent normal liver tissues were obtained."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34277775"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE121248"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE121248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34277775", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-21-2085", "sha256": 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