Identification of common genes and pathways underlying imatinib and nilotinib treatment in CML: a bioinformatics study

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dc.contributor.authorHekmatshoar, Yalda
dc.contributor.authorSaadat, Yalda Rahbar
dc.contributor.authorÖzkan, Tülin
dc.contributor.authorBozkurt, Süreyya
dc.contributor.authorGürel, Aynur Karadağ
dc.date.accessioned2023-12-28T08:07:35Z
dc.date.available2023-12-28T08:07:35Z
dc.date.issued2023en_US
dc.departmentFakülteler, Tıp Fakültesi, Temel Tıp Bilimleri, Tıbbi Biyoloji Ana Bilim Dalıen_US
dc.description.abstractImatinib (IMA) and nilotinib are the first and second generations of BCR-ABL tyrosine kinase inhibitors, which widely applied in chronic myeloid leukemia (CML) treatment. Here we aimed to provide new targets for CML treatment by transcriptome analysis. Microarray data GSE19567 was downloaded and analyzed from Gene Expression Omnibus (GEO) to identify common genes, which are downregulated or upregulated in K562-imatinib and K562-nilotinib treated cells. The differentially expressed genes (DEGs) were assessed, and STRING and Cytoscape were used to create the protein-protein interaction (PPI) network. In imatinib and nilotinib treated groups' comparison, there were common 626 upregulated and 268 downregulated genes, which were differentially expressed. The GO analysis represented the enrichment of DEGs in iron ion binding, protein tyrosine kinase activity, transcription factor activity, ATP binding, sequence-specific DNA binding, cytokine activity, the mitochondrion, sequence-specific DNA binding, plasma membrane and cell-cell adherens junction. KEGG pathway analysis revealed that downregulated DEGs were associated with pathways including microRNAs in cancer and PI3K-Akt signaling pathway. Furthermore, upregulated DEGs were involved in hematopoietic cell lineage, lysosome and chemical carcinogenesis. Among the upregulated genes, MYH9, MYH14, MYL10, MYL7, MYL5, RXRA, CYP1A1, FECH, AKR1C3, ALAD, CAT, CITED2, CPT1A, CYP3A5, CYP3A7, FABP1, HBD, HMBS and PPOX genes were found as hub genes. Moreover, 20 downregulated genes, YARS, AARS, SARS, GARS, CARS, IARS, RRP79, CEBPB, RRP12, UTP14A, PNO1, CCND1, DDX10, MYC, WDR43, CEBPG, DDIT3, VEGFA, PIM1 and TRIB3 were identified as hub genes. These genes have the potential to become target genes for diagnosis and therapy of CML patients.en_US
dc.identifier.citationHekmatshoar, Y., Saadat, Y. R., Özkan, T., Bozkurt, S., Gürel, A. K. (2023). Identification of common genes and pathways underlying imatinib and nilotinib treatment in CML: a bioinformatics study. Nucleosides, Nucleotides & Nucleic Acids, 43(7), 664-684.en_US
dc.identifier.endpage684en_US
dc.identifier.issn1525-7770
dc.identifier.issn1532-2335
dc.identifier.issue7en_US
dc.identifier.scopus2-s2.0-85180168402
dc.identifier.scopusqualityQ4
dc.identifier.startpage664en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12939/4467
dc.identifier.volume43en_US
dc.identifier.wosWOS:001128390300001
dc.identifier.wosqualityQ4
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorHekmatshoar, Yalda
dc.language.isoen
dc.relation.ispartofNucleosides, Nucleotides & Nucleic Acids
dc.relation.isversionof10.1080/15257770.2023.2296021en_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectChronic myeloid leukemiaen_US
dc.subjectBioinformaticsen_US
dc.subjectgEOen_US
dc.subjectGene expressionen_US
dc.subjectImatiniben_US
dc.subjectNilotiniben_US
dc.titleIdentification of common genes and pathways underlying imatinib and nilotinib treatment in CML: a bioinformatics study
dc.typeArticle

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