메뉴 건너뛰기




Volumn 13, Issue , 2014, Pages 5-17

Functional annotation of putative regulatory elements at cancer susceptibility loci

Author keywords

Bioinformatics; Functional follow up; Regulatory prediction; Variant annotation

Indexed keywords

BIOINFORMATICS; CANCER RISK; CANCER SUSCEPTIBILITY; EPIGENETICS; GENE LOCUS; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HUMAN; PROTEIN STRUCTURE; QUANTITATIVE TRAIT LOCUS; REGULATORY SEQUENCE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84907533564     PISSN: None     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/CIN.S13789     Document Type: Review
Times cited : (6)

References (96)
  • 2
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano MT, Humbert R, Rynes E, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012;337(6099):1190-5.
    • (2012) Science , vol.337 , Issue.6099 , pp. 1190-1195
    • Maurano, M.T.1    Humbert, R.2    Rynes, E.3
  • 3
    • 70349956433 scopus 로고    scopus 로고
    • Finding the missing heritability of complex diseases
    • Manolio TA, Collins FS, Cox NJ, et al. Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747-53.
    • (2009) Nature , vol.461 , Issue.7265 , pp. 747-753
    • Manolio, T.A.1    Collins, F.S.2    Cox, N.J.3
  • 5
    • 34248336122 scopus 로고    scopus 로고
    • PhenCode: Connecting ENCODE data with mutations and phenotype
    • Giardine B, Riemer C, Hefferon T, et al. PhenCode: connecting ENCODE data with mutations and phenotype. Hum Mutat. 2007;28(6):554-62.
    • (2007) Hum Mutat , vol.28 , Issue.6 , pp. 554-562
    • Giardine, B.1    Riemer, C.2    Hefferon, T.3
  • 6
    • 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
  • 7
    • 0033976585 scopus 로고    scopus 로고
    • ProTherm, version 2.0: Thermodynamic database for proteins and mutants
    • Gromiha MM, An J, Kono H, et al. ProTherm, version 2.0: thermodynamic database for proteins and mutants. Nucleic Acids Res. 2000;28(1):283-5.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 283-285
    • Gromiha, M.M.1    An, J.2    Kono, H.3
  • 8
    • 0035176895 scopus 로고    scopus 로고
    • Thermodynamic database for protein-nucleic acid interactions (ProNIT)
    • Prabakaran P, An J, Gromiha MM, et al. Thermodynamic database for protein-nucleic acid interactions (ProNIT). Bioinformatics. 2001;17(11):1027-34.
    • (2001) Bioinformatics , vol.17 , Issue.11 , pp. 1027-1034
    • Prabakaran, P.1    An, J.2    Gromiha, M.M.3
  • 9
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • ENCODE Project Consortium, Bernstein BE, Birney E, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2
  • 10
    • 84862263248 scopus 로고    scopus 로고
    • The NIH roadmap epigenomics program data resource
    • Chadwick LH. The NIH roadmap epigenomics program data resource. Epigenomics. 2012;4(3):317-24.
    • (2012) Epigenomics , vol.4 , Issue.3 , pp. 317-324
    • Chadwick, L.H.1
  • 11
    • 84879786890 scopus 로고    scopus 로고
    • A brief review on the human encyclopedia of DNA elements (ENCODE) project
    • Qu H, Fang X. A brief review on the human encyclopedia of DNA elements (ENCODE) project. Genomics Proteomics Bioinformatics. 2013;11(3):135-41.
    • (2013) Genomics Proteomics Bioinformatics , vol.11 , Issue.3 , pp. 135-141
    • Qu, H.1    Fang, X.2
  • 12
    • 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, Cooper GM, Sidow A, Batzoglou S. 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    Cooper, G.M.4    Sidow, A.5    Batzoglou, S.6
  • 13
    • 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(8):1034-50.
    • (2005) Genome Res , vol.15 , Issue.8 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.S.3
  • 14
    • 79952901680 scopus 로고    scopus 로고
    • Enhancer function: New insights into the regulation of tissue-specific gene expression
    • Ong CT, Corces VG. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet. 2011;12(4):283-93.
