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POTENTIAL GENETIC BIOMARKERS FOR DILATED CARDIOMYOPATHY USING GENOMIC DATA

Eljack, Ammar F
http://orcid.org/0000-0002-5936-9668
http://rave.ohiolink.edu/etdc/view?acc_num=mco1588564733943116

Abstract Details

2020, Master of Science in Biomedical Sciences (MSBS), University of Toledo, Biomedical Sciences (Bioinformatics and Proteomics/Genomics).
Dilated cardiomyopathy (DCM) belongs to the heterogeneous group of heart muscle disorders called cardiomyopathies, characterize by left ventricular dilatation and reduce myocardial muscle contractility that leads to a reduced ejection fraction of the heart. There are several causes of DCM; genetic, toxic, metabolic, endocrine, infiltrative, and idiopathic disorders. Forty causative genes encoding for a variety of proteins have been identified up to date. The objective of this study is to identify potential biomarkers related to the disease process of DCM. Microarray and RNA-Seq profiles of cardiac tissue were used to identify differentially expressed genes (DEGs). Four Microarray datasets (GSE 3585, GSE3586, GSE9800, and GSE42955), and three RNA-Seq datasets were selected (GSE55296, GSE65466, and GSE71613) from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was used to explore the hub genes involved in the disease process of DCM. A total of 51 modules for microarray datasets and 15 modules for RNA-Seq datasets were identified using correlation network analysis. Four common statistically- significant genes were identified among these modules, including AP3M2, ECM2, ERBB2, and ZNF83. AP3M2 gene, which involves protein trafficking to lysosomes and specialized organelles, ECM2 gene, which affects in extracellular matrix protein function, ERBB2 gene, which involves in Erb-B2 Receptor Tyrosine Kinase 2 signaling pathway, and ZNF83 gene which involves in transcriptional regulation in the cell. A total of 9 hub genes that were differentially over-expressed significantly in cardiac tissue from RNA-Seq datasets, including EIF4GA which is related to viral myocarditis, HACD1, MYOM3, PTPN4, and NRBP1 are associated with muscular disorders, CELSR which play an essential role for planar cell polarity, SLC27A6 which is transporter involve in LCFA uptake process, SCMH1 involves in negative regulation of gene expression, and DCAF11 encodes WD repeat-containing protein, that involves in protein modification pathway . We identified four hub genes from microarray and nine hub genes from RNA-Seq datasets using weighted gene co-expression networks analysis. We propose that these hub genes play an essential role in DCM pathogenesis and disease progression and could be a useful tools as genetic markers for the disease. Further studies and validations of these hub genes are needed to confirm our findings and to improve our understanding of the disease process.
Sadik Khuder (Committee Chair)
Robert Blumenthal (Committee Member)
Jiang Tian (Committee Member)
73 p.
Bioinformatics; Biomedical Research; Genetics
Dilated Cardiomyopathy; microarray; RNAseq

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Citations

  • Eljack, A. F. (2020). POTENTIAL GENETIC BIOMARKERS FOR DILATED CARDIOMYOPATHY USING GENOMIC DATA [Master's thesis, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=mco1588564733943116

    APA Style (7th edition)

  • Eljack, Ammar. POTENTIAL GENETIC BIOMARKERS FOR DILATED CARDIOMYOPATHY USING GENOMIC DATA . 2020. University of Toledo, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=mco1588564733943116.

    MLA Style (8th edition)

  • Eljack, Ammar. "POTENTIAL GENETIC BIOMARKERS FOR DILATED CARDIOMYOPATHY USING GENOMIC DATA ." Master's thesis, University of Toledo, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=mco1588564733943116

    Chicago Manual of Style (17th edition)

mco1588564733943116
205
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This open access ETD is published by University of Toledo Health Science Campus and OhioLINK.