Integration of METU-SNP databases via RDF for PI_SNP web service

Download
index.pdf
2014
Gedikoğlu, Ceyhun
Show full item record
229
views
80
downloads
Single Nucleotide Polymorphism (SNP) is a variation which occurs after a nucleotide mutates between members of a species or paired chromosomes in DNA sequence. SNP data is especially important for identifying genetic variations underlying complex diseases. The need for collection and service of this data under a standard format and globally normalized and structured metadata that houses the structured SNP data is becoming more important while recent advances in high-throughput genotyping technologies are resulting in data accumulation at large scales. This means every new research can result with new data and we need all the new data for our computations. Offline databases can only offer a collection of data but cannot provide access to updated information. So we have built an integrated (iSNP) database that is a regularly updated. This machine curated database that holds SNP and its associated metadata from publicly available databases under a structured standard format can be efficiently utilized within different applications. Also the adaptation of the METU-SNP desktop application(SNP prioritization tool for complex diseases) to the web environment, which is supported by the iSNP database is included as a part of the study. This study will help bioinformaticians from all over the world reach the METU-SNP application with the upto date SNP information used in it via web environment.
Single nucleotide polymorphisms., Genetics, Semantic Web., Semantic integration (Computer systems)., Medical genetics
http://etd.lib.metu.edu.tr/upload/12616830/index.pdf
https://hdl.handle.net/11511/23307
Graduate School of Informatics, Thesis

Suggestions

iSNP: An integrated, automatically updated SNP database
Çarkacioǧlu, Levent; Gedikoǧlu, Ceyhun; Aydın Son, Yeşim (2012-06-29)
Single Nucleotide Polymorphisms (SNP) is a DNA sequence variation that occurs when a single nucleotide differs between members of a biological species or paired chromosomes in an individual. Studies on SNP data are important for scientists to shed light on identifying genetic variations underlying complex diseases. While recent advances in high-throughput genotyping technologies are resulting in data accumulation at large scales, the need for collection and service of this data under a standard format and g...
Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters
SHIN, Ilchung; RAY, Judhajeet; Gupta, Vinayak; İlgü, Müslüm; Beasley, Jonathan; BENDICKSON, Lee; MEHANOVIC, Samir; Kraus, George A.; Nilsen-Hamilton, Marit (Oxford University Press (OUP), 2014-01-01)
We describe a ribonucleic acid (RNA) reporter system for live-cell imaging of gene expression to detect changes in polymerase II activity on individual promoters in individual cells. The reporters use strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags) that can be expressed from a promoter of choice. For imaging, the cells are incubated with their ligands that are separately conjugated with one of the FRET pair, Cy3 and Cy5. The IMAGEtags were expressed in yeast from ...
Predicting the disease of Alzheimer (AD) with SNP biomarkers and clinical data based decision support system using data mining classification approaches
Erdoğan, Onur; Aydın Son, Yeşim; Department of Health Informatics (2012)
Single Nucleotide Polymorphisms (SNPs) are the most common DNA sequence variations where only a single nucleotide (A, T, C, G) in the human genome differs between individuals. Besides being the main genetic reason behind individual phenotypic differences, SNP variations have the potential to exploit the molecular basis of many complex diseases. Association of SNPs subset with diseases and analysis of the genotyping data with clinical findings will provide practical and affordable methodologies for the predi...
Functional characterization of microrna-125b expression in MCF7 breast cancer cell line
Tuna, Serkan; Erson Bensan, Ayşe Elif; Department of Biology (2010)
microRNA dependent gene expression regulation has roles in diverse processes such as differentiation, proliferation and apoptosis. Therefore, deregulated miRNA expression has functional importance for various diseases, including cancer. miR-125b is among the commonly downregulated miRNAs in breast cancer cells . Therefore we aimed to characterize the effects of miR-125b expression in MCF7 breast cancer cell line (BCCL) to better understand its roles in tumorigenesis. Here, we investigated mir-125 family mem...
Predicting the Disease of Alzheimer With SNP Biomarkers and Clinical Data Using Data Mining Classification Approach: Decision Tree
Erdogan, Onur; Aydın Son, Yeşim (2014-09-03)
Single Nucleotide Polymorphisms (SNPs) are the most common genomic variations where only a single nucleotide differs between individuals. Individual SNPs and SNP profiles associated with diseases can be utilized as biological markers. But there is a need to determine the SNP subsets and patients' clinical data which is informative for the diagnosis. Data mining approaches have the highest potential for extracting the knowledge from genomic datasets and selecting the representative SNPs as well as most effec...
Citation Formats
C. Gedikoğlu, “Integration of METU-SNP databases via RDF for PI_SNP web service,” M.S. - Master of Science, Middle East Technical University, 2014.
METU IIS - Integrated Information Service open@metu.edu.tr