    • (2011) Nat Rev Genet , vol.12 , Issue.4 , pp. 283-293
    • Ong, C.T.1    Corces, V.G.2
  • 15
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • Thurman RE, Rynes E, Humbert R, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489(7414):75-82.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 75-82
    • Thurman, R.E.1    Rynes, E.2    Humbert, R.3
  • 16
    • 84864627693 scopus 로고    scopus 로고
    • Personal and population genomics of human regulatory variation
    • Vernot B, Stergachis AB, Maurano MT, et al. Personal and population genomics of human regulatory variation. Genome Res. 2012;22(9):1689-97.
    • (2012) Genome Res , vol.22 , Issue.9 , pp. 1689-1697
    • Vernot, B.1    Stergachis, A.B.2    Maurano, M.T.3
  • 17
    • 84891808382 scopus 로고    scopus 로고
    • JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles
    • Database issue
    • Mathelier A, Zhao X, Zhang AW, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42(Database issue):D142-7.
    • (2014) Nucleic Acids Res , vol.42 , pp. 142-147
    • Mathelier, A.1    Zhao, X.2    Zhang, A.W.3
  • 18
    • 3242891274 scopus 로고    scopus 로고
    • ConSite: Web-based prediction of regulatory elements using cross-species comparison
    • Web Server issue
    • Sandelin A, Wasserman WW, Lenhard B. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 2004;32(Web Server issue):W249-52.
    • (2004) Nucleic Acids Res , vol.32 , pp. 249-252
    • Sandelin, A.1    Wasserman, W.W.2    Lenhard, B.3
  • 19
    • 84858779229 scopus 로고    scopus 로고
    • HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    • Database issue
    • Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012;40(Database issue):D930-4.
    • (2012) Nucleic Acids Res , vol.40 , pp. 930-934
    • Ward, L.D.1    Kellis, M.2
  • 20
    • 20844461337 scopus 로고    scopus 로고
    • LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    • Karchin R, Diekhans M, Kelly L, et al. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005;21(12):2814-20.
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2814-2820
    • Karchin, R.1    Diekhans, M.2    Kelly, L.3
  • 21
    • 84885303367 scopus 로고    scopus 로고
    • WS-SNPs&GO: A web server for predicting the deleterious effect of human protein variants using functional annotation
    • Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R. WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics. 2013;14(suppl 3):S6.
    • (2013) BMC Genomics , vol.14 , pp. S6
    • Capriotti, E.1    Calabrese, R.2    Fariselli, P.3    Martelli, P.L.4    Altman, R.B.5    Casadio, R.6
  • 24
    • 84862785201 scopus 로고    scopus 로고
    • Unsupervised pattern discovery in human chromatin structure through genomic segmentation
    • Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012;9(5):473-6.
    • (2012) Nat Methods , vol.9 , Issue.5 , pp. 473-476
    • Hoffman, M.M.1    Buske, O.J.2    Wang, J.3    Weng, Z.4    Bilmes, J.A.5    Noble, W.S.6
  • 25
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9(3):215-6.
    • (2012) Nat Methods , vol.9 , Issue.3 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 26
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46(3):310-5.
    • (2014) Nat Genet , vol.46 , Issue.3 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O’roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 27
    • 66149167455 scopus 로고    scopus 로고
    • ChIP-based methods for the identification of long-range chromatin interactions
    • Fullwood MJ, Ruan Y. ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem. 2009;107(1):30-9.
    • (2009) J Cell Biochem , vol.107 , Issue.1 , pp. 30-39
    • Fullwood, M.J.1    Ruan, Y.2
  • 28
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295(5558):1306-11.
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 29
    • 31344477982 scopus 로고    scopus 로고
    • The three ‘C’ s of chromosome conformation capture: Controls, controls, controls
    • Dekker J. The three ‘C’ s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006;3(1):17-21.
    • (2006) Nat Methods , vol.3 , Issue.1 , pp. 17-21
    • Dekker, J.1
  • 30
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    • Simonis M, Klous P, Splinter E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006;38(11):1348-54.
