Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32587798", "kind": "science-record", "revision": 7, "content_hash": "sha256:a67ad98bb545f17969ffb95745210457f79a44515fec35a45eca42f7651f2faa", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T22:01:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis.", "doi": "10.7717/peerj.9301", "pmid": "32587798", "authors": ["Dandan Jin", "Yujie Jiao", "Jie Ji", "Wei Jiang", "Wenkai Ni", "Yingcheng Wu", "Runzhou Ni", "Cuihua Lu", "Lishuai Qu", "Hongbing Ni", "Jinxia Liu", "Weisong Xu", "MingBing Xiao"], "journal": "PeerJ", "year": 2020, "abstract": "BACKGROUND: Pancreatic cancer is one of the most common malignant cancers worldwide. Currently, the pathogenesis of pancreatic cancer remains unclear; thus, it is necessary to explore its precise molecular mechanisms.\nMETHODS: To identify candidate genes involved in the tumorigenesis and proliferation of pancreatic cancer, the microarray datasets GSE32676, GSE15471 and GSE71989 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between Pancreatic ductal adenocarcinoma (PDAC) and nonmalignant samples were screened by GEO2R. The Database for Annotation Visualization and Integrated Discovery (DAVID) online tool was used to obtain a synthetic set of functional annotation information for the DEGs. A PPI network of the DEGs was established using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and a combination of more than 0.4 was considered statistically significant for the PPI. Subsequently, we visualized the PPI network using Cytoscape. Functional module analysis was then performed using Molecular Complex Detection (MCODE). Genes with a degree ≥10 were chosen as hub genes, and pathways of the hub genes were visualized using ClueGO and CluePedia. Additionally, GenCLiP 2.0 was used to explore interactions of hub genes. The Literature Mining Gene Networks module was applied to explore the cocitation of hub genes. The Cytoscape plugin iRegulon was employed to analyze transcription factors regulating the hub genes. Furthermore, the expression levels of the 13 hub genes in pancreatic cancer tissues and normal samples were validated using the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Moreover, overall survival and disease-free survival analyses according to the expression of hub genes were performed using Kaplan-Meier curve analysis in the cBioPortal online platform. The relationship between expression level and tumor grade was analyzed using the online database Oncomine. Lastly, the eight snap-frozen tumorous and adjacent noncancerous adjacent tissues of pancreatic cancer patients used to detect the CDK1 and CEP55 protein levels by western blot.\nCONCLUSIONS: Altogether, the DEGs and hub genes identified in this work can help uncover the molecular mechanisms underlying the tumorigenesis of pancreatic cancer and provide potential targets for the diagnosis and treatment of this disease.", "claims": [{"id": "claim-method", "statement": "DEGs between PDAC and nonmalignant samples were screened by GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) (Shao et al., 2018), which is an online tool that can be used to compare two or more datasets in a GEO series to identify DEGs according to experimental conditions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32587798", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "DEGs between PDAC and nonmalignant samples were screened by GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) (Shao et al., 2018), which is an online tool that can be used to compare two or more datasets in a GEO series to identify DEGs according to experimental conditions."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The microarray datasets are available at Gene Expression Omnibus (GEO): GSE32676, GSE15471 and GSE71989.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32587798", "locator": "sections[31] \"Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:The microarray datasets are available at Gene Expression Omnibus (GEO): GSE32676, GSE15471 and GSE71989."}], "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:32587798"], "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:32587798", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.9301", "sha256": "sha256:2b54ded6e9d51a394729609ddb563ee6092664c1f9e834243b82c1818734b719", "bytes": 50172, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.9301", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7301898", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15471", "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=GSE15471", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15471", "version": null, "note": "The following information was supplied regarding data availability:The microarray datasets are available at Gene Expression Omnibus (GEO): GSE32676, GSE15471 and GSE71989.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The microarray datasets are available at Gene Expression Omnibus (GEO): GSE32676, GSE15471 and GSE71989.