Identification of key regulators of pancreatic ductal adenocarcinoma using bioinformatics analysis of microarray data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30633213", "kind": "science-record", "revision": 8, "content_hash": "sha256:007ddb03c22679ba82faaa08a6eb52f5d553d6ca8d356f8a500ac30b52229bc2", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T22:00:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key regulators of pancreatic ductal adenocarcinoma using bioinformatics analysis of microarray data.", "doi": "10.1097/MD.0000000000014074", "pmid": "30633213", "authors": ["Nan Li", "Xin Zhao", "Shengyi You"], "journal": "Medicine", "year": 2019, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal forms of cancer, and its etiology remains largely unknown. This study aimed to screen a panel of key genes and to identify their potential impact on the molecular pathways associated with the development of PDAC. Four gene expression profiles, GSE28735, GSE15471, GSE102238, and GSE43795, were downloaded from the Gene Expression Omnibus (GEO) database. The intersection of the differentially expressed genes (DEGs) in each dataset was obtained using Venn analysis. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis were subsequently carried out. To screen for hub genes, a protein-protein interaction (PPI) network was constructed.The intersection of the DEGs revealed 7 upregulated and 9 downregulated genes. Upon relaxation of the selection criteria, 58 upregulated and 32 downregulated DEGs were identified. The top 5 biological processes identified by GO analysis involved peptide cross-linking, extracellular matrix (ECM) disassembly, regulation of the fibroblast growth factor receptor signaling pathway, mesoderm morphogenesis, and lipid digestion. The results of KEGG analysis revealed that the DEGs were significantly enriched in pathways involved in protein digestion and absorption, ECM-receptor interaction, pancreatic secretion, and fat digestion and absorption. The top ten hub genes were identified based on the PPI network.In conclusion, the identified hub genes may contribute to the elucidation of the underlying molecular mechanisms of PDAC and serve as promising candidates that can be utilized for the early diagnosis and prognostic prediction of PDAC. However, further experimental validation is required to confirm these results.", "claims": [{"id": "claim-method", "statement": "The P-values, which were used to assess the significance of the differences, were calculated using a paired samples t test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30633213", "locator": "sections[4] \"Data preprocessing and DEG identification\" paragraph 3", "quote": "The P-values, which were used to assess the significance of the differences, were calculated using a paired samples t test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray gene expression profile GSE28735,[5,7] GSE15471,[13] GSE102238, and GSE43795[14] related to PDAC were downloaded from GEO (http://www.ncbi.nlm.nih.gov/geo/), which were based on the platform of GPL6244 Affymetrix Human Gene 1.0 ST Array, GPL570 Affymetrix Human Genome U133 Plus 2.0 Array, GPL19072 Agilent-052909 CBC_lncRNAmRNA_V3, and GPL10558 Illumina HumanHT-12 V4.0 expression beadchip, respectively. GSE28735 dataset contained 45 PADC tumors and 45 matching normal pancreatic tissue samples; GSE15471 contained 39 PDAC samples and 39 normal controls; GSE102238 contained 22 PDAC samples and 22 normal controls; and GSE43795 contained 6 PDAC samples and 5 normal controls were selected for subsequent analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30633213", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "The microarray gene expression profile GSE28735,[5,7] GSE15471,[13] GSE102238, and GSE43795[14] related to PDAC were downloaded from GEO (http://www.ncbi.nlm.nih.gov/geo/), which were based on the platform of GPL6244 Affymetrix Human Gene 1.0 ST Array, GPL570 Affymetrix Human Genome U133 Plus 2.0 Array, GPL19072 Agilent-052909 CBC_lncRNAmRNA_V3, and GPL10558 Illumina HumanHT-12 V4.0 expression beadchip, respectively. GSE28735 dataset contained 45 PADC tumors and 45 matching normal pancreatic tissue samples; GSE15471 contained 39 PDAC samples and 39 normal controls; GSE102238 contained 22 PDAC samples and 22 normal controls; and GSE43795 contained 6 PDAC samples and 5 normal controls were selected for subsequent analyses."}], "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:30633213"], "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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GSE28735 dataset contained 45 PADC tumors and 45 matching normal pancreatic tissue samples; GSE15471 contained 39 PDAC samples and 39 normal controls; GSE102238 contained 22 PDAC samples and 22 normal controls; and GSE43795 contained 6 PDAC samples and 5 normal controls were selected for subsequent analyses.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray gene expression profile GSE28735,[5,7] GSE15471,[13] GSE102238, and GSE43795[14] related to PDAC were downloaded from GEO (http://www.ncbi.nlm.nih.gov/geo/), which were based on the platform of GPL6244 Affymetrix Human Gene 1.0 ST Array, GPL570 Affymetrix Human Genome U133 Plus 2.0 Array, GPL19072 Agilent-052909 CBC_lncRNAmRNA_V3, and GPL10558 Illumina HumanHT-12 V4.0 expression beadchip, respectively. GSE28735 dataset contained 45 PADC tumors and 45 matching normal pancreatic tissue samples; GSE15471 contained 39 PDAC samples and 39 normal controls; GSE102238 contained 22 PDAC samples and 22 normal controls; and GSE43795 contained 6 PDAC samples and 5 normal controls were selected for subsequent analyses.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM711904", "GSM711905", "GSM711906", "GSM711907", "GSM711908", "GSM711909", "GSM711910", "GSM711911", "GSM711912", "GSM711913", "GSM711914", "GSM711915", "GSM711916", "GSM711917", "GSM711918", "GSM711919", "GSM711920", "GSM711921", "GSM711922", "GSM711923", "GSM711924", "GSM711925", "GSM711926", "GSM711927", "GSM711928", "GSM711929", "GSM711930", "GSM711931", "GSM711932", "GSM711933", "GSM711934", "GSM711935", "GSM711936", "GSM711937", "GSM711938", "GSM711939", "GSM711940", "GSM711941", "GSM711942", "GSM711943", "GSM711944", "GSM711945", "GSM711946", "GSM711947", "GSM711948", "GSM711949", "GSM711950", "GSM711951", "GSM711952", "GSM711953", "GSM711954", "GSM711955", "GSM711956", "GSM711957", "GSM711958", "GSM711959", "GSM711960", "GSM711961", "GSM711962", "GSM711963", "GSM711964", "GSM711965", "GSM711966", "GSM711967", "GSM711968", "GSM711969", "GSM711970", "GSM711971", "GSM711972", "GSM711973", "GSM711974", "GSM711975", "GSM711976", "GSM711977", "GSM711978", "GSM711979", "GSM711980", "GSM711981", "GSM711982", "GSM711983", "GSM711984", "GSM711985", "GSM711986", "GSM711987", "GSM711988", "GSM711989", "GSM711990", "GSM711991", "GSM711992", "GSM711993"], "sample_count": 90, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues from 45 patients with pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE43795", "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=GSE43795", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43795", "version": null, "note": "The microarray gene expression profile GSE28735,[5,7] GSE15471,[13] GSE102238, and GSE43795[14] related to PDAC were downloaded from GEO (http://www.ncbi.nlm.nih.gov/geo/), which were based on the platform of GPL6244 Affymetrix Human Gene 1.0 ST Array, GPL570 Affymetrix Human Genome U133 Plus 2.0 Array, GPL19072 Agilent-052909 CBC_lncRNAmRNA_V3, and GPL10558 Illumina HumanHT-12 V4.0 expression beadchip, respectively. 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