SNPnexus: A web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

Bioinformatics

Volumn 25, Issue 5, 2009, Pages 655-661

  Chelala, Claude ^a   Khan, Arshad ^a   Lemoine, Nicholas R ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ARTICLE; BIOINFORMATICS; CHROMOSOME; CLONE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; GENE FREQUENCY; GENE LOCATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HUMAN COMPUTER INTERACTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SNPNEXUS DATABASE;

EID: 61449107734     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn653     Document Type: Article

References (46)

1. Ashurst,J.L. et al. (2005) The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res., 33, D459-D465.
2. Bairoch,A. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
3. Becker,K.G. et al. (2004) The genetic association database. Nat. Genet., 36, 431-432.
4. Benson,D.A. et al. (2005) GenBank. Nucleic Acids Res., 33 D34-D38.
5. Chelala,C. et al. (2007) PTPN22 R620W functional variant in type 1 diabetes and autoimmunity related traits. Diabetes, 56, 522-526.
6. Cohen,J.C. et al. (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science, 305, 869-872.
7. Conde,L. et al. (2006) PupaSuite: Finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res., 34, W621-W625.
8. Conrad,D.F. et al. (2006) A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet., 38, 75-81.
9. Davuluri,R.V. et al. (2001) Computational identification of promoters and first exons in the human genome. Nat. Genet., 29 412-417.
10. Feuk,L. et al. (2006) Structural variation in the human genome. Nat. Rev. Genet., 7, 85-97.
11. Frazer,K.A. et al. (2007)Asecond generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
12. Griffiths-Jones,S. (2004) The microRNA registry. Nucleic Acids Res. 32, D109-D111.
13. Grimson,A. et al. (2007) MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol. Cell, 27, 91-105.
14. Hinds,D.A. et al. (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet., 38, 82-85.
15. Hsu,F. et al. (2006) The UCSC Known Genes. Bioinformatics, 22, 1036-1046.
16. Huang,M. et al. (2007) High-order interactions among genetic variants in DNA base excision repair pathway genes and smoking in bladder cancer susceptibility. Cancer Epidemiol. Biomarkers Prev., 16, 84-91.
17. Hubbard,T.J. et al. (2007) Ensembl 2007. Nucleic Acids Res., 35, D610-D617.
18. Iafrate,A.J. et al. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36, 949-951.
19. Iorio,M.V. et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res., 65, 7065-7070.
20. Jorgenson,E. and Witte,J.S. (2006) A gene-centric approach to genome-wide association studies. Nat. Rev. Genet., 7, 885-891.
21. Kawakubo,H. et al. (2004) Expression of the NF-kappaB-responsive gene BTG2 is aberrantly regulated in breast cancer. Oncogene, 23, 8310-8319.
22. Kawasaki,E. et al. (2006) Systematic search for single nucleotide polymorphisms in a lymphoid tyrosine phosphatase gene (PTPN22): association between a promoter polymorphism and type 1 diabetes in Asian populations. Am. J. Med. Genet. A, 140, 586-593.
23. Lewis,B.P. et al. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
24. Lewis,B.P. et al. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
25. Li,D. et al. (2007a) Effects of base excision repair gene polymorphisms on pancreatic cancer survival. Int. J. Cancer, 120, 1748-1754.
26. Li,S. et al. (2007b) Snap: An integrated SNP annotation platform. Nucleic Acids Res., 35, D707-D710.
27. Locke,D.P. et al. (2006) Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet., 79, 275-290.
28. McCarroll,S.A. et al. (2006) Common deletion polymorphisms in the human genome. Nat. Genet., 38, 86-92.
29. Pruitt,K.D. et al. (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
30. Ramensky,V. et al. (2002) Human non-synonymous SNPs: Server and survey. Nucleic Acids Res., 30, 3894-3900.
31. Redon,R. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
32. Romeo,S. et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat. Genet., 39, 513-516.
33. Sangrajrang,S. et al. (2008) Polymorphisms in three base excision repair genes and breast cancer risk in Thai women. Breast Cancer Res. Treat., 111, 279-288.
34. Sebat,J. et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305, 525-528.
35. Sharp,A.J. et al. (2005) Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet., 77, 78-88.
36. Sherry,S.T. et al. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
37. Siddiq,A. et al. (2005) A synonymous coding polymorphism in the alpha2-Heremans-schmid glycoprotein gene is associated with type 2 diabetes in French Caucasians. Diabetes, 54, 2477-2481.
38. Smyth,D. et al. (2004) Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes, and evidence for its role as a general autoimmunity locus. Diabetes 53, 3020-3023.
39. Stranger,B.E. et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science, 315 848-853.
40. Thierry-Mieg,D. and Thierry-Mieg,J. (2006) AceView: A comprehensive cDNA-supported gene and transcripts annotation. Genome Biol., 7 (Suppl. 1), S12 1-14.
41. Tuzun,E. et al. (2005) Fine-scale structural variation of the human genome. Nat. Genet., 37, 727-732.
42. Weber,M.J. (2005) New human and mouse microRNA genes found by homology search. FEBS J., 272, 59-73.
43. Wiltshire,S. et al. (2006) The value of gene-based selection of tag SNPs in genome-wide association studies. Eur. J. Hum. Genet., 14, 1209-1214.
44. Wingender,E. et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.
45. Yoon,S. and De Micheli,G. (2005) Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics, 21 (Suppl. 2), ii93-ii100.
46. Zhang,W. et al. (2008) The HapMap resource is providing new insights into ourselves and its application to pharmacogenomics. Bioinform. Biol. Insights, 2, 15-23.