Differentially Expressed mRNAs and Their Long Noncoding RNA Regulatory Network with Helicobacter pylori-Associated Diseases including Atrophic Gastritis and Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33282942", "kind": "science-record", "revision": 6, "content_hash": "sha256:a25ea91aa19baea92fdf7698793d2058bc997be20e35f7fdd6810ce1af81051a", "created_at": "2026-11-01T15:41:18Z", "updated_at": "2026-11-01T21:24:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differentially Expressed mRNAs and Their Long Noncoding RNA Regulatory Network with Helicobacter pylori-Associated Diseases including Atrophic Gastritis and Gastric Cancer.", "doi": "10.1155/2020/3012193", "pmid": "33282942", "authors": ["Songyi Liu", "Honghao Yin", "Shuwen Zheng", "Aining Chu", "Yizhi Li", "Chengzhong Xing", "Yuan Yuan", "Yuehua Gong"], "journal": "BioMed research international", "year": 2020, "abstract": "BACKGROUND: Helicobacter pylori (Hp) infection is the strongest risk factor for gastric cancer (GC). However, the mechanisms of Hp-associated GC remain to be explored.\nMETHODS: The gene expression profiling (GSE111762) data were downloaded from the GEO database. Differentially expressed genes (DEGs) between normal samples (NO) and Hp-atrophic gastritis (GA) or Hp-GA and Hp-GC were identified by GEO2R. Gene Ontology and pathway enrichment analysis were performed using the DAVID database. lncRNA-TF-mRNA and ceRNA regulation networks were constructed using Cytoscape. The cross-networks were obtained by overlapping molecules of the above two networks. GSE27411 and GSE116312 datasets were employed for validation.\nRESULTS: DEGs between NO and Hp-GA are linked to the activity of inward rectifying potassium channels, digestion, etc. DEGs between Hp-GA and Hp-GC were associated with digestion, positive regulation of cell proliferation, etc. According to the lncRNA-TF-mRNA network, 63 lncRNAs, 12 TFs, and 209 mRNAs were involved in Hp-GA while 16 lncRNAs, 11 TFs, and 92 mRNAs were contained in the Hp-GC network. In terms of the ceRNA network, 120 mRNAs, 18 miRNAs, and 27 lncRNAs were shown in Hp-GA while 72 mRNAs, 8 miRNAs, and 1 lncRNA were included in the Hp-GC network. In the cross-network, we found that immune regulation and differentiation regulation were important in the process of NO-GA. Neuroendocrine regulation was mainly related to the process of GA-GC. In the end, we verified that CDX2 plays an important role in the pathological process of NO to Hp-GA. Comparing Hp-GA with Hp-GC, DEGs (FPR1, TFF2, GAST, SST, FUT9, and SHH), TF, and GATA5 were of great significance.\nCONCLUSIONS: We identified the DEGs, and their lncRNA regulatory network of Hp-associated diseases might provide insights into the mechanism between Hp infection and GC. Furthermore, in-depth studies of the molecules might be useful to explore the multistep process of gastric diseases.", "claims": [{"id": "claim-method", "statement": "Coexpression relationships between the lncRNAs and mRNAs were estimated by Spearman's correlation test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33282942", "locator": "sections[9] \"2.7. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["spearman_rho"], "assets": ["source:pmid:33282942", "data:geo:GSE111762", "asset:table:pmid:33282942:1", "asset:table:pmid:33282942:2", "asset:table:pmid:33282942:3", "asset:table:pmid:33282942:4", "asset:table:pmid:33282942:5", "asset:table:pmid:33282942:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE111762"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39106, "completion_tokens": 1295, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33282942", "type": "paper", "label": "pmid:33282942"}, {"id": "source:pmid:33282942", "type": "manuscript", "label": "PMID 33282942 full text"}, {"id": "data:geo:GSE111762", "type": "dataset", "label": "GEO GSE111762"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33282942", "type": "paper", "label": "pmid:33282942"}, {"id": "source:pmid:33282942", "type": "manuscript", "label": "PMID 33282942 full text"}, {"id": "data:geo:GSE111762", "type": "dataset", "label": "GEO GSE111762"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33282942", "type": "extraction", "used": ["source:pmid:33282942"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE111762", "type": "accession_resolution", "used": ["data:geo:GSE111762"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33282942", "parent_hash": "sha256:590586b11fbcd04bf1b0d1d4d73433d589164ba3fb929d182f558ead71b61c49", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE111762 licence not read", "asset:data:geo:GSE111762 not downloaded", "asset:data:geo:GSE116312 licence not read", "asset:data:geo:GSE116312 not downloaded", "asset:data:geo:GSE27411 licence not read", "asset:data:geo:GSE27411 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["spearman_rho"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Coexpression relationships between the lncRNAs and mRNAs were estimated by Spearman's correlation test."], "order_basis": "analysis_only", "id": "assay:1"}]}