메뉴 건너뛰기




Volumn 14, Issue 4, 2013, Pages 437-447

A practical guide for the functional annotation of genetic variations using SNPnexus

Author keywords

Functional annotation; Genetic variant

Indexed keywords

ARTICLE; COMPUTER PROGRAM; FUNCTIONAL ANNOTATION; GENETIC DATABASE; GENETIC VARIABILITY; GENOMICS; HAPLOTYPE MAP; METHODOLOGY; MOLECULAR GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84889062907     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbt004     Document Type: Article
Times cited : (76)

References (33)
  • 1
    • 33750386813 scopus 로고    scopus 로고
    • The value of gene-based selection of tag SNPs in genome-wide association studies
    • Wiltshire S, de Bakker PI, Daly MJ. The value of gene-based selection of tag SNPs in genome-wide association studies. EurJ Hum Genet 2006;14:1209-14.
    • (2006) EurJ Hum Genet , vol.14 , pp. 1209-1214
    • Wiltshire, S.1    de Bakker, P.I.2    Daly, M.J.3
  • 2
    • 61449107734 scopus 로고    scopus 로고
    • SNP nexus: a web database for functional annotation of newly discovered and public domain Single Nucleotide Polymorphisms
    • Chelala C, Khan A, Lemoine NR. SNPnexus: a web database for functional annotation of newly discovered and public domain Single Nucleotide Polymorphisms. Bioinformatics 2009;25(5):655-61.
    • (2009) Bioinformatics , vol.25 , Issue.5 , pp. 655-661
    • Chelala, C.1    Khan, A.2    Lemoine, N.R.3
  • 3
    • 84864454040 scopus 로고    scopus 로고
    • SNP nexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)
    • Dayem Ullah AZ, Lemoine NR, Chelala C. SNP nexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). Nucleic Acids Res 2012;40(W1):W65-70.
    • (2012) Nucleic Acids Res , vol.40 , Issue.W1
    • Dayem Ullah, A.Z.1    Lemoine, N.R.2    Chelala, C.3
  • 4
    • 0035173378 scopus 로고    scopus 로고
    • dbSNP: the NCBI database of genetic variation
    • Sherry ST, Ward MH, Kholodov M, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001;29:308-11.
    • (2001) Nucleic Acids Res , vol.29 , pp. 308-311
    • Sherry, S.T.1    Ward, M.H.2    Kholodov, M.3
  • 5
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • The International Hap Map Consortium.
    • The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007;449:851-61.
    • (2007) Nature , vol.449 , pp. 851-861
  • 6
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007;35:D61-5.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 10
    • 33748486517 scopus 로고    scopus 로고
    • AceView: a comprehensive cDNA supported gene and transcripts annotation
    • Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA supported gene and transcripts annotation. Genome Biol 2006;7(Suppl 1):S12.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1
    • Thierry-Mieg, D.1    Thierry-Mieg, J.2
  • 11
    • 75549085982 scopus 로고    scopus 로고
    • H-InvDB in 2009: extended database and data mining resources for human genes and transcripts
    • Yamasaki C, Murakami K, Takeda J, et al. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res 2010;38: D626-32.
    • (2010) Nucleic Acids Res , vol.38
    • Yamasaki, C.1    Murakami, K.2    Takeda, J.3
  • 12
    • 67650064594 scopus 로고    scopus 로고
    • The consensus coding sequence (CCDS) project: Identifying a common proteincoding gene set for the human and mouse genomes
    • Pruitt KD, Harrow J, Harte RA, et al. The consensus coding sequence (CCDS) project: Identifying a common proteincoding gene set for the human and mouse genomes. Genome Res 2009;19:1316-23.
    • (2009) Genome Res , vol.19 , pp. 1316-1323
    • Pruitt, K.D.1    Harrow, J.2    Harte, R.A.3
  • 13
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009;4:1073-81.
    • (2009) Nat Protoc , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 14
    • 77951640946 scopus 로고    scopus 로고
    • A method and server for predicting damaging missense mutations
    • Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods 2010;7(4):248-9.
    • (2010) Nat Methods , vol.7 , Issue.4 , pp. 248-249
    • Adzhubei, I.A.1    Schmidt, S.2    Peshkin, L.3
  • 15
    • 44949243936 scopus 로고    scopus 로고
    • The HapMap resource is providing new insights into ourselves and its application to pharmacogenomics
    • Zhang W, Ratain MJ, Dolan ME. The HapMap resource is providing new insights into ourselves and its application to pharmacogenomics. Bioinform Biol Insights 2008;2:15-23.
    • (2008) Bioinform Biol Insights , vol.2 , pp. 15-23
    • Zhang, W.1    Ratain, M.J.2    Dolan, M.E.3
  • 16
    • 0035172256 scopus 로고    scopus 로고
    • The TRANSFAC system on gene expression regulation