    • (2006) Nat Genet , vol.38 , Issue.11 , pp. 1348-1354
    • Simonis, M.1    Klous, P.2    Splinter, E.3
  • 31
    • 33750203582 scopus 로고    scopus 로고
    • Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions
    • Zhao Z, Tavoosidana G, Sjölinder M, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat Genet. 2006;38(11):1341-7.
    • (2006) Nat Genet , vol.38 , Issue.11 , pp. 1341-1347
    • Zhao, Z.1    Tavoosidana, G.2    Sjölinder, M.3
  • 32
    • 33749400168 scopus 로고    scopus 로고
    • Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements
    • Dostie J, Richmond TA, Arnaout RA, et al. Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16(10):1299-309.
    • (2006) Genome Res , vol.16 , Issue.10 , pp. 1299-1309
    • Dostie, J.1    Richmond, T.A.2    Arnaout, R.A.3
  • 33
    • 84860684566 scopus 로고    scopus 로고
    • Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation
    • Goh Y, Fullwood MJ, Poh HM, et al. Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation. J Vis Exp. 2012;62:ii:3770.
    • (2012) J Vis Exp , vol.62 , Issue.2 , pp. 3770
    • Goh, Y.1    Fullwood, M.J.2    Poh, H.M.3
  • 34
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489(7414):109-13.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 109-113
    • Sanyal, A.1    Lajoie, B.R.2    Jain, G.3    Dekker, J.4
  • 35
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • 1000 GenomesProject Consortium
    • 1000 GenomesProject Consortium, Abecasis GR, Altshuler D, et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061-73.
    • (2010) Nature , vol.467 , Issue.7319 , pp. 1061-1073
    • Abecasis, G.R.1    Altshuler, D.2
  • 36
    • 13444269543 scopus 로고    scopus 로고
    • Haploview: Analysis and visualization of LD and haplotype maps
    • Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21(2):263-5.
    • (2005) Bioinformatics , vol.21 , Issue.2 , pp. 263-265
    • Barrett, J.C.1    Fry, B.2    Maller, J.3    Daly, M.J.4
  • 37
    • 0347755531 scopus 로고    scopus 로고
    • The UCSC table browser data retrieval tool
    • Database issue
    • Karolchik D, Hinrichs AS, Furey TS, et al. The UCSC table browser data retrieval tool. Nucleic Acids Res. 2004;32(Database issue):D493-6.
    • (2004) Nucleic Acids Res , vol.32 , pp. D493-D496
    • Karolchik, D.1    Hinrichs, A.S.2    Furey, T.S.3
  • 38
    • 79960405019 scopus 로고    scopus 로고
    • The variant call format and VCFtools
    • Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-8.
    • (2011) Bioinformatics , vol.27 , Issue.15 , pp. 2156-2158
    • Danecek, P.1    Auton, A.2    Abecasis, G.3
  • 39
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
    • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
    • (2010) Nucleic Acids Res , vol.38 , Issue.16
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 40
    • 84857831329 scopus 로고    scopus 로고
    • AnnTools: A comprehensive and versatile annotation toolkit for genomic variants
    • Makarov V, O’Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S. AnnTools: a comprehensive and versatile annotation toolkit for genomic variants. Bioinformatics. 2012;28(5):724-5.
    • (2012) Bioinformatics , vol.28 , Issue.5 , pp. 724-725
    • Makarov, V.1    O’grady, T.2    Cai, G.3    Lihm, J.4    Buxbaum, J.D.5    Yoon, S.6
  • 41
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the catalogue of somatic mutations in cancer
    • Database issue
    • 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(Database issue):D945-50.
    • (2011) Nucleic Acids Res , vol.39 , pp. D945-D950
    • Forbes, S.A.1    Bindal, N.2    Bamford, S.3
  • 43
    • 79953158399 scopus 로고    scopus 로고
    • Exploring the genomes of cancer cells: Progress and promise
    • Stratton MR. Exploring the genomes of cancer cells: progress and promise. Science. 2011;331(6024):1553-8.
