Identification of potential hub genes associated with the pathogenesis and prognosis of pancreatic duct adenocarcinoma using bioinformatics meta-analysis of multi-platform datasets.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31807183", "kind": "science-record", "revision": 5, "content_hash": "sha256:068eb22cfebbf5fc43950727b07814df1cfaf0a0dfae90adde074e974be01d27", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:01:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential hub genes associated with the pathogenesis and prognosis of pancreatic duct adenocarcinoma using bioinformatics meta-analysis of multi-platform datasets.", "doi": "10.3892/ol.2019.11042", "pmid": "31807183", "authors": ["Yufan Ma", "Yinquan Pu", "Li Peng", "Xujuan Luo", "Jin Xu", "Yan Peng", "Xiaowei Tang"], "journal": "Oncology letters", "year": 2019, "abstract": "Pancreatic duct adenocarcinoma (PDAC) is a highly malignant type of cancer with a low five-year survival rate. Gene alterations are crucial to the molecular pathogenesis of PDAC. Therefore, the present study analyzed gene expression profiles to reveal genes involved in the tumorigenesis of PDAC. A total of eight gene expression profiles (GSE15471, GSE16515, GSE41368, GSE62165, GSE62452, GSE71729, GSE71989 and GSE91035) and a PDAC dataset were acquired from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) database, respectively. Differentially expressed genes (DEGs) were screened using functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) network construction. A Cox proportional hazards model was then constructed and used to analyze the data. A total of 136 DEGs (67 up- and 69 downregulated genes) were identified between PDAC tissues and normal tissues. The 'extracellular matrix-related' genes were the most enriched in the GO term analysis. 'Pancreatic secretion', 'phosphoinositide-3-kinase-protein kinase B/Akt (PI3K-Akt) signaling pathway', 'protein digestion and absorption' and 'ECM-receptor interaction' were the most enriched categories in KEGG pathway analysis. Following PPI network construction, the 10 most significant genes [albumin, epidermal growth factor, matrix metalloproteinase (MMP) 9, epidermal growth factor receptor, fibronectin 1, MMP1, plasminogen activator inhibitor-1, tissue inhibitor of metalloproteinase 1, plasminogen activator urokinase (PLAU) and PLAU receptor) exhibiting a high degree of connectivity, were identified as the hub genes likely to be associated with the pathogenesis of PDAC. In addition, a prognostic predictive system for PDAC, composed of five genes (laminin subunit γ 2, laminin subunit β 3, serpin family B member 5, amphiregulin and secreted frizzled related protein 4), was constructed. This was validated in the GSE62452 dataset (using 66 PDAC samples with outcome data) and TCGA PDAC dataset (using 146 PDAC samples with outcome data). In conclusion, the present study revealed potential hub genes involved in PDAC progression, providing directive significance for individualized clinical decision-making and molecular-targeting therapy in patients with PDAC.", "claims": [{"id": "claim-method", "statement": "The RRA package was used for gene integration analysis of the DEGs in the eight datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31807183", "locator": "sections[5] \"Data pre-processing and DEG analysis\" paragraph 2", "quote": "The RRA package was used for gene integration analysis of the DEGs in the eight datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A total of 8 gene expression profiles [GSE15471 (10), GSE16515 (11), GSE41368 (12), GSE62165 (13), GSE62452 (14), GSE71729 (15), GSE71989 (16) and GSE91035 (17)] from two platforms (Affymetrix and Agilent) were retrieved from the GEO (http://www.ncbi.nlm.nih.gov/geo/) database, using the keywords ‘pancreatic ductal adenocarcinoma’, ‘Homo sapiens’ and ‘microarray’.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31807183", "locator": "sections[4] \"Selection and retrieval of microarray datasets\" paragraph 2", "quote": "A total of 8 gene expression profiles [GSE15471 (10), GSE16515 (11), GSE41368 (12), GSE62165 (13), GSE62452 (14), GSE71729 (15), GSE71989 (16) and GSE91035 (17)] from two platforms (Affymetrix and Agilent) were retrieved from the GEO (http://www.ncbi.nlm.nih.gov/geo/) database, using the keywords ‘pancreatic ductal adenocarcinoma’, ‘Homo sapiens’ and ‘microarray’."}], "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:31807183"], "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:GSE15471"], "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:GSE15471"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31807183", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2019.11042", "sha256": 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