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

Chelala, Claude, Khan, Arshad, Lemoine, Nicholas R·2009·Bioinformatics
DOI 10.1093/bioinformatics/btn653PMC PMC2647830
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Abstract

Motivation: Design a new computational tool allowing scientists to functionally annotate newly discovered and public domain single nucleotide polymorphisms in order to help in prioritizing targets in further disease studies and large-scale genotyping projects. Summary: SNPnexus database provides functional annotation for both novel and public SNPs. Possible effects on the transcriptome and proteome levels are characterized and reported from five major annotation systems providing the most extensive information on alternative splicing. Additional information on HapMap genotype and allele frequency, overlaps with potential regulatory elements or structural variations as well as related genetic diseases can be also retrieved. The SNPnexus database has a user-friendly web interface, providing single or batch query options using SNP identifiers from dbSNP as well as genomic location on clones, contigs or chromosomes. Therefore, SNPnexus is the only database currently providing a complete set of functional annotations of SNPs in public databases and newly detected from sequencing projects. Hence, we describe SNPnexus, provide details of the query options, the annotation categories as well as biological examples of use. Availability: The SNPnexus database is freely available at http://www.snp-nexus.org. Contact: claude.chelala@cancer.org.uk

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  • APOC1 SNPs perform similar functions as APOE, including roles in signal transduction, plasma lipoprotein regulation, and the transport of small molecules.

    “APOC1 SNPs perform similar functions as APOE, including roles in signal transduction, plasma lipoprotein regulation, and the transport of small molecules [35].”

    From Association of APOC1 with cortical atrophy during conversion to Alzheimer’s disease (2025) · cites this paper as [35]

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Research works printed but not linked: 40

