Identification of hub genes in colon cancer via bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32961078", "kind": "science-record", "revision": 8, "content_hash": "sha256:3bfea52aa9dd47b28ade8b99cad83697d766079567c900bbcee87a551fa2d886", "created_at": "2026-11-01T15:41:11Z", "updated_at": "2026-11-01T22:02:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes in colon cancer via bioinformatics analysis.", "doi": "10.1177/0300060520953234", "pmid": "32961078", "authors": ["Jun Liu", "Gui-Li Sun", "Shang-Ling Pan", "Meng-Bin Qin", "Rong Ouyang", "Jie-An Huang"], "journal": "The Journal of international medical research", "year": 2020, "abstract": "OBJECTIVES: This study aimed to investigate hub genes and their prognostic value in colon cancer via bioinformatics analysis.\nMETHODS: Differentially expressed genes (DEGs) of expression profiles (GSE33113, GSE20916, and GSE37364) obtained from Gene Expression Omnibus (GEO) were identified using the GEO2R tool and Venn diagram software. Function and pathway enrichment analyses were performed, and a protein-protein interaction (PPI) network was constructed. Hub genes were verified based on The Cancer Genome Atlas (TCGA) and Human Protein Atlas (HPA) databases.\nRESULTS: We identified 207 DEGs, 62 upregulated and 145 downregulated genes, enriched in Gene Ontology terms \"organic anion transport,\" \"extracellular matrix,\" and \"receptor ligand activity\", and in the Kyoto Encyclopedia of Genes and Genomes pathway \"cytokine-cytokine receptor interaction.\" The PPI network was constructed and nine hub genes were selected by survival analysis and expression validation. We verified these genes in the TCGA database and selected three potential predictors (ZG16, TIMP1, and BGN) that met the independent predictive criteria. TIMP1 and BGN were upregulated in patients with a high cancer risk, whereas ZG16 was downregulated. The immunostaining results from HPA supported these findings.\nCONCLUSION: This study indicates that these hub genes may be promising prognostic indicators or therapeutic targets for colon cancer.", "claims": [{"id": "claim-method", "statement": "DEGs of expression profiles were identified via GEO2R online tools (www.ncbi.nlm.nih.gov/geo/geo2r) and Venn diagrams (bioinformatics.psb.ugent.be/webtools/Venn).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32961078", "locator": "sections[5] \"DEG identification\" paragraph 2", "quote": "DEGs of expression profiles were identified via GEO2R online tools (www.ncbi.nlm.nih.gov/geo/geo2r) and Venn diagrams (bioinformatics.psb.ugent.be/webtools/Venn)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Expression profiles of GSE33113, GSE20916, and GSE37364 based on the GPL570 platform were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The three datasets included 90, 66, and 27 colon cancer tissues and 6, 34, and 38 normal tissues, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32961078", "locator": "sections[4] \"Data collection\" paragraph 2", "quote": "Expression profiles of GSE33113, GSE20916, and GSE37364 based on the GPL570 platform were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The three datasets included 90, 66, and 27 colon cancer tissues and 6, 34, and 38 normal tissues, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:32961078"], "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:GSE20916"], "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:GSE20916"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32961078", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/0300060520953234", "sha256": "sha256:80fd9231faa2c89428b789ee0026f5f6a3acff2445cdf7cc0d23db330fc891c6", "bytes": 18702, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/0300060520953234", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7513414", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20916", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20916", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20916", "version": null, "note": "Expression profiles of GSE33113, GSE20916, and GSE37364 based on the GPL570 platform were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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