328 research outputs found
Investigation of common pathways and putative biomarker candidates of colorectal cancer and insomnia by using integrative in-silico approaches
No full textBackground: Colorectal cancer (CRC) is one of the leading causes of cancer -related mortalities across the globe. Accumulating evidence shows that individuals having sleep disorders such as insomnia are at high risk of developing CRC, yet the association of sleep disorders with CRC risk is still unclear. Here, we investigated the potential molecular connections between CRC and insomnia using integrative in silico approaches. Objective: This study aims to explore the potential molecular connections between CRC and insomnia utilizing integrative in-silico methodologies. Methods and Methods: Gene expression microarray datasets for CRC and insomnia samples were retrieved from the NCBI-GEO database and analyzed using R. Functional enrichment analysis of common differentially expressed genes (DEGs) was performed by the g: Profiler tool. Cytoscape software was used to construct a protein -protein interaction network and hub gene identification. Expression profiles of hub genes in TCGA datasets were also determined, and predicted miRNAs targeting hub genes were analyzed by miRNA target prediction tools. Results: Our results revealed a total of 113 shared DEGs between the CRC and insomnia datasets. Six genes ( HSP8A , GAPDH , HSP90AA1 , EEF1G , RPS6 , and RPLP0), which were also differently expressed in TCGA datasets, were prioritized as hub genes and were found to be enriched in pathways related to protein synthesis. hsa-miR-324-3p, hsamiR-769-3p, and hsa-miR-16-5p were identified as promising miRNA biomarkers for two diseases. Conclusions: Our in-silico analysis provides promising evidence of the molecular link between CRC and insomnia and highlights multiple potential molecular biomarkers and pathways. Validation of the results by wet lab work can be utilized for novel translational and precision medicine applications to alleviate the public health burden of CRC
The preliminary data of gene expressions and bioinformatics analysis of mir-146b-5p and mir-4510 in the turkish population in hbv-related hepatocellular carcinoma
No full textBackground and Aim: It is reported that miRNAs play an important role in hepatocellular carcinogenesis and may serve as non-invasive biomarkers for hepatocellular carcinoma (HCC). MiR-4510 and miR-146b-5p expression levels have been found to be associated with HCC. However, their associations with hepatitis B virus (HBV)-related HCC (HBV-HCC) are yet to be explored. We aimed to assess the predictive value of expression levels of serum miR-4510 and miR-146b-5p in patients with HBV-HCC and performed bioinformatics analyses based on the miRNA expression profile. Materials and Methods: This cross-sectional study used the serum of 16 patients with Chronic Hepatitis B (CHB), 15 hepatitis B virus-related cirrhosis (HBV-cirrhosis), 15 HBV-HCC, and 16 healthy subjects. The total RNA was isolated from serum, and the expression of miRNAs was measured by qRT-PCR, calculated using the 2-Delta Delta Ct methods. MIENTURNET was used to predict miRNA-target gene interactions. The Network Analyst was used to build protein-protein interactions. Results: There was a significant difference in miR-146b-5p between study groups (p=0.009). MiR-146b-5p expression was found to be significantly reduced in HBV-HCC compared to the HBV-cirrhosis group and healthy controls (p=0.005 and p=0.006, respectively). Conclusion: The serum miR-146b-5p levels might be a promising tool to be used as a non-invasive diagnostic biomarker for HCC. Our findings shed light on potential biomarkers for the diagnosis of HBV-HCC in terms of selected miRNAs. The target pathways of miR-146b-5p identified by our in-silico analysis to reveal the functional mechanism are "MAPK signaling pathways" and "Pathways in cancer.
Dilek Güngör: Ich bin Özlem
No full textThis paper analyzes the novel "Ich bin Özlem" of Dilek Güngör, author of post-migration German literature. This article analyzes: structure and narrative style, the complex personality of the protagonist and the first steps towards the perception of one's own identit
In Silico Approach to Identify the Relationships between COVID-19 and Coronary Artery Disease/Rheumatoid Arthritis
No full textGlobal public has been threatened by the coronavirus disease 2019 (COVID-19) pandemic which led to nearly 15 million deaths around the world. People with complex and chronic diseases usually have more severe COVID-19 symptoms than the general population. Mounting evidence indicates individuals with coronary artery disease (CAD) and rheumatoid arthritis (RA) have worse COVID-19 outcomes yet the underlying mechanism still needs to be explored. The aim of our study is to reveal in silico evidence for the molecular mechanisms shared by COVID-19, CAD and RA pathogenesis which may aggravate the COVID-19 disease severity. Public datasets (GSE164805 and GSE23561) were downloaded from the Gene Expression Omnibus (GEO) database and analyzed for differential expression analysis (DEG). Identified differential expressed genes (DEGs) were further analyzed to find common DEGs, common pathways, hub genes, transcription factors (TFs) and microRNAs (miRNAs). Our study identified common hub genes, miRNAs, TFs and shared mechanisms in both mild and severe COVID-19-CAD patients and mild and severe COVID-19-RA patients. We also uncovered that mild and severe forms of COVID-19 differ in potential biomarkers, mechanisms, miRNAs and TFs in both CAD and RA patients. Our study is the first study investigating the potential shared mechanisms, biomarkers, TFs and miRNAs between COVID-19 and CAD patients and COVID-19 and RA patients. Our results could shed on light to the patient management strategies with CAD with COVID-19 and patients with RA with COVID-19 based on the severity of the COVID-19 disease. © 2023 by the authors. Submitted for possible open access publication under the terms and conditions of the Creative Commons Attribution (CC BY NC) license (https://creativecommons.org/licenses/by-nc/4.0/)
