Gene Expression Characteristics of Tumor and Adjacent Non-Tumor Tissues of Pancreatic Ductal Adenocarcinoma (PDAC) In-Silico

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dc.authoridGüven, Emine/0000-0001-9324-0879
dc.contributor.authorGüven, Emine
dc.date.accessioned2023-07-26T11:50:03Z
dc.date.available2023-07-26T11:50:03Z
dc.date.issued2022
dc.departmentDÜ, Mühendislik Fakültesi, Biyomedikal Mühendisliği Bölümüen_US
dc.description.abstractBackground: One of the deadliest and most prevalent cancer is pancreatic ductal adenocarcinoma (PDAC). Microarray has become an important tool in the research of PDAC genes and target therapeutic drugs. Objectives: This study intends to clarify the promising prognostic and biomarker targets in PDAC using GSE78229 and GSE62452 datasets, publicly accessible at the Gene Expression Omnibus database. Materials and Methods: Utilizing GEOquery, Bio base, gplots, and ggplot2 packages in the R program, this study detects 428 differentially expressed genes that are further applied to build a co-expression network by the weighted correlation network analysis (WGCNA). The turquoise module presented a higher correlation with PDAC progression. 79 candidate genes were selected based on the co-expression and protein-protein interaction (PPI) networks. In addition, the functional enrichment analysis was studied. Results: Five significant KEGG pathways linked to PDAC were detected, in which the endoplasmic reticulum protein processing pathway was remarked to be vital. The resulting 19 hub genes as HSPA4, PABPC1, HSP90B1, PPP1CC, and PDIA6 were identified by the Network Analyst web tool founded on PPI network by the STRING. These were identified as the most connected hub proteins. The quantification of the expression of levels and survival probabilities were analyzed overall survival (OS) of the real hub genes and were investigated by Kaplan-Meier (KM) plotter through The Cancer Genome Atlas Program (TCGA) database. Conclusions: The protein-protein interactions and KEGG pathway enrichment by DAVID indicated that some pathways were involved in PDAC, such as pathways in cancer (hsa05200), protein processing in the endoplasmic reticulum (hsa04141), antigen processing and presentation (hsa04612), dopaminergic synapse (hsa04728), and measles (hsa05162); in which these pathways, the protein processing in endoplasmic reticulum (hsa04141), was further studied because of its closely relationship with PDAC. The rest of the hub genes reviewed throughout the study might be promising targets for diagnosing and treating PDAC and relevant diseases.en_US
dc.identifier.doi10.30498/ijb.2021.292558.3092
dc.identifier.issn1728-3043
dc.identifier.issue1en_US
dc.identifier.pmid35891953en_US
dc.identifier.scopus2-s2.0-85126300951en_US
dc.identifier.scopusqualityQ3en_US
dc.identifier.urihttps://doi.org/10.30498/ijb.2021.292558.3092
dc.identifier.urihttps://hdl.handle.net/20.500.12684/12215
dc.identifier.volume20en_US
dc.identifier.wosWOS:000770698500006en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.institutionauthorGüven, Emine
dc.language.isoenen_US
dc.publisherNatl Inst Genetic Engineering & Biotechnologyen_US
dc.relation.ispartofIranian Journal of Biotechnologyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.snmz$2023V1Guncelleme$en_US
dc.subjectBiomarker; Co-Expression; Differentially Expressed Genes; Endoplasmic Reticulum; Gene Ontology Pathway Enrichment; Pancreatic Ductal Adenocarcinomaen_US
dc.subjectMicroarray Data; Cancer; Pathogenesis; Networks; Proteinsen_US
dc.titleGene Expression Characteristics of Tumor and Adjacent Non-Tumor Tissues of Pancreatic Ductal Adenocarcinoma (PDAC) In-Silicoen_US
dc.typeArticleen_US

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