    • (2011) Science , vol.331 , Issue.6024 , pp. 1553-1558
    • Stratton, M.R.1
  • 44
    • 79957604678 scopus 로고    scopus 로고
    • Principles for the post-GWAS functional characterization of cancer risk loci
    • Freedman ML, Monteiro AN, Gayther SA, et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet. 2011;43(6):513-8.
    • (2011) Nat Genet , vol.43 , Issue.6 , pp. 513-518
    • Freedman, M.L.1    Monteiro, A.N.2    Gayther, S.A.3
  • 45
    • 77953098883 scopus 로고    scopus 로고
    • 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC
    • Ahmadiyeh N, Pomerantz MM, Grisanzio C, et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A. 2010;107(21):9742-6.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.21 , pp. 9742-9746
    • Ahmadiyeh, N.1    Pomerantz, M.M.2    Grisanzio, C.3
  • 46
    • 84896443312 scopus 로고    scopus 로고
    • Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing
    • Zhang J, Liu J, Sun J, Chen C, Foltz G, Lin B. Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing. Brief Bioinform. 2014;15(2):244-55.
    • (2014) Brief Bioinform , vol.15 , Issue.2 , pp. 244-255
    • Zhang, J.1    Liu, J.2    Sun, J.3    Chen, C.4    Foltz, G.5    Lin, B.6
  • 47
    • 84869455546 scopus 로고    scopus 로고
    • A novel missense-mutation-related feature extraction scheme for ‘driver’ mutation identification
    • Tan H, Bao J, Zhou X. A novel missense-mutation-related feature extraction scheme for ‘driver’ mutation identification. Bioinformatics. 2012;28(22):2948-55.
    • (2012) Bioinformatics , vol.28 , Issue.22 , pp. 2948-2955
    • Tan, H.1    Bao, J.2    Zhou, X.3
  • 48
    • 77957154710 scopus 로고    scopus 로고
    • Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM)
    • Carter H, Samayoa J, Hruban RH, Karchin R. Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biol Ther. 2010;10(6):582-7.
    • (2010) Cancer Biol Ther , vol.10 , Issue.6 , pp. 582-587
    • Carter, H.1    Samayoa, J.2    Hruban, R.H.3    Karchin, R.4
  • 49
    • 53749105617 scopus 로고    scopus 로고
    • SNAP predicts effect of mutations on protein function
    • Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics. 2008;24(20):2397-8.
    • (2008) Bioinformatics , vol.24 , Issue.20 , pp. 2397-2398
    • Bromberg, Y.1    Yachdav, G.2    Rost, B.3
  • 50
    • 84891771466 scopus 로고    scopus 로고
    • The UCSC genome browser database: 2014 update
    • Database issue
    • Karolchik D, Barber GP, Casper J, et al. The UCSC genome browser database: 2014 update. Nucleic Acids Res. 2014;42(Database issue):D764-70.
    • (2014) Nucleic Acids Res , vol.42 , pp. 764-770
    • Karolchik, D.1    Barber, G.P.2    Casper, J.3
  • 51
    • 84876552099 scopus 로고    scopus 로고
    • The UCSC cancer genomics browser: Update 2013
    • Database issue
    • Goldman M, Craft B, Swatloski T, et al. The UCSC cancer genomics browser: update 2013. Nucleic Acids Res. 2013;41(Database issue):D949-54.
    • (2013) Nucleic Acids Res , vol.41 , pp. 949-954
    • Goldman, M.1    Craft, B.2    Swatloski, T.3
  • 52
    • 84875253066 scopus 로고    scopus 로고
    • Identification of genetic susceptibility loci for colorectal tumors in a genome-wide meta-analysis
    • Peters U, Jiao S, Schumacher FR, et al. Identification of genetic susceptibility loci for colorectal tumors in a genome-wide meta-analysis. Gastroenterology. 2013;144(4):799-807.e24.
    • (2013) Gastroenterology , vol.144 , Issue.4 , pp. 799-807
    • Peters, U.1    Jiao, S.2    Schumacher, F.R.3
  • 53
    • 15944413013 scopus 로고    scopus 로고
    • Online, OMIM Web site
    • Johns Hopkins University (Baltimore, MD). McKusick-Nathans Institute of Genetic Medicine. Online Mendelian Inheritance in Man, OMIM Web site: http://omim.org/2014, 2014.
