ICSNPathway: Identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Zhang, Kunlin ^a   Chang, Suhua ^a,b   Cui, Sijia ^a,b   Guo, Liyuan ^a   Zhang, Liuyan ^a,b   Wang, Jing ^a  

^a INSTITUTE OF PSYCHOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DATA ANALYSIS; FEASIBILITY STUDY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; INTERNET; PRIORITY JOURNAL; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM; WEB SERVER;

ARTHRITIS, RHEUMATOID; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INTERNET; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 79959928376     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr391     Document Type: Article

References (32)

1. McCarthy, M.I., Abecasis, G.R., Cardon, L.R., Goldstein, D.B., Little, J., Ioannidis, J.P. and Hirschhorn, J.N. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet., 9, 356-369. (Pubitemid 351556063)
2. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S. and Manolio, T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
3. McCarthy, M.I. and Hirschhorn, J.N. (2008) Genome-wide association studies: potential next steps on a genetic journey. Hum. Mol. Genet., 17, R156-R165.
4. Johnson, A.D., Handsaker, R.E., Pulit, S.L., Nizzari, M.M., O'Donnell, C.J. and de Bakker, P.I. (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics, 24, 2938-2939.
5. Adzhubei, I.A., Schmidt, S., Peshkin, L., Ramensky, V.E., Gerasimova, A., Bork, P., Kondrashov, A.S. and Sunyaev, S.R. (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248-249.
6. Kumar, P., Henikoff, S. and Ng, P.C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073-1081.
7. Yue, P., Melamud, E. and Moult, J. (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics, 7, 166.
8. Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S. and Thomas, P.D. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204-D210.
9. Yuan, H.Y., Chiou, J.J., Tseng, W.H., Liu, C.H., Liu, C.K., Lin, Y.J., Wang, H.H., Yao, A., Chen, Y.T. and Hsu, C.N. (2006) FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res., 34, W635-W641. (Pubitemid 44529848)
10. Lee, P.H. and Shatkay, H. (2008) F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res., 36, D820-D824. (Pubitemid 351149829)
11. Schmitt, A.O., Assmus, J., Bortfeldt, R.H. and Brockmann, G.A. (2010) CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. Bioinformatics, 26, 969-970.
12. Saccone, S.F., Bolze, R., Thomas, P., Quan, J., Mehta, G., Deelman, E., Tischfield, J.A. and Rice, J.P. (2010) SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. Nucleic Acids Res., 38, W201-W209.
13. Xu, Z. and Taylor, J.A. (2009) SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res., 37, W600-W605.
14. Wang, K., Li, M. and Hakonarson, H. (2010) Analysing biological pathways in genome-wide association studies. Nat. Rev. Genet., 11, 843-854.
15. Cantor, R.M., Lange, K. and Sinsheimer, J.S. (2010) Prioritizing GWAS results: A review of statistical methods and recommendations for their application. Am. J. Hum. Genet., 86, 6-22.
16. 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.
17. Nam, D., Kim, J., Kim, S.Y. and Kim, S. (2010) GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res., 38, W749-W754.
18. Zhang, K., Cui, S., Chang, S., Zhang, L. and Wang, J. (2010) i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res., 38, W90-W95.
19. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
20. Altshuler, D.M., Gibbs, R.A., Peltonen, L., Dermitzakis, E., Schaffner, S.F., Yu, F., Bonnen, P.E., de Bakker, P.I., Deloukas, P., Gabriel, S.B. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52-58.
21. Flicek, P., Aken, B.L., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S. et al. (2010) Ensembl's 10th year. Nucleic Acids Res., 38, D557-D562.
22. Reiner, A., Yekutieli, D. and Benjamini, Y. (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 19, 368-375. (Pubitemid 36284936)
23. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
24. 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. (Pubitemid 41528093)
25. WTCCC. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.
26. Plenge, R.M., Seielstad, M., Padyukov, L., Lee, A.T., Remmers, E.F., Ding, B., Liew, A., Khalili, H., Chandrasekaran, A., Davies, L.R. et al. (2007) TRAF1-C5 as a risk locus for rheumatoid arthritis-a genomewide study. N. Engl. J. Med., 357, 1199-1209. (Pubitemid 47443179)
27. Gregersen, P.K., Amos, C.I., Lee, A.T., Lu, Y., Remmers, E.F., Kastner, D.L., Seldin, M.F., Criswell, L.A., Plenge, R.M., Holers, V.M. et al. (2009) REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat. Genet., 41, 820-823.
28. Stahl, E.A., Raychaudhuri, S., Remmers, E.F., Xie, G., Eyre, S., Thomson, B.P., Li, Y., Kurreeman, F.A., Zhernakova, A., Hinks, A. et al. (2010) Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat. Genet., 42, 508-514.
29. Kochi, Y., Okada, Y., Suzuki, A., Ikari, K., Terao, C., Takahashi, A., Yamazaki, K., Hosono, N., Myouzen, K., Tsunoda, T. et al. (2010) A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility. Nat. Genet., 42, 515-519.
30. Fiorillo, E., Orru, V., Stanford, S.M., Liu, Y., Salek, M., Rapini, N., Schenone, A.D., Saccucci, P., Delogu, L.G., Angelini, F. et al. (2010) Autoimmune-associated PTPN22 R620W variation reduces phosphorylation of lymphoid phosphatase on an inhibitory tyrosine residue. J. Biol. Chem., 285, 26506-26518.
31. Musone, S.L., Taylor, K.E., Lu, T.T., Nititham, J., Ferreira, R.C., Ortmann, W., Shifrin, N., Petri, M.A., Kamboh, M.I., Manzi, S. et al. (2008) Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat. Genet., 40, 1062-1064.
32. Schadt, E.E. (2009) Molecular networks as sensors and drivers of common human diseases. Nature, 461, 218-223.