Identification of Hub genes with prognostic values in colorectal cancer by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38393891", "kind": "science-record", "revision": 3, "content_hash": "sha256:fce829a2e91eb0e31727f88a93923841c8ab533721100570511a84a88b154e23", "created_at": "2026-11-01T19:20:20Z", "updated_at": "2026-11-01T22:11:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub genes with prognostic values in colorectal cancer by integrated bioinformatics analysis.", "doi": "10.3233/CBM-230113", "pmid": "38393891", "authors": ["Shan Li", "Ting Li", "Yan-Qing Shi", "Bin-Jie Xu", "Yu-Yong Deng", "Xu-Guang Sun"], "journal": "Cancer biomarkers : section A of Disease markers", "year": 2024, "abstract": "BACKGROUND: Our study aimed to investigate the Hub genes and their prognostic value in colorectal cancer (CRC) via bioinformatics analysis.\nMETHODS: The data set of colorectal cancer was downloaded from the GEO database (GSE21510, GSE110224 and GSE74602) for differential expression analysis using the GEO2R tool. Hub genes were screened by protein-protein interaction (PPI) comprehensive analysis. GEPIA was used to verify the expression of Hub genes and evaluate its prognostic value. The protein expression of Hub gene in CRC was analyzed using the Human Protein Atlas database. The cBioPortal was used to analyze the type and frequency of Hub gene mutations, and the effects of mutation on the patients' prognosis. The TIMER database was used to study the correlation between Hub genes and immune infiltration in CRC. Gene set enrichment analysis (GSEA) was used to explore the biological function and signal pathway of the Hub genes and corresponding co-expressed genes.\nRESULTS: We identified 346 differentially expressed genes (DEGs), including 117 upregulated and 229 downregulated. Four Hub genes (AURKA, CCNB1, EXO1 and CCNA2) were selected by survival analysis and differential expression validation. The protein and mRNA expression levels of AURKA, CCNB1, EXO1 and CCNA2 were higher in CRC tissues than in adjacent tissues. There were varying degrees of immune cell infiltration and gene mutation of Hub genes, especially B cells and CD8+ T cells. The results of GSEA showed that Hub genes and their co-expressed genes mainly participated in chromosome segregation, DNA replication, translational elongation and cell cycle.\nCONCLUSION: Overexpression of AURKA, CCNB1, CCNA2 and EXO1 had a better prognosis for CRC and this effect was correlation with gene mutation and infiltration of immune cells.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) were filtered using a threshold of adjusted P values < 0.05 and an absolute log2FC (fold change) > 1 by GEO2R online tools (http://www.ncbi.nlm.nih.gov/geo/geo2r) [22].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38393891", "locator": "sections[5] \"Differential expressed gene analysis\" paragraph 2", "quote": "The differentially expressed genes (DEGs) were filtered using a threshold of adjusted P values < 0.05 and an absolute log2FC (fold change) > 1 by GEO2R online tools (http://www.ncbi.nlm.nih.gov/geo/geo2r) [22]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38393891", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four Hub genes (AURKA, CCNB1, EXO1 and CCNA2) were selected by survival analysis and differential expression validation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38393891", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Four Hub genes (AURKA, CCNB1, EXO1 and CCNA2) were selected by survival analysis and differential expression validation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four Hub genes (AURKA, CCNB1, EXO1 and CCNA2) were selected by survival analysis and differential expression validation.", "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:38393891"], "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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