Literature DB >> 19620097

The SNP ratio test: pathway analysis of genome-wide association datasets.

Colm O'Dushlaine1, Elaine Kenny, Elizabeth A Heron, Ricardo Segurado, Michael Gill, Derek W Morris, Aiden Corvin.   

Abstract

UNLABELLED: We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs within genes that are part of a pathway and computes an empirical P-value based on comparisons to ratios in datasets where the assignment of case/control status has been randomized. We applied the SRT to a Parkinson's disease GWAS dataset, using the KEGG database, revealing significance for Parkinson's disease and related pathways. AVAILABILITY: https://sourceforge.net/projects/snpratiotest/

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Mesh：

Year:  2009        PMID： 19620097     DOI： 10.1093/bioinformatics/btp448

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  76 in total

1.  Pathway analysis of genome-wide association study and transcriptome data highlights new biological pathways in colorectal cancer.

Authors:  Baoku Quan; Xingsi Qi; Zhihui Yu; Yongshuai Jiang; Mingzhi Liao; Guangyu Wang; Rennan Feng; Liangcai Zhang; Zugen Chen; Qinghua Jiang; Guiyou Liu
Journal:  Mol Genet Genomics       Date:  2014-11-02       Impact factor: 3.291

2.  Genetic analysis of biological pathway data through genomic randomization.

Authors:  Brian L Yaspan; William S Bush; Eric S Torstenson; Deqiong Ma; Margaret A Pericak-Vance; Marylyn D Ritchie; James S Sutcliffe; Jonathan L Haines
Journal:  Hum Genet       Date:  2011-01-30       Impact factor: 4.132

Review 3.  Network biology methods integrating biological data for translational science.

Authors:  Gurkan Bebek; Mehmet Koyutürk; Nathan D Price; Mark R Chance
Journal:  Brief Bioinform       Date:  2012-03-05       Impact factor: 11.622

4.  Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.

Authors:  Qing Xiong; Nicola Ancona; Elizabeth R Hauser; Sayan Mukherjee; Terrence S Furey
Journal:  Genome Res       Date:  2011-09-22       Impact factor: 9.043

5.  Locus category based analysis of a large genome-wide association study of rheumatoid arthritis.

Authors:  Jan Freudenberg; Annette T Lee; Katherine A Siminovitch; Christopher I Amos; David Ballard; Wentian Li; Peter K Gregersen
Journal:  Hum Mol Genet       Date:  2010-07-16       Impact factor: 6.150

6.  The regulation-of-autophagy pathway may influence Chinese stature variation: evidence from elder adults.

Authors:  Feng Pan; Xiao-Gang Liu; Yan-Fang Guo; Yuan Chen; Shan-Shan Dong; Chuan Qiu; Zhi-Xin Zhang; Qi Zhou; Tie-Lin Yang; Yan Guo; Xue-Zhen Zhu; Hong-Wen Deng
Journal:  J Hum Genet       Date:  2010-05-07       Impact factor: 3.172

7.  dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.

Authors:  Peilin Jia; Siyuan Zheng; Jirong Long; Wei Zheng; Zhongming Zhao
Journal:  Bioinformatics       Date:  2010-11-02       Impact factor: 6.937

8.  Testing SNPs and sets of SNPs for importance in association studies.

Authors:  Holger Schwender; Ingo Ruczinski; Katja Ickstadt
Journal:  Biostatistics       Date:  2010-07-02       Impact factor: 5.899

Review 9.  Analysing biological pathways in genome-wide association studies.

Authors:  Kai Wang; Mingyao Li; Hakon Hakonarson
Journal:  Nat Rev Genet       Date:  2010-12       Impact factor: 53.242

Review 10.  Pathways to neurodegeneration: mechanistic insights from GWAS in Alzheimer's disease, Parkinson's disease, and related disorders.

Authors:  Vijay K Ramanan; Andrew J Saykin
Journal:  Am J Neurodegener Dis       Date:  2013-09-18
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