    • (2014) Mendelian Inheritance in Man
  • 54
    • 79951841312 scopus 로고    scopus 로고
    • Replication and functional genomic analyses of the breast cancer susceptibility locus at 6q25.1 generalize its importance in women of Chinese, Japanese, and European ancestry
    • Cai Q, Wen W, Qu S, et al. Replication and functional genomic analyses of the breast cancer susceptibility locus at 6q25.1 generalize its importance in women of Chinese, Japanese, and European ancestry. Cancer Res. 2011;71(4):1344-55.
    • (2011) Cancer Res , vol.71 , Issue.4 , pp. 1344-1355
    • Cai, Q.1    Wen, W.2    Qu, S.3
  • 55
    • 77954153479 scopus 로고    scopus 로고
    • Identification of a functional genetic variant at 16q12.1 for breast cancer risk: Results from the Asia breast cancer consortium
    • Long J, Cai Q, Shu XO, et al. Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia breast cancer consortium. PLoS Genet. 2010;6(6):e1001002.
    • (2010) PLoS Genet , vol.6 , Issue.6
    • Long, J.1    Cai, Q.2    Shu, X.O.3
  • 56
    • 68149180901 scopus 로고    scopus 로고
    • The 8q24 cancer risk variant rs6983267shows long-range interaction with MYC in colorectal cancer
    • Pomerantz MM, Ahmadiyeh N, Jia L, et al. The 8q24 cancer risk variant rs6983267shows long-range interaction with MYC in colorectal cancer. Nat Genet. 2009;41(8):882-4.
    • (2009) Nat Genet , vol.41 , Issue.8 , pp. 882-884
    • Pomerantz, M.M.1    Ahmadiyeh, N.2    Jia, L.3
  • 57
    • 0042242582 scopus 로고    scopus 로고
    • ESEfinder: A web resource to identify exonic splicing enhancers
    • Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 2003;31(13):3568-71.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3568-3571
    • Cartegni, L.1    Wang, J.2    Zhu, Z.3    Zhang, M.Q.4    Krainer, A.R.5
  • 58
    • 8144225362 scopus 로고    scopus 로고
    • Variation in sequence and organization of splicing regulatory elements in vertebrate genes
    • Yeo G, Hoon S, Venkatesh B, Burge CB. Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci U S A. 2004;101(44):15700-5.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.44 , pp. 15700-15705
    • Yeo, G.1    Hoon, S.2    Venkatesh, B.3    Burge, C.B.4
  • 59
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science. 2002;297(5583):1007-13.
    • (2002) Science , vol.297 , Issue.5583 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.F.2    Sharp, P.A.3    Burge, C.B.4
  • 62
    • 79959851441 scopus 로고    scopus 로고
    • Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer
    • Tomlinson IP, Carvajal-Carmona LG, Dobbins SE, et al. Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. PLoS Genet. 2011;7(6):e1002105.
    • (2011) PLoS Genet , vol.7 , Issue.6
    • Tomlinson, I.P.1    Carvajal-Carmona, L.G.2    Dobbins, S.E.3
  • 63
    • 34247548755 scopus 로고    scopus 로고
    • Genome-wide association study of prostate cancer identifies a second risk locus at 8q24
    • Yeager M, Orr N, Hayes RB, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet. 2007;39(5):645-9.
    • (2007) Nat Genet , vol.39 , Issue.5 , pp. 645-649
    • Yeager, M.1    Orr, N.2    Hayes, R.B.3
  • 64
    • 79955860324 scopus 로고    scopus 로고
    • Common variant in 6q26-q27 is associated with distal colon cancer in an ASIAn population
    • Cui R, Okada Y, Jang SG, et al. Common variant in 6q26-q27 is associated with distal colon cancer in an ASIAn population. Gut. 2011;60(6):799-805.
