[Screening and identification of key genes ATP1B3 and ENAH in the progression of hepatocellular carcinoma: based on data mining and clinical validation].

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35790431", "kind": "science-record", "revision": 3, "content_hash": "sha256:278103717cf31a8c82d30cd6800174038368e29f0c282b162304373527e8f9cf", "created_at": "2026-11-01T18:14:50Z", "updated_at": "2026-11-01T21:28:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Screening and identification of key genes ATP1B3 and ENAH in the progression of hepatocellular carcinoma: based on data mining and clinical validation].", "doi": "10.12122/j.issn.1673-4254.2022.06.04", "pmid": "35790431", "authors": ["X Yang", "Y Li", "D Wu", "Y Ma", "S Zhou"], "journal": "Nan fang yi ke da xue xue bao = Journal of Southern Medical University", "year": 2022, "abstract": "OBJECTIVE: To explore the marker genes correlated with the prognosis, progression and clinical diagnosis of hepatocellular carcinoma (HCC) based on bioinformatics methods.\nMETHODS: The TCGA-LIHC, GSE84432, GSE143233 and GSE63898 datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed. The differentially expressed genes (DEGs) shared by different disease types were obtained using GEO2R and edge R packages, and Gene Ontology (GO) and Kyoto Gene and Genome Encyclopedia (KEGG) enrichment analyses of the DEGs were performed. The expression levels of these DEGs in normal and cancerous tissues were verified in TCGA-LIHC to identify the upregulated genes in HCC. Survival analysis, receiver-operating characteristic (ROC) curve analysis, and correlation analysis between the key genes and the clinical features of the patients were carried out using the R language. The differential expressions of 15 key genes were verified in clinical samples of HCC and adjacent tissues using RT-qPCR.\nRESULTS: A total of 118 common DEGs were obtained in the database, and among them two genes, namely ATPase Na +/K + transport subunit beta 3 (ATP1B3) and actin regulator (ENAH), showed increased expressions with disease progression. Survival analysis combined with the TCGA-LIHC dataset suggested that high expressions of ATP1B3 and ENAH were both significantly correlated with a poor prognosis of HCC patients (P < 0.05), and their AUC values were 0.821 and 0.933, respectively. A high expression of ATP1B3 was correlated with T stage, pathological stage and pathological grade of the tumors (P < 0.05), while that of ENAH was associated only with an advanced tumor grade (P < 0.05). The results of RT-qPCR showed that ATP1B3 and ENAH were both significantly upregulated in clinical HCC tissues (P < 0.05).\nCONCLUSION: ATPIB3 and ENAH are both upregulated in HCC, and their high expressions may serve as biomarkers of progression of liver diseases and a poor prognosis of HCC.", "claims": [{"id": "claim-method", "statement": "利用GEO2R和edge R包获得各疾病类型之间共同差异基因（DEG），并对DEG进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35790431", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "利用GEO2R和edge R包获得各疾病类型之间共同差异基因（DEG），并对DEG进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "分析来自癌症基因组图谱数据库（TCGA）和基因表达综合（GEO）的TCGA-LIHC、GSE84432、GSE14323和GSE63898数据集。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35790431", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "分析来自癌症基因组图谱数据库（TCGA）和基因表达综合（GEO）的TCGA-LIHC、GSE84432、GSE14323和GSE63898数据集。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "ATP1B3和ENAH在临床HCC组织中表达上调（P＜0.05）。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35790431", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "RT-qPCR结果发现，ATP1B3和ENAH在临床HCC组织中表达上调（P＜0.05）。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ATP1B3和ENAH在临床HCC组织中表达上调（P＜0.05）。", "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:35790431"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35790431", "data:geo:GSE14323"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14323"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:53:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1998, "completion_tokens": 1153, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35790431", "type": "paper", "label": "pmid:35790431"}, {"id": "source:pmid:35790431", "type": "manuscript", "label": "PMID 35790431 full text"}, {"id": "data:geo:GSE14323", "type": "dataset", "label": "GEO GSE14323"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35790431", "type": "paper", "label": "pmid:35790431"}, {"id": "source:pmid:35790431", "type": "manuscript", "label": "PMID 35790431 full text"}, {"id": "data:geo:GSE14323", "type": "dataset", "label": "GEO GSE14323"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35790431", "type": "extraction", "used": ["source:pmid:35790431"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14323", "type": "accession_resolution", "used": ["data:geo:GSE14323"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35790431", "parent_hash": "sha256:2a89cc1a1804aa2207a2ea60f7b6ff32bb7e30161e7b1d44a943207ac1629c14", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE14323 licence not read", "asset:data:geo:GSE14323 not downloaded", "asset:data:geo:GSE63898 licence not read", "asset:data:geo:GSE63898 not downloaded", "asset:data:geo:GSE84432 licence not read", "asset:data:geo:GSE84432 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["al samples of HCC and adjacent tissues using RT-qPCR. RESULTS: A total of 118 common DEGs were ob", "anced tumor grade (P < 0.05). The results of RT-qPCR showed that ATP1B3 and ENAH were both signif", "samples of HCC and adjacent tissues using RT-qPCR. RESULTS: A total of 118 common DEGs were ob", "ed tumor grade (P < 0.05). The results of RT-qPCR showed that ATP1B3 and ENAH were both signif"], "order_basis": "paper_text_order:1125", "id": "assay:1"}]}