Kruskal's minimum spanning tree approach to brain fiber tractography computation
No full textGöksel Duru, Dilek (Arel Author) --- Conference: 22nd Signal Processing and Communications Applications Conference, SIU 2014
The rs139226362 (delGATT) variant in the NTS gene alters plasma neurotensin levels in schizophrenia
No full textNeurotensin (NTS) is a critical neuropeptide involved in multiple pathways in the central nervous and peripheral systems. We assessed the possible functional relevance of NTS in SCZ pathogenesis by focusing on the rs139226362 (delGATT) located in the 3' untranslated region (UTR) of the NTS. A total of 88 Turkish individuals with known genotypes for the delGATT allele were included in the study. Differences in NTS mRNA expression and circulating NTS protein levels were evaluated by RT-qPCR and ELISA, respectively. The stability of RNA secondary structures and the binding patterns of RNA-binding protein (RBPs) interactions were evaluated by analysis. Plasma NTS protein levels were significantly higher ( = 0.0003) in SCZ patients carrying the delGATT variant compared to those with wild-type genotype. This genotype-protein association was not observed in healthy controls, indicating a disease-specific effect. Moreover, plasma NTS levels were correlated with PANSS scores ( = -0.290, = 0.041) and BMI ( = 0.306, = 0.031) in SCZ patients. These findings suggest that rs139226362 may influence post-transcriptional regulation, with the indel potentially associated with milder SCZ symptoms through altered molecular pathways. Further validation in experimental models may support the development of NTS-based personalized treatment strategies for SCZ management
Erratum: Improvement of design of a surgical interface using an eye tracking device Bioinformatics (Theoretical Biology and Medical Modelling 11:48 (2014))
No full text#nofulltext# --- Duru, Dilek Göksel (Arel Author)
Association study of coronary artery disease-associated genome-wide significant SNPS with coronary stenosis in Pakistani population
No full textGenome-wide association studies (GWAS) of coronary artery disease (CAD) have revealed multiple genetic risk loci. We assessed the association of 47 genome-wide significant single-nucleotide polymorphisms (SNPs) at 43 CAD loci with coronary stenosis in a Pakistani sample comprising 663 clinically ascertained and angiographically confirmed cases. Genotypes were determined using the iPLEX Gold technology. All statistical analyses were performed using R software. Linkage disequilibrium (LD) between significant SNPs was determined using SNAP web portal, and functional annotation of SNPs was performed using the RegulomeDB and Genotype-Tissue Expression (GTEx) databases. Genotyping comparison was made between cases with severe stenosis (>= 70%) and mild/minimal stenosis (<30%). Five SNPs demonstrated significant associations: three with additive genetic modelsPLG/rs4252120 (p=0.0078),KIAA1462/rs2505083 (p=0.005), andSLC22A3/rs2048327 (p=0.045) and two with recessive modelsSORT1/rs602633 (p=0.005) andUBE2Z/rs46522 (p=0.03).PLG/rs4252120 was in LD with two functionalPLGvariants (rs4252126 and rs4252135), each with a RegulomeDB score of 1f. Likewise,KIAA1462/rs2505083 was in LD with a functional SNP,KIAA1462/rs3739998, having a RegulomeDB score of 2b. In the GTEx database,KIAA1462/rs2505083,SLC22A3/rs2048327,SORT1/rs602633, andUBE2Z/rs46522 SNPs were found to be expression quantitative trait loci (eQTLs) in CAD-associated tissues. In conclusion, five genome-wide significant SNPs previously reported in European GWAS were replicated in the Pakistani sample. Further association studies on larger non-European populations are needed to understand the worldwide genetic architecture of CAD.Higher Education Commission of Pakistan - Higher Education Commission of Pakista
Source concordance analysis of simultaneously recorded steady state visual evoked potentials and fMRI
No full textGöksel Duru, Dilek (Arel Author) --- Conference: OHBM 2014 Annual Meeting. Hamburg, Germany, 8-12 June 2014.
Apolipoprotein <i>E-C1-C4-C2</i> gene cluster region and inter-individual variation in plasma lipoprotein levels: a comprehensive genetic association study in two ethnic groups
No full textThe apolipoprotein E-C1-C4-C2 gene cluster at 19q13.32 encodes four amphipathic apolipoproteins. The influence of APOE common polymorphisms on plasma lipid/lipoprotein profile, especially on LDL-related traits, is well recognized; however, little is known about the role of other genes/variants in this gene cluster. In this study, we evaluated the role of common and uncommon/rare genetic variation in this gene region on inter-individual variation in plasma lipoprotein levels in non-Hispanic Whites (NHWs) and African blacks (ABs). In the variant discovery step, the APOE, APOC1, APOC4, APOC2 genes were sequenced along with their flanking and hepatic control regions (HCR1 and HCR2) in 190 subjects with extreme HDL-C/TG levels. The next step involved the genotyping of 623 NHWs and 788 ABs for the identified uncommon/rare variants and common tagSNPs along with additional relevant SNPs selected from public resources, followed by association analyses with lipid traits. A total of 230 sequence variants, including 15 indels were identified, of which 65 were novel. A total of 70 QC-passed variants in NHWs and 108 QC-passed variants in ABs were included in the final association analyses. Single-site association analysis of SNPs with MAF>1% revealed 20 variants in NHWs and 24 variants in ABs showing evidence of association with at least one lipid trait, including several variants exhibiting independent associations from the established APOE polymorphism even after multiple-testing correction. Overall, our study has confirmed known associations and also identified novel associations in this genomic region with various lipid traits. Our data also support the contribution of both common and uncommon/rare variation in this gene region in affecting plasma lipid profile in the general population.</div
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