    • (2011) Gut , vol.60 , Issue.6 , pp. 799-805
    • Cui, R.1    Okada, Y.2    Jang, S.G.3
  • 65
    • 39749118602 scopus 로고    scopus 로고
    • Multiple loci identified in a genome-wide association study of prostate cancer
    • Thomas G, Jacobs KB, Yeager M, et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet. 2008;40(3):310-5.
    • (2008) Nat Genet , vol.40 , Issue.3 , pp. 310-315
    • Thomas, G.1    Jacobs, K.B.2    Yeager, M.3
  • 66
    • 39749129053 scopus 로고    scopus 로고
    • Multiple newly identified loci associated with prostate cancer susceptibility
    • Eeles RA, Kote-Jarai Z, Giles GG, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet. 2008;40(3):316-21.
    • (2008) Nat Genet , vol.40 , Issue.3 , pp. 316-321
    • Eeles, R.A.1    Kote-Jarai, Z.2    Giles, G.G.3
  • 67
    • 80052716147 scopus 로고    scopus 로고
    • Genome-wide association study identifies new prostate cancer susceptibility loci
    • Schumacher FR, Berndt SI, Siddiq A, et al. Genome-wide association study identifies new prostate cancer susceptibility loci. Hum Mol Genet. 2011;20(19):3867-75.
    • (2011) Hum Mol Genet , vol.20 , Issue.19 , pp. 3867-3875
    • Schumacher, F.R.1    Berndt, S.I.2    Siddiq, A.3
  • 68
    • 30944435031 scopus 로고    scopus 로고
    • Telomere length of normal leukocytes is affected by a functional polymorphism of hTERT
    • Matsubara Y, Murata M, Yoshida T, et al. Telomere length of normal leukocytes is affected by a functional polymorphism of hTERT. Biochem Biophys Res Commun. 2006;341(1):128-31.
    • (2006) Biochem Biophys Res Commun , vol.341 , Issue.1 , pp. 128-131
    • Matsubara, Y.1    Murata, M.2    Yoshida, T.3
  • 69
    • 84872145398 scopus 로고    scopus 로고
    • TERT polymorphisms modify the risk of acute lymphoblastic leukemia in chinese children
    • Sheng X, Tong N, Tao G, et al. TERT polymorphisms modify the risk of acute lymphoblastic leukemia in chinese children. Carcinogenesis. 2013;34(1):228-35.
    • (2013) Carcinogenesis , vol.34 , Issue.1 , pp. 228-235
    • Sheng, X.1    Tong, N.2    Tao, G.3
  • 71
    • 63149133163 scopus 로고    scopus 로고
    • Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk
    • Chang BL, Cramer SD, Wiklund F, et al. Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum Mol Genet. 2009;18(7):1368-75.
    • (2009) Hum Mol Genet , vol.18 , Issue.7 , pp. 1368-1375
    • Chang, B.L.1    Cramer, S.D.2    Wiklund, F.3
  • 72
    • 66049160161 scopus 로고    scopus 로고
    • Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility
    • Lou H, Yeager M, Li H, et al. Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility. Proc Natl Acad Sci U S A. 2009;106(19):7933-8.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.19 , pp. 7933-7938
    • Lou, H.1    Yeager, M.2    Li, H.3
  • 73
    • 84869056823 scopus 로고    scopus 로고
    • Why transcription factor binding sites are ten nucleotides long
    • Stewart AJ, Hannenhalli S, Plotkin JB. Why transcription factor binding sites are ten nucleotides long. Genetics. 2012;192(3):973-85.
    • (2012) Genetics , vol.192 , Issue.3 , pp. 973-985
    • Stewart, A.J.1    Hannenhalli, S.2    Plotkin, J.B.3
  • 74
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812-4.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 75
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; iso-2; iso-3
    • Cingolani P, Platts A, Wang Le L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2):80-92.
    • (2012) Fly (Austin) , vol.6 , Issue.2 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    Wang Le, L.3
  • 77
    • 84875945705 scopus 로고    scopus 로고
    • ENCODE data in the UCSC genome browser: Year 5 update
    • Database issue
    • Rosenbloom KR, Sloan CA, Malladi VS, et al. ENCODE data in the UCSC genome browser: year 5 update. Nucleic Acids Res. 2013;41(Database issue):D56-63.
