Identification of significant genes associated with prognosis of gastric cancer by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36567425", "kind": "science-record", "revision": 3, "content_hash": "sha256:c993f682a8ff9143df1719fecd4b7eb238221b2218f1160afd28f79ca7cb8f28", "created_at": "2026-11-01T19:01:07Z", "updated_at": "2026-11-01T22:08:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of significant genes associated with prognosis of gastric cancer by bioinformatics analysis.", "doi": "10.1186/s43046-022-00157-w", "pmid": "36567425", "authors": ["Shuanhu Wang", "Song Tao", "Yakui Liu", "Yi Shi", "Mulin Liu"], "journal": "Journal of the Egyptian National Cancer Institute", "year": 2022, "abstract": "BACKGROUND: Gastric cancer (GC) ranks second in mortality among all malignant diseases worldwide. However, the cause and molecular mechanism underlying gastric cancer are not clear. Here, we used integrated bioinformatics to identify possible key genes and reveal the pathogenesis and prognosis of gastric cancer.\nMETHODS: The gene expression profiles of GSE118916, GSE79973, and GSE29272 were available from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between GC and normal gastric tissues were screened by R software and Venn diagram software. GO and KEGG pathway enrichment of DEGs was performed using the DAVID database. A protein-protein interaction (PPI) network was established by STRING and visualized using Cytoscape software. Then the influence of hub genes on expression and survival was assessed using TCGA database.\nRESULTS: A total of 83 DEGs were found in the three datasets, including 41 up-regulated genes and 42 down-regulated genes. These DEGs were mainly enriched in extracellular matrix organization and cell adhesion. The enriched pathways obtained in the KEGG pathway analysis were extracellular matrix (ECM)-receptor interaction and focal adhesion. A PPI network of DEGs was analyzed using the Molecular Complex Detection (MCODE) app of Cytoscape. Four genes were considered hub genes, including COL5A1, FBN1, SPARC, and LUM. Among them, LUM was found to have a significantly worse prognosis based on TCGA database.\nCONCLUSIONS: We screened DEGs associated with GC by integrated bioinformatics analysis and found one potential biomarker that may be involved in the progress of GC. This hub gene may serve as a guide for further molecular biological experiments.", "claims": [{"id": "claim-method", "statement": "The data were log2 transformed. |Log2 fold change (FC)| > 1 and adjusted P < 0.01 were considered the cutoff criteria for DEG screening.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36567425", "locator": "sections[3] \"Microarray data and identification of DEGs\" paragraph 2", "quote": "The data were log2 transformed. |Log2 fold change (FC)| > 1 and adjusted P < 0.01 were considered the cutoff criteria for DEG screening."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/detail.php).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36567425", "locator": "sections[19] \"notes\" paragraph 1", "quote": "The data that support the findings of this study are available from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/detail.php)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "83 common differentially expressed genes were identified across the three GEO gastric cancer datasets, including 41 upregulated and 42 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36567425", "locator": "sections[8] \"Microarray data information and identification of DEGs\" paragraph 2", "quote": "A total of 83 genes were screened out in all three datasets for further analysis (Fig. 1d). There were 41 upregulated genes and 42 downregulated genes in GC tissues compared to adjacent tissues (Table 2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "83 common differentially expressed genes were identified across the three GEO gastric cancer datasets, including 41 upregulated and 42 downregulated genes.", "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:36567425"], "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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