Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
Optimization of weights and features in use of AHP for SNP prioritization
Date
2018
Author
Yılmaz, Arif
Metadata
Show full item record
Item Usage Stats
223
views
0
downloads
Cite This
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 statistically significant SNPs provides valuable features for further selection of SNPs. Analytical Hierarchy Process (AHP) based SNP prioritization approach is a method developed for this purpose. However, AHP requires expert knowledge, which results in subjective decisions. In this work, we propose a novel approach for AHP design and optimization by utilizing Random Forest based AHP (RF-AHP) assessment on categories. We utilized the results of previously developed genomic model on Prostate Cancer. Proposed RF-AHP approach was compared with Delphi-AHP based method on Schizophrenia, Prostate Cancer, Type 2 Diabetes and Alzheimer’s disease genomic datasets and same performance was achieved. Additionally, RegulomeDB database was integrated to RF-AHP. While similar performance was obtained in most of the datasets better prioritization scoring is achieved for Schizophrenia disease.
Subject Keywords
Single nucleotide polymorphisms.
,
Prostate
,
Diabetes.
,
Bioinformatics.
URI
http://etd.lib.metu.edu.tr/upload/12621874/index.pdf
https://hdl.handle.net/11511/27086
Collections
Graduate School of Informatics, Thesis
Suggestions
OpenMETU
Core
A multi-layered graphical model of the relation among SNPS, GENES, and pathways based on subgraph search
Ersoy, Gökhan; Aydın Son, Yeşim; Can, Tolga; Department of Bioinformatics (2015)
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...
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...
Association of-174G/C interleukin-6 gene polymorphism with the risk of chronic lymphocytic, chronic myelogenous and acute myelogenous leukemias in Turkish patients
Mutlu, Pelin; Elci, Pinar; Yildirim, Murat; Cetin, A. Turker; Avcu, Ferit (2014-07-01)
Purpose: The purpose of this study was to evaluate the relationship between -174G/C interleukin-6 (IL-6) gene promoter polymorphism and susceptibility to chronic lymphocytic (CLL), chronic myelogenous (CML) and acute myelogenous leukemia (AML) in Turkish patients.
Training of ANFIS Network by Genetic Algorithm for Diagnosis of Leukemia Cancer Subtypes Using Gene Expression Profile
Arslan, Mustafa Turan; Haznedar, Bülent; Kalınlı, Adem (2017-05-12)
In this study, subtypes of Leukemia cancer has classified by using microarray gene expression profiles. An approach is proposed to train Adaptive Neuro Fuzzy Inference System (ANFIS) network by using a population-based Genetic Algorithm (GA) to classify this cancer data. The classification success of the proposed model has compared with the successes of Backpropagation (BP)-ANFIS and Hybrid-ANFIS, which are derivative based ANFIS models. According to obtained results, GA-ANFIS model has performed ve...
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...
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
A. Yılmaz, “Optimization of weights and features in use of AHP for SNP prioritization,” Ph.D. - Doctoral Program, Middle East Technical University, 2018.
