Exploration of the link between COVID-19 and gastric cancer from the perspective of bioinformatics and systems biology.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39371335", "kind": "science-record", "revision": 4, "content_hash": "sha256:194fac560e9c3a22ac29c856aa5825d858f03f2370e57c2e45f0eb455f003b00", "created_at": "2026-11-01T20:29:34Z", "updated_at": "2026-11-01T22:55:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of the link between COVID-19 and gastric cancer from the perspective of bioinformatics and systems biology.", "doi": "10.3389/fmed.2024.1428973", "pmid": "39371335", "authors": ["Xiao Ma", "Tengda Huang", "Xiaoquan Li", "Xinyi Zhou", "Hongyuan Pan", "Ao Du", "Yong Zeng", "Kefei Yuan", "Zhen Wang"], "journal": "Frontiers in medicine", "year": 2024, "abstract": "Background: Coronavirus disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has caused a global pandemic. Gastric cancer (GC) poses a great threat to people's health, which is a high-risk factor for COVID-19. Previous studies have found some associations between GC and COVID-19, whereas the underlying molecular mechanisms are not well understood.\nMethods: We employed bioinformatics and systems biology to explore these links between GC and COVID-19. Gene expression profiles of COVID-19 (GSE196822) and GC (GSE179252) were obtained from the Gene Expression Omnibus (GEO) database. After identifying the shared differentially expressed genes (DEGs) for GC and COVID-19, functional annotation, protein-protein interaction (PPI) network, hub genes, transcriptional regulatory networks and candidate drugs were analyzed.\nResults: We identified 209 shared DEGs between COVID-19 and GC. Functional analyses highlighted immune-related pathways as key players in both diseases. Ten hub genes (CDK1, KIF20A, TPX2, UBE2C, HJURP, CENPA, PLK1, MKI67, IFI6, IFIT2) were identified. The transcription factor/gene and miRNA/gene interaction networks identified 38 transcription factors (TFs) and 234 miRNAs. More importantly, we identified ten potential therapeutic agents, including ciclopirox, resveratrol, etoposide, methotrexate, trifluridine, enterolactone, troglitazone, calcitriol, dasatinib and deferoxamine, some of which have been reported to improve and treat GC and COVID-19.\nConclusion: This research offer valuable insights into the molecular interplay between COVID-19 and GC, potentially guiding future therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "The DEseq2 package (29) of R software (version 4.2.1) was used to identify the DEGs with false-discovery rate (FDR) < 0.05 and | log2 Fold Change| > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39371335", "locator": "sections[4] \"2.2 Identification of DEGs and common DEGs between COVID-19 and gastric cancer\" paragraph 2", "quote": "The DEseq2 package (29) of R software (version 4.2.1) was used to identify the DEGs with false-discovery rate (FDR) < 0.05 and | log2 Fold Change| > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39371335", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 209 shared DEGs between COVID-19 and GC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39371335", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 209 shared DEGs between COVID-19 and GC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 209 shared DEGs between COVID-19 and GC.", "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:39371335"], "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:GSE179252"], "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:GSE179252"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39371335", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2024.1428973", "sha256": 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inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5412496", "GSM5412497", "GSM5412498", "GSM5412499", "GSM5412500", "GSM5412501", "GSM5412502", "GSM5412503", "GSM5412504", "GSM5412505", "GSM5412506", "GSM5412507", "GSM5412508", "GSM5412509", "GSM5412510", "GSM5412511", "GSM5412512", "GSM5412513", "GSM5412514", "GSM5412515", "GSM5412516", "GSM5412517", "GSM5412518", "GSM5412519", "GSM5412520", "GSM5412521", "GSM5412522", "GSM5412523", "GSM5412524", "GSM5412525", "GSM5412526", "GSM5412527", "GSM5412528", "GSM5412529", "GSM5412530", "GSM5412531", "GSM5412532", "GSM5412533", "GSM5412534", "GSM5412535", "GSM5412536", "GSM5412537", 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