  1. Ashurst, 2005, The Vertebrate Genome Annotation (Vega) database, Nucleic Acids Res., 33, D459, 10.1093/nar/gki135 · DOI
  2. Bairoch, 2005, The Universal Protein Resource (UniProt), Nucleic Acids Res., 33, D154, 10.1093/nar/gki070 · DOI · Paper page
  3. Becker, 2004, The genetic association database, Nat. Genet., 36, 431, 10.1038/ng0504-431 · DOI
  4. Benson, 2005, GenBank, Nucleic Acids Res., 33, D34, 10.1093/nar/gki063 · DOI
  5. Chelala, 2007, PTPN22 R620W functional variant in type 1 diabetes and autoimmunity related traits, Diabetes, 56, 522, 10.2337/db06-0942 · DOI
  6. Conde, 2006, PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes, Nucleic Acids Res., 34, W621, 10.1093/nar/gkl071 · DOI
  7. Conrad, 2006, A high-resolution survey of deletion polymorphism in the human genome, Nat. Genet., 38, 75, 10.1038/ng1697 · DOI
  8. Davuluri, 2001, Computational identification of promoters and first exons in the human genome, Nat. Genet., 29, 412, 10.1038/ng780 · DOI
  9. Feuk, 2006, Structural variation in the human genome, Nat. Rev. Genet., 7, 85, 10.1038/nrg1767 · DOI
  10. Griffiths-Jones, 2004, The microRNA registry, Nucleic Acids Res., 32, D109, 10.1093/nar/gkh023 · DOI
  11. Grimson, 2007, MicroRNA targeting specificity in mammals: determinants beyond seed pairing, Mol. Cell, 27, 91, 10.1016/j.molcel.2007.06.017 · DOI · Paper page
  12. Hsu, 2006, The UCSC Known Genes, Bioinformatics, 22, 1036, 10.1093/bioinformatics/btl048 · DOI
  13. Huang, 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, 10.1158/1055-9965.EPI-06-0712 · DOI
  14. Hubbard, 2007, Ensembl 2007, Nucleic Acids Res., 35, D610, 10.1093/nar/gkl996 · DOI
  15. Iorio, 2005, MicroRNA gene expression deregulation in human breast cancer, Cancer Res., 65, 7065, 10.1158/0008-5472.CAN-05-1783 · DOI · Paper page
  16. Jorgenson, 2006, A gene-centric approach to genome-wide association studies, Nat. Rev. Genet., 7, 885, 10.1038/nrg1962 · DOI
  17. Kawakubo, 2004, Expression of the NF-kappaB-responsive gene BTG2 is aberrantly regulated in breast cancer, Oncogene, 23, 8310, 10.1038/sj.onc.1208008 · DOI
  18. Kawasaki, 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, 10.1002/ajmg.a.31124 · DOI
  19. Lewis, 2003, Prediction of mammalian microRNA targets, Cell, 115, 787, 10.1016/S0092-8674(03)01018-3 · DOI · Paper page
  20. Lewis, 2005, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120, 15, 10.1016/j.cell.2004.12.035 · DOI · Paper page
  21. Li, 2007, Effects of base excision repair gene polymorphisms on pancreatic cancer survival, Int. J. Cancer, 120, 1748, 10.1002/ijc.22301 · DOI
  22. Li, 2007, Snap: an integrated SNP annotation platform, Nucleic Acids Res., 35, D707, 10.1093/nar/gkl969 · DOI
  23. Locke, 2006, Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome, Am. J. Hum. Genet., 79, 275, 10.1086/505653 · DOI
  24. Pruitt, 2007, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res., 35, D61, 10.1093/nar/gkl842 · DOI
  25. Ramensky, 2002, Human non-synonymous SNPs: server and survey, Nucleic Acids Res., 30, 3894, 10.1093/nar/gkf493 · DOI
  26. Redon, 2006, Global variation in copy number in the human genome, Nature, 444, 444, 10.1038/nature05329 · DOI
  27. Romeo, 2007, Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL, Nat. Genet., 39, 513, 10.1038/ng1984 · DOI · Paper page
  28. Sangrajrang, 2008, Polymorphisms in three base excision repair genes and breast cancer risk in Thai women, Breast Cancer Res. Treat., 111, 279, 10.1007/s10549-007-9773-7 · DOI
  29. Sebat, 2004, Large-scale copy number polymorphism in the human genome, Science, 305, 525, 10.1126/science.1098918 · DOI · Paper page
  30. Sharp, 2005, Segmental duplications and copy-number variation in the human genome, Am. J. Hum. Genet., 77, 78, 10.1086/431652 · DOI
  31. Sherry, 2001, dbSNP: the NCBI database of genetic variation, Nucleic Acids Res., 29, 308, 10.1093/nar/29.1.308 · DOI · Paper page
  32. Siddiq, 2005, A synonymous coding polymorphism in the alpha2-Heremans-schmid glycoprotein gene is associated with type 2 diabetes in French Caucasians, Diabetes, 54, 2477, 10.2337/diabetes.54.8.2477 · DOI
  33. Smyth, 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, 10.2337/diabetes.53.11.3020 · DOI
  34. Stranger, 2007, Relative impact of nucleotide and copy number variation on gene expression phenotypes, Science, 315, 848, 10.1126/science.1136678 · DOI
  35. Tuzun, 2005, Fine-scale structural variation of the human genome, Nat. Genet., 37, 727, 10.1038/ng1562 · DOI
  36. Weber, 2005, New human and mouse microRNA genes found by homology search, FEBS J., 272, 59, 10.1111/j.1432-1033.2004.04389.x · DOI
  37. Wiltshire, 2006, The value of gene-based selection of tag SNPs in genome-wide association studies, Eur. J. Hum. Genet., 14, 1209, 10.1038/sj.ejhg.5201678 · DOI
  38. Wingender, 2001, The TRANSFAC system on gene expression regulation, Nucleic Acids Res., 29, 281, 10.1093/nar/29.1.281 · DOI
  39. Yoon, 2005, Prediction of regulatory modules comprising microRNAs and target genes, Bioinformatics, 21, ii93, 10.1093/bioinformatics/bti1116 · DOI
  40. Zhang, 2008, The HapMap resource is providing new insights into ourselves and its application to pharmacogenomics, Bioinform. Biol. Insights, 2, 15, 10.4137/BBI.S455 · DOI

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Metadata

Authors
Chelala, C., Khan, A., & Lemoine, N. R.
Affiliations
Centre for Molecular Oncology and Imaging, Institute of Cancer & CR-UK Clinical Centre, Barts & The London School of Medicine (QMUL), Charterhouse Square, London EC1M 6BQ, UK
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2008-12-19
Volume
25
Issue
5
Pages
655-661
ISSN
  • 1367-4811
  • 1367-4803
DOI
10.1093/bioinformatics/btn653
PMC
PMC2647830
Cited by
200
References
7
Language
en
Licence
creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2844 d)

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