CDK1 and CCNA2 play important roles in oral squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38640322", "kind": "science-record", "revision": 4, "content_hash": "sha256:7b25875b20b2d09616fdec9633f346ce38490eae58e5f0da55701287a8d19b83", "created_at": "2026-11-01T19:20:36Z", "updated_at": "2026-11-01T22:54:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CDK1 and CCNA2 play important roles in oral squamous cell carcinoma.", "doi": "10.1097/MD.0000000000037831", "pmid": "38640322", "authors": ["Junbo Zhang", "Yongbin Di", "Bohao Zhang", "Tianke Li", "Dan Li", "Haolei Zhang"], "journal": "Medicine", "year": 2024, "abstract": "Oral squamous cell carcinoma (OSCC) is a malignant tumor that occurs in oral cavity and is dominated by squamous cells. The relationship between CDK1, CCNA2, and OSCC is still unclear. The OSCC datasets GSE74530 and GSE85195 configuration files were downloaded from the Gene Expression Omnibus (GEO) database and were derived from platforms GPL570 and GPL6480. Differentially expressed genes (DEGs) were screened. The weighted gene co-expression network analysis, functional enrichment analysis, gene set enrichment analysis, construction and analysis of protein-protein interaction (PPI) network, Comparative Toxicogenomics Database analysis were performed. Gene expression heatmap was drawn. TargetScan was used to screen miRNAs that regulate central DEGs. A total of 1756 DEGs were identified. According to Gene Ontology (GO) analysis, they were predominantly enriched in processes related to organic acid catabolic metabolism, centromeric, and chromosomal region condensation, and oxidoreductase activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the DEGs were mainly concentrated in metabolic pathways, P53 signaling pathway, and PPAR signaling pathway. Weighted gene co-expression network analysis was performed with a soft-thresholding power set at 9, leading to the identification of 6 core genes (BUB1B, CCNB1, KIF20A, CCNA2, CDCA8, CDK1). The gene expression heatmap revealed that core genes (CDK1, CCNA2) were highly expressed in OSCC samples. Comparative Toxicogenomics Database analysis demonstrated associations between the 6 genes (BUB1B, CCNB1, KIF20A, CCNA2, CDCA8, CDK1) and oral tumors, precancerous lesions, inflammation, immune system disorders, and tongue tumors. The associated miRNAs for CDK1 gene were hsa-miR-203a-3p.2, while for CCNA2 gene, they were hsa-miR-6766-3p, hsa-miR-4782-3p, and hsa-miR-219a-5p. CDK1 and CCNA2 are highly expressed in OSCC. The higher the expression of CDK1 and CCNA2, the worse the prognosis.", "claims": [{"id": "claim-method", "statement": "The “limma” R package was employed for probe summarization and background correction of the GSE74530 and GSE85195 matrices. The Benjamini-Hochberg method was used to adjust the raw P values, and the fold change (FC) was calculated using the false discovery rate (FDR).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38640322", "locator": "sections[4] \"2.2. Selection of DEGs\" paragraph 2", "quote": "The “limma” R package was employed for probe summarization and background correction of the GSE74530 and GSE85195 matrices. The Benjamini-Hochberg method was used to adjust the raw P values, and the fold change (FC) was calculated using the false discovery rate (FDR)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38640322", "locator": "sections[28] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1756 DEGs were identified, and CDK1 and CCNA2 were highly expressed in OSCC samples, with higher expression associated with worse prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38640322", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 1756 DEGs were identified."}, {"asset": "source:pmid:38640322", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene expression heatmap revealed that core genes (CDK1, CCNA2) were highly expressed in OSCC samples."}, {"asset": "source:pmid:38640322", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "CDK1 and CCNA2 are highly expressed in OSCC. The higher the expression of CDK1 and CCNA2, the worse the prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1756 DEGs were identified, and CDK1 and CCNA2 were highly expressed in OSCC samples, with higher expression associated with worse prognosis.", "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:38640322"], "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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