Conjoint analysis for hepatic carcinoma with hub genes and multi-slice spiral CT.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33157984", "kind": "science-record", "revision": 7, "content_hash": "sha256:31a196a1e4dd1be2d58614d9ba83e2bf4acfd76b82d21b2f9101b7abd6d06763", "created_at": "2026-11-01T15:41:15Z", "updated_at": "2026-11-01T22:02:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Conjoint analysis for hepatic carcinoma with hub genes and multi-slice spiral CT.", "doi": "10.1097/MD.0000000000023099", "pmid": "33157984", "authors": ["Shuang Zhang", "Ruchen Peng", "Ruiqiang Xin", "Xiuzhi Shen", "Jingli Zheng"], "journal": "Medicine", "year": 2020, "abstract": "Hepatic carcinoma (HCC) is a common malignant tumor, with insidious onset and poor prognosis. However, more hub genes associated with hepatocellular carcinoma are unknown. And there are few researches about the conjoint analysis with the hub genes and multi-slice spiral computerized tomography (CT).A total of 100 HCC participates were recruited, who all received the examination of multi-slice spiral CT. Two expression profile data sets (GSE101728 and GSE101685) were downloaded from the Gene Expression Omnibus (GEO) database. GEO2R can perform a command to compare gene expression profiles between groups in order to identify differently expressed genes (DEGs). Functional annotation of DEGs via Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was made with Database for Annotation, Visualization, and Integrated Discovery (DAVID). Construction and analysis of protein-protein interaction network were performed. Furthermore, the study could mine of hub genes and explore the correlation with the multi-slice CT. Real-time quantitative polymerase chain reaction (RT-qPCR) assay was used the exam the expression of hub genes.A total of 10 genes were identified as hub genes with degrees ≥10. The hub genes (NIMA Related Kinase 2 [NEK2], Anillin Actin Binding Protein [ANLN], DNA Topoisomerase II Alpha [TOP2A], Centromere Protein F [CENPF], Assembly Factor For Spindle Microtubules [ASPM], Cell Division Cycle 20 [CDC20], Cyclin Dependent Kinase 1 [CDK1], Cyclin B1 [CCNB1], Epithelial Cell Transforming 2 [ECT2], Cyclin B2 [CCNB2]) were identified from the Molecular Complex Detection (MCODE) network. These hub genes were highly expressed in HCC tissues, and when these genes were highly expressed, the survival prognosis of HCC patients was poor. The type of CT enhancement was significantly related with the expression of NEK2 (P < .001), ANLN (P < .001), and TOP2A (P = .006).The combination between the gene expression (NEK2, ANLN, and TOP2A) and type of CT enhancement might provide a new idea for future basic research and targeted therapy of HCC.", "claims": [{"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the present study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33157984", "locator": "sections[23] \"Footnotes\" paragraph 2", "quote": "The datasets generated during and/or analyzed during the present study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33157984"], "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:GSE101685"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE101685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33157984", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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"version": null, "note": "The gene expression in patients with HCC and multi-slice CT.", "structure": {"pmcid": "PMC7647627", "section_index": 18, "section_title": "The correlation between the gene expression and type of multi-slice CT enhancement", "row_count": 33, "column_count": 6}, "table": {"label": "Table 1", "caption": "The gene expression in patients with HCC and multi-slice CT.", "rows": [["Gene symbol", "Type of CT enhancement", ""], ["", "", ""], ["", "", "Tumor parenchymal enhancement", "Tumor vascular enhancement", "Nontumor enhancement", "P"], ["NEK2"], ["Low", "34", "4 (11.76%)", "6 (17.65%)", "24 (70.59%)", "<.001∗"], ["High", "66", "36 (54.55%)", "20 (30.30%)", "10 (15.15%)", ""], ["ANLN", "", "", "", "", ""], ["Low", "35", "3 (8.57%)", "9 (25.71%)", "23 (65.71%)", "<.001∗"], ["High", "65", "38 (58.46%)", "21 (32.31%)", "6 (9.23%)", ""], ["TOP2A"], ["Low", "29", "7 (24.14%)", "10 (34.48%)", "12 (41.38%)", ".006∗"], ["High", "71", "35 (49.30%)", "26 (36.62%)", "10 (14.08%)", ""], ["CENPF"], ["Low", "38", "10 (26.32%)", "13 (34.21%)", "15 (39.47%)", ".393"], ["High", "62", "24 (38.71%)", "20 (32.26%)", "18 (29.03%)", ""], ["ASPM"], ["Low", "41", "12 (29.27%)", "11 (26.83%)", "18 (43.90%)", ".481"], ["High", "59", "22 (37.29%)", "18 (30.51%)", "19 (32.20%)", ""], ["CDC20"], ["Low", "67", "19 (28.36%)", "23 (34.33%)", "25 (37.31%)", ".260"], ["High", "33", "11 (33.33%)", "15 (45.45%)", "7 (21.21%)", ""], ["CDK1"], ["Low", "46", "18 (39.13%)", "12 (26.09%)", "16 (34.78%)", ".106"], ["High", "54", "25 (46.30%)", "20 (37.04%)", "9 (16.67%)", ""], ["CCNB1"], ["Low", "52", "14 (26.92%)", "20 (38.46%)", "18 (34.62%)", ".211"], ["High", "48", "21 (43.75%)", "14 (29.17%)", "13 (27.08%)", ""], ["ECT2"], ["Low", "54", "21 (38.89%)", "16 (29.63%)", "17 (31.48%)", ".924"], ["High", "46", "19 (41.30%)", "12 (26.09%)", "15 (32.61%)", ""], ["CCNB2"], ["Low", "49", "15 (30.61%)", "13 (26.53%)", "21 (42.86%)", ".731"], ["High", "51", "17 (33.33%)", "16 (31.37%)", 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