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM388076", "GSM388077", "GSM388078", "GSM388079", "GSM388080", "GSM388081", "GSM388082", "GSM388083", "GSM388084", "GSM388085", "GSM388086", "GSM388087", "GSM388088", "GSM388089", "GSM388090", "GSM388091", "GSM388092", "GSM388093", "GSM388094", "GSM388095", "GSM388096", "GSM388097", "GSM388098", "GSM388099", "GSM388100", "GSM388101", "GSM388102", "GSM388103", "GSM388104", "GSM388105", "GSM388106", "GSM388107", "GSM388108", "GSM388109", "GSM388110", "GSM388111", "GSM388112", "GSM388113", "GSM388114", "GSM388115", "GSM388116", "GSM388117", "GSM388118", "GSM388119", "GSM388120", "GSM388121", "GSM388122", 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Involving in chromosome condensation, chromatid separation, and the relief of torsional stress."], ["2", "CDK1", "Cyclin dependent kinase 1", "Essential for G1/S and G2/M phase transitions of eukaryotic cell cycle and mitotic cyclins."], ["3", "RRM2", "Ribonucleotide reductase regulatory subunit M2", "Catalyzing the formation of deoxyribonucleotides from ribonucleotides."], ["4", "PRC1", "Protein regulator of cytokinesis 1", "A substrate of several CDKs and necessary for polarizing parallel microtubules and concentrating the factors responsible for contractile ring assembly."], ["5", "NEK2", "NIMA related kinase 2", "A serine/threonine-protein kinase that is involved in mitotic regulation."], ["6", "ZWINT", "ZW10 interacting kinetochore protein", "Clearly involved in kinetochore function."], ["7", "DTL", "Denticleless E3 ubiquitin protein ligase homolog", "Cellular response to DNA damage stimulus."], ["8", "MELK", "Maternal embryonic leucine zipper kinase", "G2/M transition of mitotic cell cycle apoptotic process."], ["9", "CENPF", "Centromere protein F", "Associating with the centromere-kinetochore complex and playing a role in chromosome segregation during mitotis."], ["10", "CEP55", "Centrosomal protein 55", "Cranial skeletal system development and establishment of protein localization."], ["11", "ANLN", "Anillin actin binding protein", "An actin-binding protein that plays a role in cell growth and migration, and in cytokinesis."], ["12", "ASPM", "Abnormal spindle microtubule assembly", "Essential for normal mitotic spindle function in embryonic neuroblasts and regulating neurogenesis."], ["13", "ECT2", "Epithelial cell transforming 2", "A guanine nucleotide exchange factor and transforming protein that is related to Rho-specific exchange factors and yeast cell cycle regulators."]], "row_count": 14, "column_count": 4, "numeric_cells": 20, "header_rows": 1, "locator": "section[16]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:32587798:2", "role": "table", 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["GO:0007160", "Cell–matrix adhesion", "8", "3.55E−05"], ["GO:0022617", "Extracellular matrix disassembly", "7", "1.20E−04"], ["GO:0048333", "Mesodermal cell differentiation", "4", "1.58E−04"], ["GO:0031581", "Hemidesmosome assembly", "4", "2.10E−04"], ["GO:0090004", "Positive regulation of establishment of protein localization to plasma membrane", "5", "2.26E−04"], ["GO:0007155", "Cell adhesion", "15", "2.45E−04"], ["GO:0007229", "Integrin-mediated signaling pathway", "7", "5.08E−04"], ["GO-CC Terms", "", "", ""], ["GO:0070062", "Extracellular exosome", "63", "1.50E−10"], ["GO:0005925", "Focal adhesion", "16", "7.65E−06"], ["GO:0005913", "Cell–cell adherens junction", "14", "1.91E−05"], ["GO:0005615", "Extracellular space", "28", "3.05E−04"], ["GO:0005886", "Plasma membrane", "61", "5.23E−04"], ["GO:0005737", "Cytoplasm", "72", "9.52E−04"], ["GO:0009986", "Cell surface", "15", "9.53E−04"], ["GO-MF Terms", "", "", ""], ["GO:0098641", "Cadherin binding involved in cell–cell adhesion", "13", "3.05E−05"], ["GO:0042803", "Protein homodimerization activity", "18", "8.70E−04"], ["GO:0005509", "Calcium ion binding", "16", "0.004808"], ["GO:0005515", "Protein binding", "102", "0.013495"]], "row_count": 24, "column_count": 4, "numeric_cells": 60, "header_rows": 1, "locator": "section[15]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:32587798:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:39ab6d6d2f685499a01a17b38b7d8165aa1608aaa677ddde6690a71d590ace4f", "bytes": 601, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#table-2", "version": null, "note": "KEGG pathway enrichment analysis of upregulated DEGs in pancreatic ductal adenocarcinoma.", "structure": {"pmcid": "PMC7301898", "section_index": 15, "section_title": "GO and KEGG pathway analyses of the PPI network", "row_count": 7, "column_count": 4}, "table": 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Involving in chromosome condensation, chromatid separation, and the relief of torsional stress."], ["2", "CDK1", "Cyclin dependent kinase 1", "Essential for G1/S and G2/M phase transitions of eukaryotic cell cycle and mitotic cyclins."], ["3", "RRM2", "Ribonucleotide reductase regulatory subunit M2", "Catalyzing the formation of deoxyribonucleotides from ribonucleotides."], ["4", "PRC1", "Protein regulator of cytokinesis 1", "A substrate of several CDKs and necessary for polarizing parallel microtubules and concentrating the factors responsible for contractile ring assembly."], ["5", "NEK2", "NIMA related kinase 2", "A serine/threonine-protein kinase that is involved in mitotic regulation."], ["6", "ZWINT", "ZW10 interacting kinetochore protein", "Clearly involved in kinetochore function."], ["7", "DTL", "Denticleless E3 ubiquitin protein ligase homolog", "Cellular response to DNA damage stimulus."], ["8", "MELK", "Maternal embryonic leucine zipper kinase", "G2/M transition of mitotic 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