A multi-layered graphical model of the relation among SNPS, GENES, and pathways based on subgraph search

Ersoy, Gökhan
The analysis of Single Nucleotide Polymorphisms (SNPs) through Genome Wide Association Studies (GWAS) presents great potential for describing disease loci and gaining insight into the underlying etiology of diseases. Recently described combined p-value approach allows identification of associations at gene and pathway level. The integrated programs like METU-SNP produce simple lists of either SNP id/gene id/pathway title and their p-values and significance status or SNP id/disease id/pathway information. In this study, starting with the SNP id, we have annotated related gene ids and pathway ids consecutively. Then we have computed the intersection of these pathways, and visualized the common sub-graphs by an interactive graphical library. The tool developed in this thesis provides a visualization of the text output as graphical knowledge networks; hence, facilitates the efficient use of the information offered by the candidate SNP Biomarkers and helping discovery of SNP associated biological networks


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Oğuz, Gökçe; Acar, Aybar Can; Aydın Son, Yeşim; Department of Bioinformatics (2014)
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 c...
Investigation of the impacts of linkage disequilibrium on SNP selection studies
Kantar Özçırpan, Ekin; Weber, Gerhard Wilhelm; İyigün, Cem; Department of Biomedical Engineering (2015)
In many Genome Wide Association Studies (GWAS), the relation between SNPs and complex diseases has being tried to reveal. Moreover it is known that, in GWAS there exist a high amount of data which include relations between SNPs, phenotypes and diseases, etc. Many algorithms have been used to be able to reach the desired information from this huge data. Therefore, in this study, an algorithm one of whose important steps is based on linkage disequilibrium(LD), was constructed to eliminate the redundant inform...
A novel SVM-ID3 Hybrid Feature Selection Method to Build a Disease Model for Melanoma using Integrated Genotyping and Phenotype Data from dbGaP
Aydın Son, Yeşim (2014-09-03)
The relations between Single Nucleotide Polymorphism (SNP) and complex diseases are likely to be non-linear and require analysis of the high dimensional data. Previous studies in the field mostly focus on genotyping and effects of various phenotypes are not considered. To fill this gap a hybrid feature selection model of support vector machine and decision tree has been designed. The designed method is tested on melanoma. We were able to select phenotypic features such as moles and dysplastic nevi, and SNPs...
A test for detecting etiologic heterogeneity in epidemiological studies
Karagulle, S.; Kalaylıoğlu Akyıldız, Zeynep Işıl (2016-02-17)
Current statistical methods for analyzing epidemiological data with disease subtype information allow us to acquire knowledge not only for risk factor-disease subtype association but also, on a more profound account, heterogeneity in these associations by multiple disease characteristics (so-called etiologic heterogeneity of the disease). Current interest, particularly in cancer epidemiology, lies in obtaining a valid p-value for testing the hypothesis whether a particular cancer is etiologically heterogene...
Optimization of weights and features in use of AHP for SNP prioritization
Yılmaz, Arif; Aydın Son, Yeşim; Department of Medical Informatics (2018)
Single Nucleotide Polymorphisms (SNP) holds a promise in identification of genomic footprints of complex diseases such as cancer and diabetes. However identification of SNPs associated to complex diseases is a challenging problem due to the high number and variety of SNPs present in individual genomes. Analysis of genome wide studies of SNP datasets mainly focus on statistical evidence. As there are close to hundred million SNPs in human genome, incorporating biological and functional knowledge about statis...
Citation Formats
G. Ersoy, “A multi-layered graphical model of the relation among SNPS, GENES, and pathways based on subgraph search,” M.S. - Master of Science, Middle East Technical University, 2015.