Identification and Interaction Analysis of Molecular Markers in Pancreatic Ductal Adenocarcinoma by Bioinformatics and Next-Generation Sequencing Data Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37529485", "kind": "science-record", "revision": 5, "content_hash": "sha256:1adae71a30533c4efd0ceedde7ab2f0dd4afa2974a621c16d615356831703ce0", "created_at": "2026-11-01T19:02:18Z", "updated_at": "2026-11-01T22:52:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Interaction Analysis of Molecular Markers in Pancreatic Ductal Adenocarcinoma by Bioinformatics and Next-Generation Sequencing Data Analysis.", "doi": "10.1177/11779322231186719", "pmid": "37529485", "authors": ["Muttanagouda Giriyappagoudar", "Basavaraj Vastrad", "Rajeshwari Horakeri", "Chanabasayya Vastrad"], "journal": "Bioinformatics and biology insights", "year": 2023, "abstract": "Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the molecular pathogenesis, but the molecular mechanisms of PDAC are still not well understood. The purpose of this study is to further explore the molecular mechanism of PDAC through integrated bioinformatics analysis.\nMethods: To identify the candidate genes in the carcinogenesis and progression of PDAC, next-generation sequencing (NGS) data set GSE133684 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and Gene Ontology (GO) and pathway enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using Integrated Interactions Database (IID) interactome database and Cytoscape. Subsequently, miRNA-DEG regulatory network and TF-DEG regulatory network were constructed using miRNet database, NetworkAnalyst database, and Cytoscape software. The expression levels of hub genes were validated based on Kaplan-Meier analysis, expression analysis, stage analysis, mutation analysis, protein expression analysis, immune infiltration analysis, and receiver operating characteristic (ROC) curve analysis.\nResults: A total of 463 DEGs were identified, consisting of 232 upregulated genes and 233 downregulated genes. The enriched GO terms and pathways of the DEGs include vesicle organization, secretory vesicle, protein dimerization activity, lymphocyte activation, cell surface, transferase activity, transferring phosphorus-containing groups, hemostasis, and adaptive immune system. Four hub genes (namely, cathepsin B [CCNB1], four-and-a-half LIM domains 2 (FHL2), major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) and tubulin beta 1 class VI (TUBB1)) were obtained via taking interaction of different analysis results.\nConclusions: On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of PDAC and provide potential targets for further investigation.", "claims": [{"id": "claim-method", "statement": "The limma package of R language was used for DEGs between PDAC and normal control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37529485", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The limma package of R language was used for DEGs between PDAC and normal control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data sets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/) repository ([GSE133684] [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133684]).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37529485", "locator": "sections[19] \"fn-group\" paragraph 1", "quote": "The data sets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/) repository ([GSE133684] [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133684])."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The limma analysis of GSE133684 identified 463 DEGs, including 232 upregulated and 231 downregulated genes in PDAC samples compared with normal controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37529485", "locator": "sections[11] \"Identification of DEGs\" paragraph 2", "quote": "We analyzed the DEGs of GSE133684 by using the limma package."}, {"asset": "source:pmid:37529485", "locator": "sections[11] \"Identification of DEGs\" paragraph 2", "quote": "We screened 463 DEGs, including 232 upregulated genes and 231 downregulated genes in PDAC samples compared with normal control samples, which are listed in Table 1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The limma analysis of GSE133684 identified 463 DEGs, including 232 upregulated and 231 downregulated genes in PDAC samples compared with normal controls.", "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:37529485"], "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:GSE133684"], "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:GSE133684"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37529485", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/11779322231186719", "sha256": 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