Screening and verifying key genes with poor prognosis in colon cancer through bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35117282", "kind": "science-record", "revision": 5, "content_hash": "sha256:39bd41597657c5be5bcba23de356f5f5dd1fbcfa07dfbc550e9f9d9152a2a2c7", "created_at": "2026-11-01T17:36:51Z", "updated_at": "2026-11-01T22:05:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and verifying key genes with poor prognosis in colon cancer through bioinformatics analysis.", "doi": "10.21037/tcr-20-2309", "pmid": "35117282", "authors": ["Buyuan Dong", "Mengyu Chai", "Hao Chen", "Qian Feng", "Rong Jin", "Sunkuan Hu"], "journal": "Translational cancer research", "year": 2020, "abstract": "BACKGROUND: Colon cancer (CC) is one of the tumors with high morbidity and mortality in the world, and has a trend of younger generation. The molecular level of CC has not been fully elaborated. The purpose of this study is to screen and identify important genes with poor prognosis and their mechanisms at different levels.\nMETHODS: GSE74602 and GSE10972 gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) database. There were 58 normal tissues and 58 CC tissues. Differentially expressed genes (DEGs) were screened out by using the GEO2R tool and Venn diagram. Then, the DAVID online database was used to perform the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Six hub genes with the highest correlation were screened out after the modular analysis of the protein-protein interaction (PPI) network by using Cytoscape's MCODE plug-in. Finally, the overall survival of key hub genes and potential pathways were verified in GEPIA and UALCAN database.\nRESULTS: A total of 78 up-regulated DEGs were enriched in the mitotic nuclear division, cell division, cell proliferation, anaphase-promoting complex-dependent catabolic process and G2/M transition of the mitotic cell cycle. In total, 130 down-regulated DEGs were enriched in muscle contraction, bicarbonate transport, cellular response to zinc ion, negative regulation of growth, negative regulation of leukocyte apoptotic process and one-carbon metabolic process. CDK1, CCNB1, CDC20, AURKA, CCNA2 and TOP2A were the top six hub genes, mainly enriched in cell cycle pathways. Among them, CCNB1, CDK1, CDC20, CCNA2 were enriched in the G2/M phase. GEPIA and UALCAN database confirmed that CCNA2 and CCNB1 had a significant relationship with the poor prognosis of CC patients. Meanwhile, there was a positive correlation between the two.\nCONCLUSIONS: Screening out genes with abnormal expression in CC help understand the initiation and progression of CC at the molecular level and explore candidate biomarkers for diagnosis, treatment and prognosis.", "claims": [{"id": "claim-method", "statement": "The GEPIA and UALCAN use the log-rank test, sometimes called the Mantel-Cox test, for the hypothesis evaluation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117282", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "The GEPIA and UALCAN use the log-rank test, sometimes called the Mantel-Cox test, for the hypothesis evaluation."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this study, we downloaded GSE74602 and GSE10972 gene expression profiles from Gene Expression Omnibus (GEO) (Affymetrix GPL6104 platform, Illumina humanRef-8 v2.0 expression beadchip).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117282", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "In this study, we downloaded GSE74602 and GSE10972 gene expression profiles from Gene Expression Omnibus (GEO) (Affymetrix GPL6104 platform, Illumina humanRef-8 v2.0 expression beadchip)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 78 up-regulated and 130 down-regulated genes were detected on the ‘Draw Venn Diagram’ website.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35117282", "locator": "sections[3] \"Identification of DEGs\" paragraph 2", "quote": "A total of 78 up-regulated and 130 down-regulated genes were detected on the ‘Draw Venn Diagram’ website."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 78 up-regulated and 130 down-regulated genes were detected on the ‘Draw Venn Diagram’ website.", "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:35117282"], "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:GSE10972"], "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:GSE10972"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35117282", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-20-2309", "sha256": 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