Exploration of a miRNA-mRNA network shared between acute pancreatitis and Epstein-Barr virus infection by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39546499", "kind": "science-record", "revision": 4, "content_hash": "sha256:97403144d19d46a682bdd62b44b7d53edbd3214bed9f2818a9b3124a5d4580c6", "created_at": "2026-11-01T20:29:48Z", "updated_at": "2026-11-01T22:55:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of a miRNA-mRNA network shared between acute pancreatitis and Epstein-Barr virus infection by integrated bioinformatics analysis.", "doi": "10.1371/journal.pone.0311130", "pmid": "39546499", "authors": ["Xing Wei", "Zhen Weng", "Xia Xu", "Jian Yao"], "journal": "PloS one", "year": 2024, "abstract": "Acute pancreatitis (AP) stands out as a primary cause of hospitalization within gastrointestinal ailments, attributed to diverse factors, including Epstein-Barr virus (EBV) infection. Nevertheless, the common miRNAs and genes shared between AP and EBV infection remain unclear. In the present study, four datasets GSE194331, GSE42455, GSE45918 and GSE109220 were selected and downloaded from the Gene Expression Omnibus (GEO) database. Differential expression analysis was performed to screen for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Target genes of overlapping DEMs were predicted, and intersections with overlapping DEGs were used to construct a miRNA-mRNA network. In addition, the enrichment analysis, drug prediction, diagnostic accuracy assessment, competitive endogenous RNA (ceRNA) network construction, transcription factor (TF)-miRNA-mRNA network construction, and immune cell infiltration analysis were also carried out. We found a total of 111 genes and 8 miRNAs shared between AP and EBV infection. A miRNA-mRNA network was constructed, which comprised 5 miRNAs and 10 genes exhibiting robust diagnostic performance. Histone deacetylase (HDAC) inhibitor was identified as a novel therapeutic intervention from drug prediction analysis. The results of immune cell infiltration analysis revealed that a consistent and significant difference could be found on activated B cell in AP and EBV-infected individuals in comparison to the controls. Taken together, our work, for the first time, revealed a miRNA-mRNA network shared between AP and EBV infection, thereby enriching a deeper comprehension of the intricate molecular mechanisms and potential therapeutic targets entwined in these two pathological conditions.", "claims": [{"id": "claim-method", "statement": "Finally, the DESeq2 (version 1.44.0) package [22], which provides methods to test for differential expression by use of negative binomial generalized linear models on un-normalized RNA-seq counts data, was employed to identify the DEGs between 76 AP patients and 32 healthy controls in the dataset GSE194331. The limma is an R package for the analysis of gene expression data, especially the use of linear models for assessment of differential expression on normalized microarray data, which was used to identify the DEGs across 8 samples before and after acquisition of EBV infection in the dataset GSE45918. Similarly, in the dataset GSE109220, the limma package was used to identify the DEMs between 5 infectious mononucleosis diagnosis samples and 3 healthy controls. 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Similarly, in the dataset GSE109220, the limma package was used to identify the DEMs between 5 infectious mononucleosis diagnosis samples and 3 healthy controls. Within the dataset GSE42455, the limma package was employed for DEMs identification between 10 AP rat models and 5 sham samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets are available from the GEO database (GSE194331, GSE42455, GSE45918 and GSE109220). All relevant data are within the paper and its supporting information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39546499", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "All datasets are available from the GEO database (GSE194331, GSE42455, GSE45918 and GSE109220). All relevant data are within the paper and its supporting information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified a shared miRNA-mRNA network between acute pancreatitis and Epstein-Barr virus infection comprising 5 miRNAs and 10 genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39546499", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A miRNA-mRNA network was constructed, which comprised 5 miRNAs and 10 genes exhibiting robust diagnostic performance."}, {"asset": "source:pmid:39546499", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found a total of 111 genes and 8 miRNAs shared between AP and EBV infection."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified a shared miRNA-mRNA network between acute pancreatitis and Epstein-Barr virus infection comprising 5 miRNAs and 10 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:39546499"], "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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