Cytokine polymorphism catalog (cytocat) for the analysis of phenotype associations

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2014

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Oğuz, Gökçe

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Currently, many studies focus on identifying disease related biological biomarkers for prediction of susceptibility, early detection, and prevention, in addition to developing new therapeutic approaches. In our study, we have investigated the single nucleotide polymorphisms (SNPs) of human cytokines and cytokine receptors, which play an important role in the immune system, as potential disease biomarkers and focused on phenotypes as they might give clue about disease symptoms. Our main aim was to create a catalog to be a guideline to early diagnosis, disease treatment, and drug discovery and design studies by storing general and specific associations between genes, SNPs and phenotypes. For that reason, firstly genetic variations on known human cytokines and cytokine receptors and then associations between these variations and phenotypes are identified. In particular, the data integration approaches were used to map single nucleotide polymorphisms (SNPs) on known cytokine and cytokine receptor genes and to extract SNPs associated to phenotypes from various biological databases. By congregating these data a new biological relational database was developed. A case study is done to further analyze and visualize the GWAS results for 3 different cancer types accessed through database of Genotypes and Phenotypes (dbGaP). This relational database enables one to search with different parameters and to analyze the associations from different aspects. As a result, a catalog of cytokine and cytokine receptor SNPs and their association with diseases is developed. This allows analysis of molecular and clinical research data from different perspectives, like identifying underlying etiology of diseases through associated polymorphisms, and SNPs common to cytokine-dependent diseases.

Subject Keywords

Cytokines, Single nucleotide polymorphisms., Phenotype, Biochemical markers., Genetics

URI

http://etd.lib.metu.edu.tr/upload/12616863/index.pdf
https://hdl.handle.net/11511/23308

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Graduate School of Informatics, Thesis

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Citation Formats

G. Oğuz, “Cytokine polymorphism catalog (cytocat) for the analysis of phenotype associations,” M.S. - Master of Science, Middle East Technical University, 2014.