메뉴 건너뛰기




Volumn 40, Issue 6, 2012, Pages 2414-2425

Gene Array Analyzer: Alternative usage of gene arrays to study alternative splicing events

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ANALYZER; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL DIFFERENTIATION; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENE EXPRESSION; GENETIC ANALYSIS; HEART DEVELOPMENT; HEART MUSCLE CELL; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL;

EID: 84859350055     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1110     Document Type: Article
Times cited : (14)

References (43)
  • 2
    • 75649102520 scopus 로고    scopus 로고
    • Sex-specific and lineage-specific alternative splicing in primates
    • Blekhman, R., Marioni, J.C., Zumbo, P., Stephens, M. and Gilad, Y. (2009) Sex-specific and lineage-specific alternative splicing in primates. Genome Res., 20, 180-189
    • (2009) Genome Res. , vol.20 , pp. 180-189
    • Blekhman, R.1    Marioni, J.C.2    Zumbo, P.3    Stephens, M.4    Gilad, Y.5
  • 3
    • 23944473342 scopus 로고    scopus 로고
    • Structural and functional diversity generated by alternative mRNA splicing
    • DOI 10.1016/j.tibs.2005.07.001, PII S0968000405001921
    • Stetefeld, J. and Ruegg, M. (2005) Structural and functional diversity generated by alternative mRNA splicing. Trends Biochem. Sci., 30, 515-521 (Pubitemid 41206507)
    • (2005) Trends in Biochemical Sciences , vol.30 , Issue.9 , pp. 515-521
    • Stetefeld, J.1    Ruegg, M.A.2
  • 6
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86
    • (2010) Genome Biol. , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 7
    • 38649143214 scopus 로고    scopus 로고
    • A comparison of Affymetrix gene expression arrays
    • Robinson, M.D. and Speed, T.P. (2007) A comparison of Affymetrix gene expression arrays. BMC Bioinformatics, 8, 449
    • (2007) BMC Bioinformatics , vol.8 , pp. 449
    • Robinson, M.D.1    Speed, T.P.2
  • 8
    • 71049131864 scopus 로고    scopus 로고
    • Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation
    • Ha, K.C., Coulombe-Huntington, J. and Majewski, J. (2009) Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation. BMC Genomics, 10, 519
    • (2009) BMC Genomics , vol.10 , pp. 519
    • Ha, K.C.1    Coulombe-Huntington, J.2    Majewski, J.3
  • 9
    • 67649729607 scopus 로고    scopus 로고
    • Differential splicing using whole-transcript microarrays
    • Robinson, M.D. and Speed, T.P. (2009) Differential splicing using whole-transcript microarrays. BMC Bioinformatics, 10, 156
    • (2009) BMC Bioinformatics , vol.10 , pp. 156
    • Robinson, M.D.1    Speed, T.P.2
  • 10
    • 75849144808 scopus 로고    scopus 로고
    • Exon Array Analyzer: A web interface for Affymetrix exon array analysis
    • Gellert, P., Uchida, S. and Braun, T. (2009) Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics, 25, 3323-3324
    • (2009) Bioinformatics , vol.25 , pp. 3323-3324
    • Gellert, P.1    Uchida, S.2    Braun, T.3
  • 13
    • 77954365140 scopus 로고    scopus 로고
    • Alternative splicing is frequent during early embryonic development in mouse
    • Revil, T., Gaffney, D., Dias, C., Majewski, J. and Jerome-Majewska, L.A. (2010) Alternative splicing is frequent during early embryonic development in mouse. BMC Genomics, 11, 399
    • (2010) BMC Genomics , vol.11 , pp. 399
    • Revil, T.1    Gaffney, D.2    Dias, C.3    Majewski, J.4    Jerome-Majewska, L.A.5
  • 17
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth, G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article3
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 18
    • 62249205133 scopus 로고    scopus 로고
    • Identifying differential exon splicing using linear models and correlation coefficients
    • Shah, S.H. and Pallas, J.A. (2009) Identifying differential exon splicing using linear models and correlation coefficients. BMC Bioinformatics, 10, 26