    • (2013) Nucleic Acids Res , vol.41 , pp. D56-D63
    • Rosenbloom, K.R.1    Sloan, C.A.2    Malladi, V.S.3
  • 79
    • 78651293534 scopus 로고    scopus 로고
    • Griffiths-Jones S. miRBase: Integrating microRNA annotation and deep-sequencing data
    • Database issue
    • Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011;39(Database issue):D152-7.
    • (2011) Nucleic Acids Res , vol.39 , pp. 152-157
    • Kozomara, A.1
  • 80
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009;19(1):92-105.
    • (2009) Genome Res , vol.19 , Issue.1 , pp. 92-105
    • Friedman, R.C.1    Farh, K.K.2    Burge, C.B.3    Bartel, D.P.4
  • 82
    • 84878682420 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) project
    • GTEx Consortium. The genotype-tissue expression (GTEx) project. Nat Genet. 2013;45(6):580-5.
    • (2013) Nat Genet , vol.45 , Issue.6 , pp. 580-585
  • 83
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • Felsenstein J, Churchill GA. A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996;13(1):93-104.
    • (1996) Mol Biol Evol , vol.13 , Issue.1 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 84
    • 68149170044 scopus 로고    scopus 로고
    • The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
    • Tuupanen S, Turunen M, Lehtonen R, et al. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet. 2009;41(8):885-90.
    • (2009) Nat Genet , vol.41 , Issue.8 , pp. 885-890
    • Tuupanen, S.1    Turunen, M.2    Lehtonen, R.3
  • 85
    • 78049415226 scopus 로고    scopus 로고
    • Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H
    • Pittman AM, Naranjo S, Jalava SE, et al. Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H. PLoS Genet. 2010;6(9):e1001126.
    • (2010) PLoS Genet , vol.6 , Issue.9
    • Pittman, A.M.1    Naranjo, S.2    Jalava, S.E.3
  • 86
    • 81855226435 scopus 로고    scopus 로고
    • Genome-wide association study identifies breast cancer risk variant at 10q21.2: Results from the Asia breast cancer consortium
    • Cai Q, Long J, Lu W, et al. Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia breast cancer consortium. Hum Mol Genet. 2011;20(24):4991-9.
    • (2011) Hum Mol Genet , vol.20 , Issue.24 , pp. 4991-4999
    • Cai, Q.1    Long, J.2    Lu, W.3
  • 87
    • 80052846746 scopus 로고    scopus 로고
    • Functional polymorphisms in the TERT promoter are associated with risk of serous epithelial ovarian and breast cancers
    • Beesley J, Pickett HA, Johnatty SE, et al. Functional polymorphisms in the TERT promoter are associated with risk of serous epithelial ovarian and breast cancers. PLoS One. 2011;6(9):e24987.
    • (2011) PLoS One , vol.6 , Issue.9
    • Beesley, J.1    Pickett, H.A.2    Johnatty, S.E.3
  • 88
    • 77957878164 scopus 로고    scopus 로고
    • A functional variant in NKX3.1 associated with prostate cancer susceptibility down-regulates NKX3.1 expression
    • Akamatsu S, Takata R, Ashikawa K, et al. A functional variant in NKX3.1 associated with prostate cancer susceptibility down-regulates NKX3.1 expression. Hum Mol Genet. 2010;19(21):4265-72.
    • (2010) Hum Mol Genet , vol.19 , Issue.21 , pp. 4265-4272
    • Akamatsu, S.1    Takata, R.2    Ashikawa, K.3
  • 89
    • 84886642986 scopus 로고    scopus 로고
    • Identification of functional nucleotide and haplotype variants in the promoter of the CEBPE gene
    • Ryoo H, Kong M, Kim Y, Lee C. Identification of functional nucleotide and haplotype variants in the promoter of the CEBPE gene. J Hum Genet. 2013;58(9):600-3.
