Identification of differentially expressed genes associated with the pathogenesis of gastric cancer by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38041130", "kind": "science-record", "revision": 2, "content_hash": "sha256:034e2a22630c292b55a3f67b1051ad0a863d48ff40bbccc4a0d5b7e5b72cda22", "created_at": "2026-11-01T19:02:58Z", "updated_at": "2026-11-01T21:32:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes associated with the pathogenesis of gastric cancer by bioinformatics analysis.", "doi": "10.1186/s12920-023-01720-7", "pmid": "38041130", "authors": ["Fatemeh Abdolahi", "Ali Shahraki", "Roghayeh Sheervalilou", "Sedigheh Sadat Mortazavi"], "journal": "BMC medical genomics", "year": 2023, "abstract": "AIM: Gastric cancer (GC) is one of the most diagnosed cancers worldwide. GC is a heterogeneous disease whose pathogenesis has not been entirely understood. Besides, the GC prognosis for patients remains poor. Hence, finding reliable biomarkers and therapeutic targets for GC patients is urgently needed.\nMETHODS: GSE54129 and GSE26942 datasets were downloaded from Gene Expression Omnibus (GEO) database to detect differentially expressed genes (DEGs). Then, gene set enrichment analyses and protein-protein interactions were investigated. Afterward, ten hub genes were identified from the constructed network of DEGs. Then, the expression of hub genes in GC was validated. Performing survival analysis, the prognostic value of each hub gene in GC samples was investigated. Finally, the databases were used to predict microRNAs that could regulate the hub genes. Eventually, top miRNAs with more interactions with the list of hub genes were introduced.\nRESULTS: In total, 203 overlapping DEGs were identified between both datasets. The main enriched KEGG pathway was \"Protein digestion and absorption.\" The most significant identified GO terms included \"primary alcohol metabolic process,\" \"basal part of cell,\" and \"extracellular matrix structural constituent conferring tensile strength.\" Identified hub modules were COL1A1, COL1A2, TIMP1, SPP1, COL5A2, THBS2, COL4A1, MUC6, CXCL8, and BGN. The overexpression of seven hub genes was associated with overall survival. Moreover, among the list of selected miRNAs, hsa-miR-27a-3, hsa-miR-941, hsa-miR-129-2-3p, and hsa-miR-1-3p, were introduced as top miRNAs targeting more than five hub genes.\nCONCLUSIONS: The present study identified ten genes associated with GC, which may help discover novel prognostic and diagnostic biomarkers as well as therapeutic targets for GC. Our results may advance the understanding of GC occurrence and progression.", "claims": [{"id": "claim-method", "statement": "The Kaplan–Meier plotter was applied to examine the correlation between the effect of the key genes and overall survival in GC patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38041130", "locator": "sections[8] \"Survival analysis\" paragraph 2", "quote": "The Kaplan–Meier plotter was applied to examine the correlation between the effect of the key genes and overall survival in GC patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All databases (including NCBI GEO, Veen Diagram maker, etc.) are Freely available on the web. The raw data of this study are obtained from the GEO database (available at https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38041130", "locator": "sections[25] \"notes\" paragraph 1", "quote": "All databases (including NCBI GEO, Veen Diagram maker, etc.) are Freely available on the web. The raw data of this study are obtained from the GEO database (available at https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 203 overlapping differentially expressed genes were identified between the two gastric cancer datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38041130", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In total, 203 overlapping DEGs were identified between both datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 203 overlapping differentially expressed genes were identified between the two gastric cancer datasets.", "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:38041130"], "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:GSE26942"], "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:GSE26942"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38041130", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-023-01720-7", "sha256": "sha256:4f33b3e0af4dc4c1f569aa3f08a3078af85aef9f973bf4a6e14aedfa06568218", "bytes": 34996, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-023-01720-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10690994", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26942", "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=GSE26942", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26942", "version": null, "note": "All databases (including NCBI GEO, Veen Diagram maker, etc.) are Freely available on the web. 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