    • (2009) BMC Bioinformatics , vol.10 , pp. 26
    • Shah, S.H.1    Pallas, J.A.2
  • 20
    • 33748486517 scopus 로고    scopus 로고
    • AceView: A comprehensive cDNA-supported gene and transcripts annotation
    • 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
    • (2006) Genome Biol. , vol.7 , Issue.SUPPL. 1
    • Thierry-Mieg, D.1    Thierry-Mieg, J.2
  • 21
    • 34547599504 scopus 로고    scopus 로고
    • ASTALAVISTA: Dynamic and flexible analysis of alternative splicing events in custom gene datasets
    • Foissac, S. and Sammeth, M. (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res., 35, W297-W299
    • (2007) Nucleic Acids Res. , vol.35
    • Foissac, S.1    Sammeth, M.2
  • 23
    • 0242468552 scopus 로고    scopus 로고
    • Generation of confluent cardiomyocyte monolayers derived from embryonic stem cells in suspension: A cell source for new therapies and screening strategies
    • DOI 10.1080/14653240310003062
    • Zweigerdt, R., Burg, M., Willbold, E., Abts, H. and Ruediger, M. (2003) Generation of confluent cardiomyocyte monolayers derived from embryonic stem cells in suspension: a cell source for new therapies and screening strategies. Cytotherapy, 5, 399-413 (Pubitemid 37369027)
    • (2003) Cytotherapy , vol.5 , Issue.5 , pp. 399-413
    • Zweigerdt, R.1    Burg, M.2    Willbold, E.3    Abts, H.F.4    Ruediger, M.5
  • 25
    • 75149150388 scopus 로고    scopus 로고
    • TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
    • Stöver, B.C. and Müller, K.F. (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics, 11, 7
    • (2010) BMC Bioinformatics , vol.11 , pp. 7
    • Stöver, B.C.1    Müller, K.F.2
  • 26
    • 56749164864 scopus 로고    scopus 로고
    • Expression of 24, 426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
    • Castle, J.C., Zhang, C., Shah, J.K., Kulkarni, A.V., Kalsotra, A., Cooper, T.A. and Johnson, J.M. (2008) Expression of 24, 426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat. Genet., 40, 1416-1425
    • (2008) Nat. Genet. , vol.40 , pp. 1416-1425
    • Castle, J.C.1    Zhang, C.2    Shah, J.K.3    Kulkarni, A.V.4    Kalsotra, A.5    Cooper, T.A.6    Johnson, J.M.7
  • 28
    • 33747865461 scopus 로고    scopus 로고
    • Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
    • DOI 10.1093/nar/gkl229
    • Thomas, P.D., Kejariwal, A., Guo, N., Mi, H., Campbell, M.J., Muruganujan, A. and Lazareva-Ulitsky, B. (2006) Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res., 34, W645-W650 (Pubitemid 44529850)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Thomas, P.D.1    Kejariwal, A.2    Guo, N.3    Mi, H.4    Campbell, M.J.5    Muruganujan, A.6    Lazareva-Ulitsky, B.7
  • 29
    • 0027959864 scopus 로고
    • Differential localization and sequence analysis of capping protein beta-subunit isoforms of vertebrates
    • Schafer, D., Korshunova, Y.O., Schroer, T. and Cooper, J. (1994) Differential localization and sequence analysis of capping protein beta-subunit isoforms of vertebrates. Cell Biol., 127, 453-465
    • (1994) Cell Biol. , vol.127 , pp. 453-465
    • Schafer, D.1    Korshunova, Y.O.2    Schroer, T.3    Cooper, J.4
  • 30
    • 0033552611 scopus 로고    scopus 로고
    • Vertebrate isoforms of actin capping protein beta have distinct functions in vivo
    • Hart, M.C. and Cooper, J. (1999) Vertebrate isoforms of actin capping protein beta have distinct functions in vivo. J. Cell Biol., 147, 128798
    • (1999) J. Cell Biol. , vol.147 , pp. 128798
    • Hart, M.C.1    Cooper, J.2
  • 32
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386
    • (2000) Methods Mol. Biol. , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 36
    • 41549118423 scopus 로고    scopus 로고
    • An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons
    • DOI 10.1002/pmic.200700741
    • Irmler, M., Hartl, D., Schmidt, T, Schuchhardt, J., Lach, C., Meyer, H.E., