Ayna Duran, Gizem
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Ayna Duran, Assist. Prof. Dr. Gizem
Ayna, Duran, G.
Duran, Gizem Ayna
Gizem Ayna Duran
Ayna, Duran, G.
Duran, Gizem Ayna
Gizem Ayna Duran
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gizem.duran@ieu.edu.tr
aynadurangizem@gmail.com
aynadurangizem@gmail.com
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05.02. Biomedical Engineering
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Current Staff
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Sustainable Development Goals
5
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0
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9
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13
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8
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14
LIFE BELOW WATER
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17
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1
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2
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4
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11
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16
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6
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10
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15
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7
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10
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177
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2
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10
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46
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22
Articles
11
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25/588
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1
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2
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2
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1
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1
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1
WoS Citations per Publication
0.09
Scopus Citations per Publication
0.09
Open Access Source
17
Supervised Theses
1
| Journal | Count |
|---|---|
| Analytical Biochemistry | 1 |
| Asian Biomedicine | 1 |
| Celal Bayar Üniversitesi Sağlık Bilimleri Enstitüsü Dergisi | 1 |
| Discover Oncology | 1 |
| European Journal of Biology | 1 |
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22 results
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Now showing 1 - 10 of 22
Article Determination of Eight Hub Genes and Functional Pathways Affecting Both the Survival of Early- and Late-Stage Colon Cancer Patients(Kare Publ, 2023) Ayna Duran, Gizem; Sert, FatmaOBJECTIVEThe stage of colon cancer (CC) and therefore the level at which the treatment is initiated affects the survival of CC patients. In our study, we aimed to identify the common survival-related genes in both early-and late-stage CC patients.METHODSInformation on the demographic characteristics of 581 patients and microarray expression profiles (GSE39582) were obtained from the gene expression omnibus database. Survival analysis was per-formed using univariate and multivariate Cox regression methods with the help of R3.53 programming language and Kaplan-Meier graphics through the R software Survival package. ShinyGO v0.741 gene ontology enrichment analysis was performed to clarify the common and functional pathways related to both early-and late-stage CC cancer patients' data.RESULTSCox regression analysis indicated that overall survival and relapse-free survival of CC patients were strongly influenced by stage. Genes that significantly affect prognosis and survival in early-and late -stage CC patients were identified. As a result of gene enrichment analysis, arginine binding, oxidore-ductase activity, and methylcytosine dioxygenase activity and related eight hub genes (TM4SF5, NOS3, Ten eleven translocation [TET1], TET3, JMJD7, AKR1C1, prenylcysteine oxidase 1 like, Methionine sulfoxide reductase A) were identified.CONCLUSIONAccording to our results, it might be considered that developing new treatment strategies based on eight hub-genes related to arginine binding, oxidoreductase activity, and methylcytosine dioxygenase activity detected at different stages of CC might increase the success of targeted therapies.Article Bioinformatics Based Drug Repurposing Approach for Breast and Gynecological Cancers: RECQL4/FAM13C Genes Address Common Hub Genes and Drugs(Galenos Publ House, 2025) Duran, Gizem AynaObjective: The prevalence of breast cancer and gynaecological cancers is high, and these cancer types can occur consecutively as secondary cancers. The aim of our study is to determine the genes commonly expressed in these cancers and to identify the common hub genes and drug components. Materials and Methods: Gene intensity values of breast cancer, gynaecological cancers such as cervical, ovarian and endometrial cancers were used from the Gene Expression Omnibus database Affymetrix Human Genome U133 Plus 2.0 Array project. Using the linear modelling method included in the R LIMMA package, genes that differ between healthy individuals and cancer patients were identified. Hub genes were determined using cytoHubba in Cytoscape program. “ShinyGo 0.80” tool was used to determine the disease-specific biological KEGG pathways. Drug.MATADOR from the ShinyGo 0.80 tool was used to predict drug-target relationships. Results: The RecQ Like Helicase 4 and Family with Sequence Similarity 13 Member C genes were found to be similarly expressed in breast cancer and gynaecological cancers. Upon KEGG pathway analyses with hub genes, Drug.MATADOR analysis with hub genes related to cancer related pathways was performed. We have determined these gene/drug interactions: NBN (targeted by Hydroxyurea), EP300 (targeted by Acetylcarnitine) and MAPK14 (targeted by Salicylate and Dibutyryl cyclic AMP). Conclusion: The drugs associated with hub genes determined in our study are not routinely used in cancer treatment. Our study offers the opportunity to identify the target genes of drugs used in breast and gynaecological cancers with the drug repurposing approach.Article Autophagy-Related Genes Affect the Survival of Multiple Myeloma Patients Depending on Chromosomal Abnormality(Walter De Gruyter Gmbh, 2022) Ayna Duran, Gizem; Benderli Cihan, YaseminBackground: Targeting autophagy at gene level may be promising in multiple myeloma (MM) treatment depending on chromosomal abnormality (ABN) status.Objectives: We aimed to investigate the role of ABN on survival of MM patients and to identify prognosis related autophagy-related genes (ARGs) for patients with or without ABN.Methods: Gene intensity values of 222 ARG for 548 MM patients were obtained from the Affymetrix Human Genome U133 Plus 2.0 Array (GPL570) platform containing 54,675 probes (GSE24080). A dataset containing data from 1576 MM patients with 1q21 amplification (GSE4204, GSE4452, GSE4581, and GSE2658) was used for validation. Survival analysis of the patients was analyzed using univariate and multivariate Cox regression method with the help of R3.53 programming language and Kaplan-Meier graphics were created. The Gene Ontology enRIchmentanaLysis and visuaLizAtion (GOrilla) tool was used to define the related biological processes and pathways.Results: The overall survival (OS) and event-free survival (EFS) in all MM patients were strongly influenced by ABN. In the group of patients with ABN, 41 ARGs were found to be important in prognosis, whereas in the group of patients without ABN, 13 ARGs were found to be important in prognosis. CDKN1A, FKBP1B, FOXO3, and NCKAP1 ARGs were commonly significant in both groups and found to be survival triggering.Conclusions: The classification of MM patients according to the absence or presence of ABN is important in the determination of survival status. Detection of survival related ARGs in patients with chromosomal anomalies may be a new therapeutic target in treatment.Article Pan-Cancer Analyses Identify the Rrm2 Gene as a Biomarker With Diagnostic and Prognostic Roles in Multiple Human Cancers Via Interactions With the Hsa-Let Mirna and Ezh2(Biolife Sas, 2023) Ayna Duran, GizemBackground: Pan-cancer research has recently been conducted to identify genomic differences in multiple cancers compared with those in normal tissues. Our aims were to determine common differentially expressed genes (DEGs) by analysing the genomes of multiple cancers and to identify common cancer biomarkers for both diagnosis and treatment by determining the effect of these commonly changed genes on survival.Methods: We performed DEG and survival analyses by considering differences in expression levels in tumour and related normal tissues using the R programme and bioinformatic webtools Gene Expression Profiling Interactive Analysis 2 (GEPIA2), UALCAN, TIMER2.0, KM-plot, ShinyGO 0.77, miRTargetLink, and CancerMIRNome.Results: In our study, 5 genes (ribonucleotide reductase regulatory subunit M2 (RRM2), enhancer of the zeste homolog 2 (EZH2), Proliferating cell nuclear antigen (PCNA) clamp associated factor (PCLAF), mitotic checkpoint serine/threonine kinase B (BUB1B), and centromere protein U (CENP-U)) were found to be upregulated in multiple cancers. Among these genes, the RRM2 gene was upregulated in more cancers and datasets. According to the gene enrichment analysis, the EZH2 gene also acted together with the RRM2 gene in terms of biological significance. Furthermore, instead of finding chemical agents that would inhibit the overexpression of both the RRM2 and EZH2 genes, miRNA screening targeting both genes were performed. As a result, hsa-let-7a-5p miRNA was found to have a strong interaction with both genes through the p53-and cell cycle-dependent pathways.Conclusion: The commonly upregulated RRM2 and EZH2 genes can be utilised as biomarkers for early diagnosis of multiple cancers. The joint interactions of the RRM2 and EZH2 genes with hsa-let-7a-5p may be a promising early treatment by inhibiting the expression levels of both genes by targeting hsa-let-7a-5p, an miRNA with low expression levels in cancers.Conference Object Identification of Differentially Expressed Genes and Potential Inhibitors in Resistant Subtypes of Acute Lymphoblastic Leukemia(2023) Başak Özay; Ezgi Yağmur Tükel; Yağmur Kiraz; Ayna Duran, GizemBook Part Biyomedikal, Biyoteknoloji ve Sağlık Bilimlerinde Biyoinformatik Analizler ve Yaklaşımlar(2022) Gizem Ayna DuranArticle Upregulated Acute Systemic Inflammation-Related Genes Based on Endotoxin Exposure Provide ‘Survival Benefit’ or Create ‘High Risk of Death’ in Leukaemia and Colon Cancer(Istanbul University, 2024) Duran, Gizem AynaObjective: Although endotoxin exposure has been shown to trigger innate immune responses and promote cancer, it has also been shown to prevent cancer formation. In our study, survival analysis was performed to determine whether the upregulated genes triggered by endotoxins have hazardous effects