    • (2013) J Hum Genet , vol.58 , Issue.9 , pp. 600-603
    • Ryoo, H.1    Kong, M.2    Kim, Y.3    Lee, C.4
  • 90
    • 84867410664 scopus 로고    scopus 로고
    • Genetic polymorphisms in the osteopontin promoter increases the risk of distance metastasis and death in Chinese patients with gastric cancer
    • Zhao F, Chen X, Meng T, Hao B, Zhang Z, Zhang G. Genetic polymorphisms in the osteopontin promoter increases the risk of distance metastasis and death in Chinese patients with gastric cancer. BMC Cancer. 2012;12:477.
    • (2012) BMC Cancer , vol.12 , pp. 477
    • Zhao, F.1    Chen, X.2    Meng, T.3    Hao, B.4    Zhang, Z.5    Zhang, G.6
  • 91
    • 58849142631 scopus 로고    scopus 로고
    • The functional-443T/C osteopontin promoter polymorphism influences osteopontin gene expression in melanoma cells via binding of c-Myb transcription factor
    • Schultz J, Lorenz P, Ibrahim SM, Kundt G, Gross G, Kunz M. The functional-443T/C osteopontin promoter polymorphism influences osteopontin gene expression in melanoma cells via binding of c-Myb transcription factor. Mol Carcinog. 2009;48(1):14-23.
    • (2009) Mol Carcinog , vol.48 , Issue.1 , pp. 14-23
    • Schultz, J.1    Lorenz, P.2    Ibrahim, S.M.3    Kundt, G.4    Gross, G.5    Kunz, M.6
  • 92
    • 84885651314 scopus 로고    scopus 로고
    • A polymorphic p53 response element in KIT ligand influences cancer risk and has undergone natural selection
    • Zeron-Medina J, Wang X, Repapi E, et al. A polymorphic p53 response element in KIT ligand influences cancer risk and has undergone natural selection. Cell. 2013;155(2):410-22.
    • (2013) Cell , vol.155 , Issue.2 , pp. 410-422
    • Zeron-Medina, J.1    Wang, X.2    Repapi, E.3
  • 93
    • 84861862859 scopus 로고    scopus 로고
    • The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type
    • Jendrzejewski J, He H, Radomska HS, et al. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci U S A. 2012;109(22):8646-51.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , Issue.22 , pp. 8646-8651
    • Jendrzejewski, J.1    He, H.2    Radomska, H.S.3
  • 94
    • 84864624041 scopus 로고    scopus 로고
    • Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus
    • Zhang X, Cowper-Sal lari R, Bailey SD, Moore JH, Lupien M. Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res. 2012;22(8):1437-46.
    • (2012) Genome Res , vol.22 , Issue.8 , pp. 1437-1446
    • Zhang, X.1    Cowper-Sal Lari, R.2    Bailey, S.D.3    Moore, J.H.4    Lupien, M.5
  • 95
    • 79957905172 scopus 로고    scopus 로고
    • LIN28B polymorphisms influence susceptibility to epithelial ovarian cancer
    • Permuth-Wey J, Kim D, Tsai YY, et al. LIN28B polymorphisms influence susceptibility to epithelial ovarian cancer. Cancer Res. 2011;71(11):3896-903.
    • (2011) Cancer Res , vol.71 , Issue.11 , pp. 3896-3903
    • Permuth-Wey, J.1    Kim, D.2    Tsai, Y.Y.3
  • 96
    • 84897103859 scopus 로고    scopus 로고
    • The has-miR-526b binding-site rs8506G.a polymorphism in the lincRNA-NR_024015 exon identified by GWASs predispose to non-cardia gastric cancer risk
    • Fan QH, Yu R, Huang WX, Cui XX, Luo BH, Zhang LY. The has-miR-526b binding-site rs8506G.a polymorphism in the lincRNA-NR_024015 exon identified by GWASs predispose to non-cardia gastric cancer risk. PLoS One. 2014;9(3):e90008.
    • (2014) PLoS One , vol.9 , Issue.3
    • Fan, Q.H.1    Yu, R.2    Huang, W.X.3    Cui, X.X.4    Luo, B.H.5    Zhang, L.Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.