METU-SNP: An Integrated Software System for SNPComplex Disease Association Analysis

2011-6
Aydın Son, Yeşim
Show full item record
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
209
views
116
downloads
Recently, there has been increasing research to discover genomic biomarkers, haplotypes, and potentially other variables that together contribute to the development of diseases. Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual's genetic variability in greatest detail. Genome-wide association studies (GWAS) of SNPs, high-dimensional case-control studies, are among the most promising approaches for identifying disease causing variants. METU-SNP software is a Java based integrated desktop application specifically designed for the prioritization of SNP biomarkers and the discovery of genes and pathways related to diseases via analysis of the GWAS case-control data. Outputs of METU-SNP can easily be utilized for the downstream biomarkers research to allow the prediction and the diagnosis of diseases and other personalized medical approaches. Here, we introduce and describe the system functionality and architecture of the METU-SNP. We believe that the METU-SNP will help researchers with the reliable identification of SNPs that are involved in the etiology of complex diseases, ultimately supporting the development of personalized medicine approaches and targeted drug discoveries.
GENOME-WIDE ASSOCIATION, IMPUTATION, DATABASE
https://hdl.handle.net/11511/50933
JOURNAL OF INTEGRATIVE BIOINFORMATICS
Graduate School of Informatics, Article

Suggestions

Systems-level analysis of genome wide association study results for a pilot juvenile idiopathic arthritis family study
Aydın Son, Yeşim; Demirkaya, Erkan; BİLGİNER, YELDA; KASAPÇOPUR, Özgür; Unsal, Erbil; ALİKAŞİFOĞLU, MEHMET; ÖZEN, SEZA (2015-01-01)
Genome wide association studies (GWAS) determine susceptibility profiles for complex diseases. In this study, GWAS was performed in 26 patients with oligo and rheumatoid factor negative polyarticular juvenile idiopathic artritis (JIA) and their healthy parents by Affymetrix 250K SNP arrays. Biological function and pathway enrichment analysis was done. This is the first GWAS reported for JIA families from the eastern Mediterranean population. Enrichment of Fc gamma R-mediated phagocytosis pathway and respons...
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences
Doğan, Tunca (PeerJ, 2018-8-2)
Analysing the relationships between biomolecules and the genetic diseases is a highly active area of research, where the aim is to identify the genes and their products that cause a particular disease due to functional changes originated from mutations. Biological ontologies are frequently employed in these studies, which provides researchers with extensive opportunities for knowledge discovery through computational data analysis. In this study, a novel approach is proposed for the identification of relatio...
COMPUTATIONAL MECHANICS FOR SOFT BIOLOGICAL TISSUES
Altun, Cem; Dal, Hüsnü; Department of Mechanical Engineering (2023-1-17)
Computational biomechanics is an active research area, not only to understand the mechanisms behind the behaviours of biological tissues but also to develop medical techniques for surgeries, rehabilitations, and diseases. The thesis mainly composed of two parts namely, growth-induced instabilities and dispersion-type anisotropic viscoelasticity for soft biological tissues. In the first part of the thesis, planar growth-induced instabilities for a three-dimensional bilayer-type confined tissue is examined. F...
Collagen scaffolds with in situ grown calcium phosphate for osteogenic differentiation of wharton’s jelly and menstrual blood stem cells
Karadaş, Özge; Hasırcı, Vasıf Nejat; Köse, Gamze Torun; Department of Biotechnology (2011)
The importance of developing new techniques for the treatment of bone and joint diseases is increasing continuosly together with the increase of human population and the average life span. Especially bone fractures as a result of osteoporosis are often seen in humans older than 50 years old. The expenses of bone and joint disease operations are very high and the duration of recovery is long. Because of these reasons World Health Organization, The United Nations and 37 countries announced that the years 2000...
Computational approaches leveraging integrated connections of multi-omic data toward clinical applications
Demirel, Habibe Cansu; Tunçbağ, Nurcan (2021-10-01)
In line with the advances in high-throughput technologies, multiple omic datasets have accumulated to study biological systems and diseases coherently. No single omics data type is capable of fully representing cellular activity. The complexity of the biological processes arises from the interactions between omic entities such as genes, proteins, and metabolites. Therefore, multi-omic data integration is crucial but challenging. The impact of the molecular alterations in multi-omic data is not local in the ...
Citation Formats
Y. Aydın Son, “METU-SNP: An Integrated Software System for SNPComplex Disease Association Analysis,” JOURNAL OF INTEGRATIVE BIOINFORMATICS, 2011, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/50933.
METU IIS - Integrated Information Service open@metu.edu.tr