Identification of Hub Genes and Potential Pathogenesis in Gastric Cancer Based on Integrated Gene Expression Profile Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38546071", "kind": "science-record", "revision": 4, "content_hash": "sha256:95bcc5ffce32fe7999463a08410430f44d40f23d6f6a2534405117dfa4538440", "created_at": "2026-11-01T19:20:30Z", "updated_at": "2026-11-01T22:53:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes and Potential Pathogenesis in Gastric Cancer Based on Integrated Gene Expression Profile Analysis.", "doi": "10.31557/APJCP.2024.25.3.885", "pmid": "38546071", "authors": ["Hung Luu Truong Thanh", "Tien-Manh Hoang", "Hieu Hoang Van"], "journal": "Asian Pacific journal of cancer prevention : APJCP", "year": 2024, "abstract": "OBJECTIVE: Gastric cancer (GC) is one of the most common malignancies and ranks third in terms of cancer-related mortality. This study aims to identify the hub genes and potential mechanisms in GC using a bioinformatics approach.\nMETHODS: Microarray data GSE54129, GSE79973, GSE55696 were extracted from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) was identified using Benjamini-Hochberg method in the limma package. GO and KEGG pathway enrichment analyses of the DEGs were conducted. Furthermore, protein-protein interaction network was constructed the STRING platform, and the hub genes were discovered using Maximal Clique Centrality method via cytoHubba. The predictive significance of hub genes was evaluated through GSE15459 dataset.\nRESULTS: A total of 73 genes was identified as DEGs in GC. Volcano plots and heatmaps of DEGs were visualized. Functional enrichment analysis revealed that the genes were mostly enriched in response to xenobiotic stimulus, digestion, cellular hormone metabolic process, extracellular matrix structural constituent, calcium-dependent cysteine-type endopeptidase activity, aromatase activity, apical part of cell, basal part of cell, and apical plasma membrane. Regarding KEGG pathway-enrichment, the genes were mainly involved in Drug metabolism-cytochrome P450, Retinol metabolism, Chemical carcinogenesis-DNA adducts, Gastric acid secretion, and Metabolism of xenobiotics by cytochrome P450. By combining the results of Cytohubba, the top five intersecting genes identified were SPP1, INHBA, MMP7, THBS2 and FAP. Kapplan-Meier analysis results showed that these 5 hub genes were highly related to the overall survival of patients.\nCONCLUSION: SPP1, INHBA, MMP7, THBS2, and FAP were identified as prospective biomarkers and therapeutic targets for GC that might be utilized for prognostic evaluation and scheme selection.", "claims": [{"id": "claim-method", "statement": "The DEGs between the normal group and the GC group were compared using the Limma package. The false discovery rate (FDR) was controlled using the Benjamini-Hochberg analysis, and DEGs were chosen using the cutoffs of FDR p-value <0.05 and absolute log2 fold-change (FC) >1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38546071", "locator": "sections[2] \"Materials and Methods\" paragraph 6", "quote": "The DEGs between the normal group and the GC group were compared using the Limma package. The false discovery rate (FDR) was controlled using the Benjamini-Hochberg analysis, and DEGs were chosen using the cutoffs of FDR p-value <0.05 and absolute log2 fold-change (FC) >1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data was obtained from the Gene Expression Omnibus (GEO), a freely accessible database available to the public.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38546071", "locator": "sections[8] \"Availability of data\" paragraph 2", "quote": "Data was obtained from the Gene Expression Omnibus (GEO), a freely accessible database available to the public."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SPP1, INHBA, MMP7, THBS2, and FAP were identified as prospective biomarkers and therapeutic targets for GC that might be utilized for prognostic evaluation and scheme selection.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38546071", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "SPP1, INHBA, MMP7, THBS2, and FAP were identified as prospective biomarkers and therapeutic targets for GC that might be utilized for prognostic evaluation and scheme selection."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SPP1, INHBA, MMP7, THBS2, and FAP were identified as prospective biomarkers and therapeutic targets for GC that might be utilized for prognostic evaluation and scheme selection.", "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:38546071"], "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:GSE15459"], "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": {"fdr_threshold": "with Benjamini-Hochberg false discovery rate control"}, "inputs": ["data:geo:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38546071", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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METHODS: Microarray data GSE54129, GSE79973, GSE55696 were extra", "Materials and Methods MicroArray Data Collection The present study used four", "dataset, which is based on GPL570 platform (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array),"], "order_basis": "paper_text_order:321", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs between the normal group and the GC group were compared using the Limma package. The false discovery rate (FDR) was controlled using the Benjamini-Hochberg analysis, and DEGs were chosen using the cutoffs of FDR p-value <0.05 and absolute log2 fold-change (FC) >1.5."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}