Identification of key microRNAs and their targets in exosomes of pancreatic cancer using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30278585", "kind": "science-record", "revision": 9, "content_hash": "sha256:5b1c182ff7285a5ba99e731f283b7d8e48d8ef357141b4777549edf7a5955602", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:43:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key microRNAs and their targets in exosomes of pancreatic cancer using bioinformatics analysis.", "doi": "10.1097/MD.0000000000012632", "pmid": "30278585", "authors": ["Xin Zhao", "Yiming Ren", "Naiqiang Cui", "Ximo Wang", "Yunfeng Cui"], "journal": "Medicine", "year": 2018, "abstract": "Pancreatic cancer (PC) is one of the most lethal tumors, due to late diagnosis and limited surgical strategies. It has been reported that serum exosomal microRNAs (S-Exo-miRNAs) play a pivotal role as signaling molecules and serve as noninvasive diagnosis methods for PC. The combination of S-Exo-miRNAs with the corresponding target also plays an important role in the tumor microenvironment.Here we investigated S-Exo-miRNAs involved in PC. The gene expression profile was downloaded from the Gene Expression Omnibus (GEO) database. The analysis was carried out using GEO2R. The targets of differentially expressed serum exosomal miRNAs (DE-S-Exo-miRNAs) were predicted by 4 bioinformatic algorithms (miRanda, miRDB, miRWalk, and Targetscan). Further analysis with gene ontology (GO) and Kyoto Encyclopedia of Genomes pathway (KEGG) enrichment analyses were performed with Cytoscape software version 3.4.0. Subsequently, the interaction regulatory network of target genes was performed with the Search Tool for the Retrieval of Interacting Genes (STRING) database (http://www.string-db.org/) and visualized using Cytoscape software.We downloaded the gene expression profile GSE50632, which was based on an Agilent microarray GPL17660 platform containing 4 eligible samples. In total 467 DE-S-Exo-miRNAs were obtained, including 7 overexpressed miRNAs (1.50%), and 460 remaining underexpressed miRNAs (98.50%). The databases miRWalk, miRDB, miRanda, and TargetScan were used to predict their potential targets, which were subsequently submitted to Cytoscape software version 3.4.0 (www.cytoscape.org). Next the functional and pathway enrichment analysis were used for the KEGG pathway and GO categories analysis. The enrichment analysis identified the genes involved in such processes as developmental and negative regulation of multicellular organismal processes, regulation of anatomical structure morphogenesis, regulation of cell death, apoptotic processes and mitogen-activated protein kinase (MAPK) signaling pathway, transforming growth factor - beta (TGF -β) signaling pathway, cyclic adenosine monophosphate (cAMP) signaling pathway, and the phosphatidylinositol-3 kinases/Akt (PI3K-Akt) signaling pathway. Subsequently according to the protein-protein interaction (PPI) network, the top 10 genes were obtained. The enrichment analyses of the genes involved in a significant module revealed that these genes were related to the TGF-β signaling pathway. After reviewing the literature, we identified the apoptosis genes, and their corresponding miRNAs that have a relationship with apoptosis of the tumor.This analysis provides a comprehensive understanding of the roles of S-Exo-miRNAs and the related targets in the development of PC. Additionally, the present study provides promising candidate targets for early diagnosis and therapeutic intervention. However, these predictions require further experimental validation in future studies.", "claims": [{"id": "claim-method", "statement": "The analysis was carried out using GEO2R, which can perform comparisons on original submitter-supplied processed data tables using the GEO query and limma R packages from the Bioconductor project.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30278585", "locator": "sections[4] \"DE-S-Exo-miRNAs in patients with or without pancreatic adenocarcinoma\" paragraph 2", "quote": "The analysis was carried out using GEO2R, which can perform comparisons on original submitter-supplied processed data tables using the GEO query and limma R packages from the Bioconductor project."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The S-Exo-miRNA profile of GSE50632 was downloaded from the GEO (www.ncbi.nlm.nih.gov/geo/), and the GEO2R method was used to identify DE-Exo-miRNAs in the PC samples compared with the control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30278585", "locator": "sections[10] \"Identification of DE-S-Exo-miRNAs\" paragraph 2", "quote": "The S-Exo-miRNA profile of GSE50632 was downloaded from the GEO (www.ncbi.nlm.nih.gov/geo/), and the GEO2R method was used to identify DE-Exo-miRNAs in the PC samples compared with the control samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30278585"], "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:GSE50632"], "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:GSE50632"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30278585", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000012632", "sha256": "sha256:419fd78dc4b5344bf6e0d4164cc706f5340106d704eba6c36f093f738de7b2d5", "bytes": 34886, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000012632", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6181532", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE50632", "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=GSE50632", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50632", "version": null, "note": "The S-Exo-miRNA profile of GSE50632 was downloaded from the GEO (www.ncbi.nlm.nih.gov/geo/), and the GEO2R method was used to identify DE-Exo-miRNAs in the PC samples compared with the control samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The S-Exo-miRNA profile of GSE50632 was downloaded from the GEO (www.ncbi.nlm.nih.gov/geo/), and the GEO2R method was used to identify DE-Exo-miRNAs in the PC samples compared with the control samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1224991", "GSM1224992", "GSM1224993", "GSM1224994", "GSM1224995", "GSM1224996", "GSM1224997", "GSM1224998", "GSM1224999", "GSM1225000", "GSM1225001", "GSM1225002", "GSM1225003"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "16294;17660", "taxon": "Human alphaherpesvirus 2; Cytomegalovirus; Lymphocryptovirus; Betapolyomavirus macacae; Murid gammaherpesvirus 4; Rattus norvegicus; JC polyomavirus; Betapolyomavirus hominis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Rhadinovirus; Human immunodeficiency virus 1; Merkel cell polyomavirus", "title": "Pancreatic cancer cell exosomal microRNA as diagnostic marker", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30278585:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:102c2bc593df278cd1283b1f484dc1f9c66ba3f180bc1a81776402887c43df9f", "bytes": 197, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "List of differentially expressed exosomal miRNAs.", "structure": {"pmcid": "PMC6181532", "section_index": 10, "section_title": "Identification of DE-S-Exo-miRNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "List of differentially expressed exosomal miRNAs.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30278585:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:36e68ba151162f24b5c3c90c9f974f7013b0cbdfdd139bfe7f3a0398a761b996", "bytes": 238, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T2", "version": null, "note": "Go function annotation of differentially expression exosomal miRNA target genes. 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