    • Wingender E, Chen X, Fricke E, et al. The TRANSFAC system on gene expression regulation. Nucleic Acids Res 2001;29:281-3.
    • (2001) Nucleic Acids Res , vol.29 , pp. 281-283
    • Wingender, E.1    Chen, X.2    Fricke, E.3
  • 17
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet 2001;29:412-7.
    • (2001) Nat Genet , vol.29 , pp. 412-417
    • Davuluri, R.V.1    Grosse, I.2    Zhang, M.Q.3
  • 18
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian microRNA targets
    • Lewis BP, Shih IH, Jones-Rhoades MW, et al. Prediction of mammalian microRNA targets. Cell 2003;115:787-98.
    • (2003) Cell , vol.115 , pp. 787-798
    • Lewis, B.P.1    Shih, I.H.2    Jones-Rhoades, M.W.3
  • 19
    • 78651293534 scopus 로고    scopus 로고
    • miRBase: integrating microRNA annotation and deep-sequencing data
    • Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011;39:D152-7.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 20
    • 33644875300 scopus 로고    scopus 로고
    • snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
    • Lestrade L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 2006;34:D158-62.
    • (2006) Nucleic Acids Res , vol.34
    • Lestrade, L.1    Weber, M.J.2
  • 21
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. JMol Biol 1987;196:261-82.
    • (1987) J Mol Biol , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 22
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • Pennacchio LA, Ahituv N, Moses AM, et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006;444:499-502.
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1    Ahituv, N.2    Moses, A.M.3
  • 23
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005;15:1034-50.
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.S.3
  • 24
    • 78651237647 scopus 로고    scopus 로고
    • Identifying a high fraction of the human genome to be under selective constraint using GERP++
    • Davydov EV, Goode DL, Sirota M, et al. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 2010;6(12). e1001025.
    • (2010) PLoS Comput Biol , vol.6 , Issue.12
    • Davydov, E.V.1    Goode, D.L.2    Sirota, M.3
  • 26
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer
    • Forbes SA, Bindal N, Bamford S, et al. COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res 2011;39:D945-50.
    • (2011) Nucleic Acids Res , vol.39
    • Forbes, S.A.1    Bindal, N.2    Bamford, S.3
  • 27
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • Hindorff LA, Bindal N, Bamford S, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009;106:9362-7.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Bindal, N.2    Bamford, S.3
  • 29
    • 4444291843 scopus 로고    scopus 로고
    • Detection of large-scale variation in the human genome
    • Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36:949-51.
    • (2004) Nat Genet , vol.36 , pp. 949-951
    • Iafrate, A.J.1    Feuk, L.2    Rivera, M.N.3
  • 30
    • 33747836301 scopus 로고    scopus 로고
    • Effects of PTPN22 C1858T polymorphism on susceptibility and clinical characteristics of British Caucasian rheumatoid arthritis patients
    • Harrison P, Pointon JJ, Farrar C, et al. Effects of PTPN22 C1858T polymorphism on susceptibility and clinical characteristics of British Caucasian rheumatoid arthritis patients. Rheumatology 2006;45(8):1009-11.
    • (2006) Rheumatology , vol.45 , Issue.8 , pp. 1009-1011
    • Harrison, P.1    Pointon, J.J.2    Farrar, C.3
  • 31
    • 34548849168 scopus 로고    scopus 로고
    • TRAF1-C5 as a risk locus for rheumatoid arthritis-a genomewide study
    • Plenge RM, Seielstad M, Padyukov L, etal. TRAF1-C5 as a risk locus for rheumatoid arthritis-a genomewide study. N Engl J Med 2007;357(12):1199-209.
    • (2007) N Engl J Med , vol.357 , Issue.12 , pp. 1199-1209
    • Plenge, R.M.1    Seielstad, M.2    Padyukov, L.3
  • 32
    • 67649880295 scopus 로고    scopus 로고
    • REL, a member of the NF-κB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis
    • Gregersen PK, Amos , Lee AT, et al. REL, a member of the NF-κB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat Genet 2009;41(7):820-3.
    • (2009) Nat Genet , vol.41 , Issue.7 , pp. 820-823
    • Gregersen, P.K.1    Amos, .2    Lee, A.T.3
  • 33
    • 33846978695 scopus 로고    scopus 로고
    • Relative impact of nucleotide and copy number variation on gene expression phenotypes
    • Stranger BE, Forrest MS, Dunning M, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007;315(5813):848-53.
    • (2007) Science , vol.315 , Issue.5813 , pp. 848-853
    • Stranger, B.E.1    Forrest, M.S.2    Dunning, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.