GSA-SNP: A general approach for gene set analysis of polymorphisms

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Nam, Dougu ^a   Kim, Jin ^b   Kim, Seon Young ^c   Kim, Sangsoo ^d  

^a Ulsan National Institute of Science and Technology   (South Korea)

^b Seoul National University   (South Korea)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^d Soongsil University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASIAN; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA POLYMORPHISM; GENETIC ASSOCIATION; GENETIC DATABASE; INTERNET; KOREA; MATHEMATICAL COMPUTING; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ADULT; BODY HEIGHT; GENETICS; HUMAN;

ADULT; BODY HEIGHT; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77954300600     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq428     Document Type: Article

References (31)

1. Hirschhorn,J.N. and Daly,M.J. (2005) Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet., 6, 95-108.
2. Wang,W.Y., Barratt,B.J., Clayton,D.G. and Todd,J.A. (2005) Genome-wide association studies: theoretical and practical concerns. Nat. Rev. Genet., 6, 109-118.
3. Mootha,V.K., Lindgren,C.M., Eriksson,K.F., Subramanian,A., Sihag,S., Lehar,J., Puigserver,P., Carlsson,E., Ridderstrale,M., Laurila,E. et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
4. Goeman,J.J. and Bühlmann,P. (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23, 980-987.
5. Nam,D. and Kim,S.Y. (2008) Gene-set approach for expression pattern analysis. Brief Bioinform., 9, 189-197.
6. Wang,K., Li,M. and Bucan,M. (2007) Pathway-Based Approaches for Analysis of Genomewide Association Studies. Am. J. Hum. Genet., 81, 1278-1283.
7. Wang,K., Zhang,H., Ma,D., Bucan,M., Glessner,J.T., Abrahams,B.S., Salyakina,D., Imielinski,M., Bradfield,J.P., Sleiman,P.M. et al. (2009) Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature, 459, 528-533.
8. Chen,L., Zhang,L., Zhao,Y., Xu,L., Shang,Y., Wang,Q., Li,W., Wang,H. and Li,X. (2009) Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. Bioinformatics, 25, 237-242.
9. Lesnick,T.G., Papapetropoulos,S., Mash,D.C., Ffrench-Mullen,J., Shehadeh,L., de Andrade,M., Henley,J.R., Rocca,W.A., Ahlskog,J.E. and Maraganore,D.M. (2007) A genomic pathway approach to a complex disease: axon guidance and Parkinson disease. PLoS Genet., 3, e98.
10. Askland,K., Read,C. and Moore,J. (2009) Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission. Hum. Genet., 125, 63-79.
11. Purcell,S., Neale,B., Todd-Brown,K., Thomas,L., Ferreira,M.A., Bender,D., Maller,J., Sklar,P., de Bakker,P.I., Daly,M.J. et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
12. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Royal Statist. Soc. Ser. B, 57, 289-300.
13. Kim,S.Y. and Volsky,D.J. (2005) PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics, 6, 144.
14. Efron,B. and Tibshirani,R. (2007) On testing the significance of sets of genes. Ann. Appl. Stat., 1, 107-129.
15. Subramanian,A., Tamayo,P., Mootha,V.K., Mukherjee,S., Ebert,B.L., Gillette,M.A., Paulovich,A., Pomeroy,S.L., Golub,T.R., Lander,E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
16. Holden,M., Deng,S., Wojnowski,L. and Kulle,B. (2008) GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics, 24, 2784-2785.
17. Rebhan,M., Chalifa-Caspi,V., Prilusky,J. and Lancet,D. (1997) GeneCards: integrating information about genes, proteins and diseases. Trends Genet., 13, 163.
18. O'Dushlaine,C., Kenny,E., Heron,E.A., Segurado,R., Gill,M., Morris,D.W. and Corvin,A. (2009) The SNP ratio test: pathway analysis of genome-wide association datasets. Bioinformatics, 25, 2762-2763.
19. Medina,I., Montaner,D., Bonifaci,N., Pujana,M.A., Carbonell,J., Tarraga,J., Al-Shahrour,F. and Dopazo,J. (2009) Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res., 37, W340-W344.
20. Cho,Y.S., Go,M.J., Kim,Y.J., Heo,J.Y., Oh,J.H., Ban,H.J., Yoon,D., Lee,M.H., Kim,D.J., Park,M. et al. (2009) A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. Nat. Genet., 41, 527-534.
21. Silventoinen,K., Sammalisto,S., Perola,M., Boomsma,D.I., Cornes,B.K., Davis,C., Dunkel,L., De Lange,M., Harris,J.R., Hjelmborg,J.V. et al. (2003) Heritability of adult body height: a comparative study of twin cohorts in eight countries. Twin Res., 6, 399-408.
22. Lettre,G., Jackson,A.U., Gieger,C., Schumacher,F.R., Berndt,S.I., Sanna,S., Eyheramendy,S., Voight,B.F., Butler,J.L., Guiducci,C. et al. (2008) Identification of ten loci associated with height highlights new biological pathways in human growth. Nat. Genet., 40, 584-591.
23. Johansson,A., Marroni,F., Hayward,C., Franklin,C.S., Kirichenko,A.V., Jonasson,I., Hicks,A.A., Vitart,V., Isaacs,A., Axenovich,T. et al. (2009) Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis. Hum. Mol. Genet., 18, 373-380.
24. Yang,T.L., Xiong,D.H., Guo,Y., Recker,R.R. and Deng,H.W. (2008) Comprehensive association analyses of IGF1, ESR2, and CYP17 genes with adult height in Caucasians. Eur. J. Hum. Genet., 16, 1380-1387.
25. Weedon,M.N., Lango,H., Lindgren,C.M., Wallace,C., Evans,D.M., Mangino,M., Freathy,R.M., Perry,J.R., Stevens,S., Hall,A.S. et al. (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet., 40, 575-583.
26. Gudbjartsson,D.F., Walters,G.B., Thorleifsson,G., Stefansson,H., Halldorsson,B.V., Zusmanovich,P., Sulem,P., Thorlacius,S., Gylfason,A., Steinberg,S. et al. (2008) Many sequence variants affecting diversity of adult human height. Nat. Genet., 40, 609-615.
27. Polasek,O., Marusic,A., Rotim,K., Hayward,C., Vitart,V., Huffman,J., Campbell,S., Jankovic,S., Boban,M., Biloglav,Z. et al. (2009) Genome-wide association study of anthropometric traits in Korcula Island, Croatia. Croat Med. J., 50, 7-16.
28. Lee,K. and Kim,S. (2009) A scheme for filtering SNPs imputed in 8,842 Korean individuals based on the International HapMap Project data. Genomics Inform., 7, 136-140.
29. Chu,Z. and Moenter,S.M. (2005) Endogenous activation of metabotropic glutamate receptors modulates GABAergic transmission to gonadotropin-releasing hormone neurons and alters their firing rate: a possible local feedback circuit. J. Neurosci., 25, 5740-5749.
30. Yanovski,J.A., Rose,S.R., Municchi,G., Pescovitz,O.H., Hill,S.C., Cassorla,F.G. and Cutler,G.B. Jr (2003) Treatment with a luteinizing hormone-releasing hormone agonist in adolescents with short stature. N. Engl. J. Med., 348, 908-917.
31. Reimer,R.J. and Edwards,R.H. (2004) Organic anion transport is the primary function of the SLC17/type I phosphate transporter family. Pflugers Arch., 447, 629-635.