Bioinformatics Advance Access originally published online on November 24, 2008
Bioinformatics 2009 25(2):237-242; doi:10.1093/bioinformatics/btn613
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
*To whom correspondence should be addressed.
 |
Abstract |
|---|
Motivation: Complex diseases are generally thought to be under the influence of one or more mutated risk genes as well as genetic and environmental factors. Many traditional methods have been developed to identify susceptibility genes assuming a single-gene disease model (‘single-locus methods’). Pathway-based approaches, combined with traditional methods, consider the joint effects of genetic factor and biologic network context. With the accumulation of high-throughput SNP datasets and human biologic pathways, it becomes feasible to search for risk pathways associated with complex diseases using bioinformatics methods. By analyzing the contribution of genetic factor and biologic network context in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, we proposed an approach to prioritize risk pathways for complex diseases: Prioritizing Risk Pathways fusing SNPs and pathways (PRP). A risk-scoring (RS) measurement was used to prioritize risk biologic pathways. This could help to demonstrate the pathogenesis of complex diseases from a new perspective and provide new hypotheses. We introduced this approach to five complex diseases and found that these five diseases not only share common risk pathways, but also have their specific risk pathways, which is verified by literature retrieval.
Availability: Genotype frequencies of five case–control samples were downloaded from the WTCCC online system and the address is https://www.wtccc.org.uk/info/access_to_data_samples.shtml
Contact: chenlina{at}ems.hrbmu.edu.cn; lixia{at}hrbmu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
The authors wish it to be known that, in their opinion, first four authors and the last author should be regarded as joint First Authors.
Associate Editor: Alex Bateman
Received on August 1, 2008; revised on October 27, 2008; accepted on November 21, 2008
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  I. Medina, D. Montaner, N. Bonifaci, M. A. Pujana, J. Carbonell, J. Tarraga, F. Al-Shahrour, and J. Dopazo Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies Nucleic Acids Res., July 1, 2009; 37(suppl_2): W340 - W344. [Abstract] [Full Text] [PDF]
|
|