on cancers or provide a survival benefit. Materials and Methods: Gene intensity values of control and bacterial endotoxin-administered individuals were obtained from the Gene Expression Omnibus database. Using the R "Linear Models for Microarray Data" package, differentially expressed gene analyses were conducted to determine genes that differ between healthy and bacterial endotoxin-administered samples. "ShinyGo 0.80" web-based tool was used to determine the disease types indicated by these genes. The "Kaplan-Meier Plotter" web-based tool was used to conduct survival analysis. Results: Genes that create an innate immune response to bacterial endotoxin exposure and are upregulated differently than in individuals without exposure were identified. According to gene enrichment analyses, the two main types of cancer identified were leukaemia/lymoma and colon cancer. We detected that MLF1, STAT5B, and BCL3 genes led to poor survival; however, the ARHGAP26 gene was protective for acute myeloid leukaemia patients. In the case of colon cancer, SMAD7 and TLR2 genes were determined as leading to "high risk of death". Conclusion: Once the systemic inflammation-related genes identified in our study are confirmed through laboratory experiments in samples taken from solid tissue in the case of colon cancer and at the level of genes obtained from blood samples in leukemias, genetically targeted treatments will also be possible.Article LEP and FOXO1 Genes, as a Proposed Tumor Suppressor Autophagic Cell Death Related Genes, Can Be Targeted by Antidiabetic Therapy in Nondiabetic Breast Cancer Patients(Springer, 2025) Duran, Gizem Ayna; Kiraz, Yagmur; Baykara, DenizIntroduction Breast cancer can be treated effectively with personalized, gene-targeted therapies due to its molecular and genetic differences. Our study aims to identify breast cancer-specific tumor suppressor genes related to autophagic cell death and discover new drugs that target these mechanisms, even if they are not breast cancer-specific. Materials and methods Gene intensity values of 457 tumor and 19 healthy breast tissues were used to determine downregulated and upregulated genes related to autophagy and apoptosis using Bioconductor R program via LIMMA package. Then, genes affecting survival were identified by survival analysis via Kaplan-Meier Plotter tool. Furthermore, the signalling pathways associated with these genes and targeting candidate drug components were determined by gene enrichment analysis using "KEGG pathway option" and Drug MATADOR in "ShinyGo 0.82" web-tool, respectively. Results Breast cancer tumor tissues showed downregulation of genes related to autophagy and apoptosis (c19orf12, CRYAB, LEP, SRPX, SNCA, FOXO1) and upregulation of others (SLC7A5, ATP2A2, INHBA, ATP5IF1). Among these, SLC7A5, c19orf12, LEP, SPRX, SNCA, and FOXO1 affected patient survival and prognosis. The AMPK signaling pathway, targeting FOXO1 and LEP, was identified as key. Only the LEP gene was targeted by Metformin, Pioglitazone, Rosiglitazone, and Troglitazone. Conclusion In our study, survival associated LEP and FOXO1 genes were identified as candidate tumor suppressor genes associated with autophagic cell death in non-obese and non-diabetic breast cancer patients. Anti-diabetic drugs such as Metformin, Pioglitazone, Rosiglitazone, Troglitazone are proposed as candidate components in the treatment processes by targeting the LEP gene in nondiabetic breast cancer patients.Article Exploring Pi3k Pathway Inhibitors for Acute Myeloid Leukemia: a Drug-Repurposing Approach(Istanbul University Press, 2023) Ergun, Cansu; Kiremitci, Buse Zeren; Arslantas, Gizem; Bozkurt, Busenur; Duran, Gizem Ayna; Kiraz, YağmurObjective: Acute myeloid leukemia (AML) is a malignant disease characterized by the uncontrolled growth, differentiation, and proliferation of immature hematopoietic cells. Patients with AML often have poor survival rates, which are associated with specific gene mutations in FLT3, CEBPA, and NPM1. The phosphatidylinositol 3-kinase (PI3K) pathway, a lipase pathway, is activated in many malignancies, including AML. Given the low survival rates in AML, this study identified candidate drugs that could inhibit the PI3K pathway, thereby offering a potential treatment for AML, by using a drug-repurposing approach. Materials and Methods: Online bioinformatics tools were utilized to identify pathway-related genes and FDA-approved drugs. Subsequently, molecular docking was performed to determine the binding affinity values. Important genes were identified by evaluating their impact on survival and their aberrant expression in the tumor. In this study, genes such as VAV1, GSK3B, MTOR, PDPK1, PRR5, TSC2, AKT3, and CREB1 were determined and docked with their potential inhibitors. Particular attention was paid to VAV1 because there were no known potential VAV1 inhibitors used in AML. Results: The docking results were ranked, and the proposed gene–drug pairs were identified as tideglusib and fostamatinib for the inhibition of GSK3B, pimecrolimus and fostamatinib for the inhibition of MTOR, and fostamatinib for the inhibition of PDPK1. Furthermore, nebivolol, darifenacin, dihydroergotamine, libanserin and entereg were identified as potential inhibitors of VAV1 in AML. Conclusion: To sum up, most effective gene–drug pairs according to binding affinities were proposed as candidate inhibitor drugs for AML.Book Part Kanser Tedavisinde Otofajik Hücre Ölümü Temelli Terapötik Uygulamalar(2020) Ayna Duran, Gizem
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