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Bioinformatics. 2014 May 1;30(9):1287-9. doi: 10.1093/bioinformatics/btt743. Epub 2014 Jan 11.

PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data.

Author information

1
Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, 34353, Besiktas, Istanbul, Turkey, Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039, Kayseri, Turkey, Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey and Department of Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.

Abstract

Genome-wide association studies (GWAS) have revolutionized the search for the variants underlying human complex diseases. However, in a typical GWAS, only a minority of the single-nucleotide polymorphisms (SNPs) with the strongest evidence of association is explained. One possible reason of complex diseases is the alterations in the activity of several biological pathways. Here we present a web server called Pathway and Network-Oriented GWAS Analysis to devise functionally important pathways through the identification of SNP-targeted genes within these pathways. The strength of our methodology stems from its multidimensional perspective, where we combine evidence from the following five resources: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.

PMID:
24413675
DOI:
10.1093/bioinformatics/btt743
[Indexed for MEDLINE]

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