Screening of the Key Genes for the Progression of Liver Cirrhosis to Hepatocellular Carcinoma Based on Bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36199789", "kind": "science-record", "revision": 5, "content_hash": "sha256:d55461ed6e0d994b17508680c4ca12f5ce166f5e44059b412291cc9aff7f9d6b", "created_at": "2026-11-01T18:15:31Z", "updated_at": "2026-11-01T22:50:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of the Key Genes for the Progression of Liver Cirrhosis to Hepatocellular Carcinoma Based on Bioinformatics.", "doi": "10.1155/2022/2515513", "pmid": "36199789", "authors": ["Yuanbin Chen", "Hongyan Qian", "Xiao He", "Jing Zhang", "Song Xue", "Yumeng Wu", "Jian Chen", "Xuming Wu", "Suqing Zhang"], "journal": "Journal of oncology", "year": 2022, "abstract": "Hepatocellular carcinoma (HCC), which is among the most globally prevalent cancers, is strongly associated with liver cirrhosis. Using a bioinformatics approach, we have identified and investigated the hub genes responsible for the progression of cirrhosis into HCC. We analyzed the Gene Expression Omnibus (GEO) microarray datasets, GSE25097 and GSE17549, to identify differentially expressed genes (DEGs) in these two conditions and also performed protein-protein interaction (PPI) network analysis. STRING database and Cytoscape software were used to analyze the modules and locate hub genes following which the connections between hub genes and the transition from cirrhosis to HCC, progression of HCC, and prognosis of HCC were investigated. We used the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to detect the molecular mechanisms underlying the action of the primary hub genes. In all, 239 DEGs were obtained, with 94 of them showing evidence of upregulation and 145 showing evidence of downregulation in HCC tissues as compared to cirrhotic liver tissues. We identified six hub genes, namely, BUB1B, NUSAP1, TTK, HMMR, CCNA2, and KIF2C, which were upregulated and had a high diagnostic value for HCC. Besides, these six hub genes were positively related to immune cell infiltration. Since these genes may play a direct role in the progression of cirrhosis to HCC, they can be considered as potential novel molecular indicators for the onset and development of HCC.", "claims": [{"id": "claim-method", "statement": "DEGs between HCC tissues and liver cirrhotic tissues were identified through GEO2R program.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36199789", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "DEGs between HCC tissues and liver cirrhotic tissues were identified through GEO2R program."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in TCGA (https://portal.gdc.cancer.gov/) and GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36199789", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The datasets analyzed during the current study are available in TCGA (https://portal.gdc.cancer.gov/) and GEO repository (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified six hub genes, namely, BUB1B, NUSAP1, TTK, HMMR, CCNA2, and KIF2C, which were upregulated and had a high diagnostic value for HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36199789", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified six hub genes, namely, BUB1B, NUSAP1, TTK, HMMR, CCNA2, and KIF2C, which were upregulated and had a high diagnostic value for HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified six hub genes, namely, BUB1B, NUSAP1, TTK, HMMR, CCNA2, and KIF2C, which were upregulated and had a high diagnostic value for HCC.", "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:36199789"], "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. 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