[CDK1, CCNB1 and NDC80 are associated with prognosis and progression of hepatitis B virus-associated hepatocellular carcinoma: a bioinformatic analysis].

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34755666", "kind": "science-record", "revision": 3, "content_hash": "sha256:c81c64d4a476cd4b2786321d7f9422af76615bc8f31f59367538bb7fff39b6c7", "created_at": "2026-11-01T17:36:27Z", "updated_at": "2026-11-01T21:26:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[CDK1, CCNB1 and NDC80 are associated with prognosis and progression of hepatitis B virus-associated hepatocellular carcinoma: a bioinformatic analysis].", "doi": "10.12122/j.issn.1673-4254.2021.10.09", "pmid": "34755666", "authors": ["Y Li", "D Wu", "C Wei", "X Yang", "S Zhou"], "journal": "Nan fang yi ke da xue xue bao = Journal of Southern Medical University", "year": 2021, "abstract": "OBJECTIVE: To identify the key genes involved in the transformation of hepatitis B virus (HBV) into hepatocellular carcinoma (HCC) and explore the underlying molecular mechanisms.\nMETHODS: We analyzed the mRNA microarray data of 119 HBV-related HCC tissues and 252 HBV-related non-tumor tissues in GSE55092, GSE84044 and GSE121248 from the GEO database, and the \"sva\" R package was used to remove the batch effects. Integration analysis was performed to identify the differentially expressed genes (DEGs) in HBV-related liver cancer and liver tissues with HBV infection. The significant DEGs were functionally annotated using GO and KEGG analyses, and the most important modules and hub genes were explored with STRING analysis. Kaplan-Meier and Oncomine databases were used to verify the HCC gene expression data in the TCGA database to explore the correlations of the hub genes with the occurrence, progression and prognosis of HCC. We also examined the expressions of the hub genes in 17 pairs of surgical specimens of HCC and adjacent tissues using RT-qPCR.\nRESULTS: We identified a total of 121 DEGs and 3 genetic markers in HCC (P < 0.01). These DEGs included cyclin1 (CDK1), cyclin B1 (CCNB1), and nuclear division cycle 80 (NDC80), which participated in cell cycle, pyrimidine metabolism and DNA replication and were highly correlated (P < 0.05). Analysis of the UALCAN database confirmed high expressions of these 3 genes in HCC tissues, which were correlated with a low survival rate of the patients, as shown by Kaplan-Meier analysis of the prognostic data from the UALCAN database. CDK1, CCNB1 and NDC80 were all correlated with the clinical grading of HCC (P < 0.05). The results of RT-qPCR on the surgical specimens verified significantly higher expressions of CDK1, CCNB1 and NDC80 mRNA in HCC tissues than in the adjacent tissues.\nCONCLUSION: CDK1, CCNB1 and NDC80 genes can be used as prognostic markers of HBV-related HCC and may serve as potential targets in preclinical studies and clinical treatment of HCC.", "claims": [{"id": "claim-method", "statement": "利用Kaplan-Meier和Oncomine数据库对TCGA数据库中肝癌基因表达数据进行验证，探讨hub基因与肝癌发生、发展和预后的关系。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34755666", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "利用Kaplan-Meier和Oncomine数据库对TCGA数据库中肝癌基因表达数据进行验证，探讨hub基因与肝癌发生、发展和预后的关系。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "分析基因表达综合（GEO）数据库中GSE55092、GSE84044和GSE121248的mRNA微阵列数据，其中包括119个HBV相关的HCC组织和252个HBV相关的非肿瘤组织。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34755666", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "分析基因表达综合（GEO）数据库中GSE55092、GSE84044和GSE121248的mRNA微阵列数据，其中包括119个HBV相关的HCC组织和252个HBV相关的非肿瘤组织。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "CDK1、CCNB1和NDC80基因可作为HBV相关肝细胞癌的预后标志物，在肝癌的基础研究和临床治疗方面有一定的应用价值。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34755666", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "CDK1、CCNB1和NDC80基因可作为HBV相关肝细胞癌的预后标志物，在肝癌的基础研究和临床治疗方面有一定的应用价值。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CDK1、CCNB1和NDC80基因可作为HBV相关肝细胞癌的预后标志物，在肝癌的基础研究和临床治疗方面有一定的应用价值。", "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:34755666"], "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:34755666", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12122/j.issn.1673-4254.2021.10.09", "sha256": 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METHODS: We analyzed the mRNA microarray data of 119 HBV-related HCC tissues and 252"], "order_basis": "paper_text_order:319", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["specimens of HCC and adjacent tissues using RT-qPCR. RESULTS: We identified a total of 121 DEGs", "al grading of HCC (P < 0.05). The results of RT-qPCR on the surgical specimens verified significa", "ecimens of HCC and adjacent tissues using RT-qPCR. RESULTS: We identified a total of 121 DEGs", "grading of HCC (P < 0.05). The results of RT-qPCR on the surgical specimens verified significa"], "order_basis": "paper_text_order:1163", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["利用Kaplan-Meier和Oncomine数据库对TCGA数据库中肝癌基因表达数据进行验证，探讨hub基因与肝癌发生、发展和预后的关系。"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}