Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31311829", "kind": "science-record", "revision": 8, "content_hash": "sha256:47dd7bf73910e30b2f006d336321b2050b05e956e1af1d2b2a8570abc4eb5a9b", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T22:00:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis.", "doi": "10.1042/BSR20190625", "pmid": "31311829", "authors": ["Jun Zhou", "Xiaoliang Hui", "Ying Mao", "Liya Fan"], "journal": "Bioscience reports", "year": 2019, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is a class of the commonest malignant carcinomas. The present study aimed to elucidate the potential biomarker and prognostic targets in PDAC. The array data of GSE41368, GSE43795, GSE55643, and GSE41369 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and differentially expressed microRNAs (DEmiRNAs) in PDAC were obtained by using GEO2R, and overlapped DEGs were acquired with Venn Diagrams. Functional enrichment analysis of overlapped DEGs and DEmiRNAs was conducted with Metascape and FunRich, respectively. The protein-protein interaction (PPI) network of overlapped DEGs was constructed by STRING and visualized with Cytoscape. Overall survival (OS) of DEmiRNAs and hub genes were investigated by Kaplan-Meier (KM) plotter (KM plotter). Transcriptional data and correlation analyses among hub genes were verified through GEPIA and Human Protein Atlas (HPA). Additionally, miRNA targets were searched using miRTarBase, then miRNA-DEG regulatory network was visualized with Cytoscape. A total of 32 DEmiRNAs and 150 overlapped DEGs were identified, and Metascape showed that DEGs were significantly enriched in cellular chemical homeostasis and pathways in cancer, while DEmiRNAs were mainly enriched in signal transduction and Glypican pathway. Moreover, seven hub genes with a high degree, namely, V-myc avian myelocytomatosis viral oncogene homolog (MYC), solute carrier family 2 member 1 (SLC2A1), PKM, plasminogen activator, urokinase (PLAU), peroxisome proliferator activated receptor γ (PPARG), MET proto-oncogene, receptor tyrosine kinase (MET), and integrin subunit α 3 (ITGA3), were identified and found to be up-regulated between PDAC and normal tissues. miR-135b, miR-221, miR-21, miR-27a, miR-199b-5p, miR-143, miR-196a, miR-655, miR-455-3p, miR-744 and hub genes predicted poor OS of PDAC. An integrative bioinformatics analysis identified several hub genes that may serve as potential biomarkers or targets for early diagnosis and precision target treatment of PDAC.", "claims": [{"id": "claim-method", "statement": "We used the KM plotter (http://kmplot.com/analysis/) [26] to perform an OS analysis of the DEmiRNAs and hub genes in 178 and 177 patients with PDAC, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31311829", "locator": "sections[7] \"Survival analysis of the DEmiRNAs and hub genes\" paragraph 2", "quote": "We used the KM plotter (http://kmplot.com/analysis/) [26] to perform an OS analysis of the DEmiRNAs and hub genes in 178 and 177 patients with PDAC, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In the present paper, we employed mRNA microarray data of GSE41368 [20], GSE43795 [21], and GSE55643 [22] and miRNA microarray data of GSE41369 [20] to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) and to explore the potential therapeutic targets as well as the prognostic value of PDAC. The gene expression profile data (GSE41368, GSE43795, GSE55643, and GSE41369) of PDAC were downloaded from the public GEO database", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31311829", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "In the present paper, we employed mRNA microarray data of GSE41368 [20], GSE43795 [21], and GSE55643 [22] and miRNA microarray data of GSE41369 [20] to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) and to explore the potential therapeutic targets as well as the prognostic value of PDAC."}, {"asset": "source:pmid:31311829", "locator": "sections[3] \"PDAC dataset preprocessing\" paragraph 2", "quote": "The gene expression profile data (GSE41368, GSE43795, GSE55643, and GSE41369) of PDAC were downloaded from the public GEO database"}], "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:31311829"], "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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The gene expression profile data (GSE41368, GSE43795, GSE55643, and GSE41369) of PDAC were downloaded from the public GEO database", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the present paper, we employed mRNA microarray data of GSE41368 [20], GSE43795 [21], and GSE55643 [22] and miRNA microarray data of GSE41369 [20] to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) and to explore the potential therapeutic targets as well as the prognostic value of PDAC. 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The gene expression profile data (GSE41368, GSE43795, GSE55643, and GSE41369) of PDAC were downloaded from the public GEO database", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the present paper, we employed mRNA microarray data of GSE41368 [20], GSE43795 [21], and GSE55643 [22] and miRNA microarray data of GSE41369 [20] to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) and to explore the potential therapeutic targets as well as the prognostic value of PDAC. 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The gene expression profile data (GSE41368, GSE43795, GSE55643, and GSE41369) of PDAC were downloaded from the public GEO database", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the present paper, we employed mRNA microarray data of GSE41368 [20], GSE43795 [21], and GSE55643 [22] and miRNA microarray data of GSE41369 [20] to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) and to explore the potential therapeutic targets as well as the prognostic value of PDAC. 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The gene expression profile data (GSE41368, GSE43795, GSE55643, and GSE41369) of PDAC were downloaded from the public GEO database", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In the present paper, we employed mRNA microarray data of GSE41368 [20], GSE43795 [21], and GSE55643 [22] and miRNA microarray data of GSE41369 [20] to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) and to explore the potential therapeutic targets as well as the prognostic value of PDAC. 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characteristics of the gene expression profiling studies", "rows": [["PMID", "Record", "mRNA/miRNA", "Tissue", "Normal", "Tumor", "Platfrom", "Reference"], ["24120476", "GSE41368", "mRNA", "PDAC", "6", "6", "GPL6244-[HuGene-1_0-st]Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]", "Frampton et al., 2014"], ["24072181", "GSE43795", "mRNA", "PDAC", "6", "6", "GPL10558-Illumina HumanHT-12 V4.0 expression beadchip", "Kim et al., 2014"], ["25415223", "GSE55643", "mRNA", "PDAC", "8", "45", "GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)", "Jamieson et al., 2014"], ["24120476", "GSE41369", "miRNA", "PDAC", "9", "9", "GPL16142 NanoString nCounter Human miRNA assay (v1)", "Frampton et al., 2014"]], "row_count": 5, "column_count": 8, "numeric_cells": 24, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31311829:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", 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