메뉴 건너뛰기




Volumn 12, Issue SUPPL. 4, 2011, Pages

Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites

Author keywords

[No Author keywords available]

Indexed keywords

ANNOTATION TOOL; GENE PREDICTION; GENE SEQUENCES; MODIFIED PROTEINS; NEXT-GENERATION SEQUENCING; OPEN READING FRAME; SINGLE NUCLEOTIDE POLYMORPHISMS; TARGET DATABASE;

EID: 79959940492     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S4-S2     Document Type: Article
Times cited : (26)

References (26)
  • 1
    • 0035865070 scopus 로고    scopus 로고
    • To a future of genetic medicine
    • 10.1038/35057281, 11236997
    • Chakravarti A. To a future of genetic medicine. Nature 2001, 409(6822):822-823. 10.1038/35057281, 11236997.
    • (2001) Nature , vol.409 , Issue.6822 , pp. 822-823
    • Chakravarti, A.1
  • 2
    • 77952301353 scopus 로고    scopus 로고
    • Pharmacogenetic biomarkers as tools for improved drug therapy; emphasis on the cytochrome P450 system
    • 10.1016/j.bbrc.2010.02.162, 20494117
    • Ingelman-Sundberg M, Sim SC. Pharmacogenetic biomarkers as tools for improved drug therapy; emphasis on the cytochrome P450 system. Biochem Biophys Res Commun 2010, 396(1):90-94. 10.1016/j.bbrc.2010.02.162, 20494117.
    • (2010) Biochem Biophys Res Commun , vol.396 , Issue.1 , pp. 90-94
    • Ingelman-Sundberg, M.1    Sim, S.C.2
  • 3
    • 20844461337 scopus 로고    scopus 로고
    • LS-SNP:Large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    • 10.1093/bioinformatics/bti442, 15827081
    • Karchin R, Diekhans M, Kelly L, Thomas D, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP:Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 2005, 21(12):2814-2820. 10.1093/bioinformatics/bti442, 15827081.
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2814-2820
    • Karchin, R.1    Diekhans, M.2    Kelly, L.3    Thomas, D.4    Pieper, U.5    Eswar, N.6    Haussler, D.7    Sali, A.8
  • 4
    • 38549158538 scopus 로고    scopus 로고
    • F-SNP: computationally predicted functional SNPs for disease association studies
    • 2238878, 17986460
    • Lee PH, Shatkay H. F-SNP: computationally predicted functional SNPs for disease association studies. Nucl Acids Res 2008, 36:D820-824. 2238878, 17986460.
    • (2008) Nucl Acids Res , vol.36
    • Lee, P.H.1    Shatkay, H.2
  • 5
    • 64549139680 scopus 로고    scopus 로고
    • An integrative scoring system for ranking SNPs by their potential deleterious effects
    • 10.1093/bioinformatics/btp103, 19228803
    • Lee PH, Shatkay H. An integrative scoring system for ranking SNPs by their potential deleterious effects. Bioinformatics 2009, 25(8):1048-1055. 10.1093/bioinformatics/btp103, 19228803.
    • (2009) Bioinformatics , vol.25 , Issue.8 , pp. 1048-1055
    • Lee, P.H.1    Shatkay, H.2
  • 6
    • 60749104999 scopus 로고    scopus 로고
    • Next generation tools for the annotation of human SNPs
    • 2638621, 19181721
    • Karchin R. Next generation tools for the annotation of human SNPs. Brief Bioinform 2009, 10(1):35-52. 2638621, 19181721.
    • (2009) Brief Bioinform , vol.10 , Issue.1 , pp. 35-52
    • Karchin, R.1
  • 7
    • 77949480756 scopus 로고    scopus 로고
    • Genomic features defining exonic variants that modulate splicing
    • 10.1186/gb-2010-11-2-r20, 2872880, 20158892
    • Woolfe A, Mullikin JC, Elnitski L. Genomic features defining exonic variants that modulate splicing. Genome Biol 2010, 11(2):R20. 10.1186/gb-2010-11-2-r20, 2872880, 20158892.
    • (2010) Genome Biol , vol.11 , Issue.2
    • Woolfe, A.1    Mullikin, J.C.2    Elnitski, L.3
  • 8
    • 77249135158 scopus 로고    scopus 로고
    • A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements
    • 10.1186/1471-2105-11-22, 3098058, 20067640
    • Churbanov A, Vorechovsky I, Hicks C. A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements. BMC Bioinformatics 2010, 11:22. 10.1186/1471-2105-11-22, 3098058, 20067640.
    • (2010) BMC Bioinformatics , vol.11 , pp. 22
    • Churbanov, A.1    Vorechovsky, I.2    Hicks, C.3
  • 9
    • 54049104382 scopus 로고    scopus 로고
    • Automatic detection of exonic splicing enhancers (ESEs) using SVMs
    • 10.1186/1471-2105-9-369, 2567995, 18783607
    • Mersch B, Gepperth A, Suhai S, Hotz-Wagenblatt A. Automatic detection of exonic splicing enhancers (ESEs) using SVMs. BMC Bioinformatics 2008, 9:369. 10.1186/1471-2105-9-369, 2567995, 18783607.
    • (2008) BMC Bioinformatics , vol.9 , pp. 369
    • Mersch, B.1    Gepperth, A.2    Suhai, S.3    Hotz-Wagenblatt, A.4
  • 10
    • 71749092105 scopus 로고    scopus 로고
    • SsSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database
    • 10.1002/humu.21128, 19760752
    • Yang JO, Kim WY, Bhak J. ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database. Hum Mutat 2009, 30(12):E1010-1020. 10.1002/humu.21128, 19760752.
    • (2009) Hum Mutat , vol.30 , Issue.12
    • Yang, J.O.1    Kim, W.Y.2    Bhak, J.3
  • 11
    • 0036021719 scopus 로고    scopus 로고
    • A T2517C polymorphism in the GSTM4 gene is associated with risk of developing lung cancer
    • 10.1016/S0169-5002(02)00078-8, 12140136
    • Liloglou T, Walters M, Maloney P, Youngson J, Field JK. A T2517C polymorphism in the GSTM4 gene is associated with risk of developing lung cancer. Lung Cancer 2002, 37(2):143-146. 10.1016/S0169-5002(02)00078-8, 12140136.
    • (2002) Lung Cancer , vol.37 , Issue.2 , pp. 143-146
    • Liloglou, T.1    Walters, M.2    Maloney, P.3    Youngson, J.4    Field, J.K.5
  • 12
    • 0029944971 scopus 로고    scopus 로고
    • Mutation of the VHL gene is associated exclusively with the development of non-papillary renal cell carcinomas
    • 10.1002/(SICI)1096-9896(199606)179:2<157::AID-PATH557>3.0.CO;2-S, 8758207
    • Kenck C, Wilhelm M, Bugert P, Staehler G, Kovacs G. Mutation of the VHL gene is associated exclusively with the development of non-papillary renal cell carcinomas. J Pathol 1996, 179(2):157-161. 10.1002/(SICI)1096-9896(199606)179:2<157::AID-PATH557>3.0.CO;2-S, 8758207.
    • (1996) J Pathol , vol.179 , Issue.2 , pp. 157-161
    • Kenck, C.1    Wilhelm, M.2    Bugert, P.3    Staehler, G.4    Kovacs, G.5
  • 13
    • 0030733022 scopus 로고    scopus 로고
    • Deletion of 11 amino acids in tuberin associated with severe tuberous sclerosis phenotypes: evidence for a new essential domain in the first third of the protein
    • Jobert S, Bragado-Nilsson E, Samolyk D, Pedespan JM, Marchal C, Reichert S, Mallet J, Pitiot G. Deletion of 11 amino acids in tuberin associated with severe tuberous sclerosis phenotypes: evidence for a new essential domain in the first third of the protein. Eur J Hum Genet 1997, 5(5):280-287.
    • (1997) Eur J Hum Genet , vol.5 , Issue.5 , pp. 280-287
    • Jobert, S.1    Bragado-Nilsson, E.2    Samolyk, D.3    Pedespan, J.M.4    Marchal, C.5    Reichert, S.6    Mallet, J.7    Pitiot, G.8
  • 15
    • 26644463218 scopus 로고    scopus 로고
    • Mutation screen and association study of EZH2 as a susceptibility gene for aggressive prostate cancer
    • 10.1002/pros.20296, 16015586
    • Bachmann N, Hoegel J, Haeusler J, Kuefer R, Herkommer K, Paiss T, Vogel W, Maier C. Mutation screen and association study of EZH2 as a susceptibility gene for aggressive prostate cancer. Prostate 2005, 65(3):252-259. 10.1002/pros.20296, 16015586.
    • (2005) Prostate , vol.65 , Issue.3 , pp. 252-259
    • Bachmann, N.1    Hoegel, J.2    Haeusler, J.3    Kuefer, R.4    Herkommer, K.5    Paiss, T.6    Vogel, W.7    Maier, C.8
  • 17
    • 33748674197 scopus 로고    scopus 로고
    • AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
    • Stanke M, Tzvetkova A, Morgenstern B. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. BMC Genome Biol 2006, 7(Suppl 1):S11.
    • (2006) BMC Genome Biol , vol.7 , Issue.SUPPL. 1
    • Stanke, M.1    Tzvetkova, A.2    Morgenstern, B.3
  • 18
    • 66249120367 scopus 로고    scopus 로고
    • Human Splicing Finder: an online bioinformatics tool to predict splicing signals
    • 10.1093/nar/gkp215, 2685110, 19339519
    • Desmet F-O, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucl Acids Res 2009, 37(9):e67. 10.1093/nar/gkp215, 2685110, 19339519.
    • (2009) Nucl Acids Res , vol.37 , Issue.9
    • Desmet, F.-O.1    Hamroun, D.2    Lalande, M.3    Collod-Béroud, G.4    Claustres, M.5    Béroud, C.6
  • 19
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 1990, 183:63-98.
    • (1990) Methods Enzymol , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 20
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • 10.1006/jmbi.1997.0951, 9149143
    • Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268(1):78-94. 10.1006/jmbi.1997.0951, 9149143.
    • (1997) J Mol Biol , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 21
    • 0030623944 scopus 로고    scopus 로고
    • Two methods for improving performance of an HMM and their application for gene finding
    • Krogh A. Two methods for improving performance of an HMM and their application for gene finding. Proc Int Conf Intell Syst Mol Biol 1997, 5:179-186.
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 179-186
    • Krogh, A.1
  • 22
    • 0034061137 scopus 로고    scopus 로고
    • GeneID in Drosophila
    • 10.1101/gr.10.4.511, 310871, 10779490
    • Parra G, Blanco E, Guigo R. GeneID in Drosophila. Genome Res 2000, 10(4):511-515. 10.1101/gr.10.4.511, 310871, 10779490.
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 511-515
    • Parra, G.1    Blanco, E.2    Guigo, R.3
  • 23
    • 33748641488 scopus 로고    scopus 로고
    • JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
    • Allen JE, Majoros WH, Pertea M, Salzberg SL. JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biol 2006, 7(Suppl 1):911-913.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1 , pp. 911-913
    • Allen, J.E.1    Majoros, W.H.2    Pertea, M.3    Salzberg, S.L.4
  • 25
    • 2442713832 scopus 로고    scopus 로고
    • GeneWise and Genomewise
    • 10.1101/gr.1865504, 479130, 15123596
    • Birney E, Clamp M, Durbin R. GeneWise and Genomewise. Genome Res 2004, 14(5):988-995. 10.1101/gr.1865504, 479130, 15123596.
    • (2004) Genome Res , vol.14 , Issue.5 , pp. 988-995
    • Birney, E.1    Clamp, M.2    Durbin, R.3
  • 26
    • 0042242582 scopus 로고    scopus 로고
    • ESEfinder: a web resource to identify exonic splicing enhancers
    • 10.1093/nar/gkg616, 169022, 12824367
    • Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: a web resource to identify exonic splicing enhancers. Nucl Acids Res 2003, 31(13):3568-3571. 10.1093/nar/gkg616, 169022, 12824367.
    • (2003) Nucl 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.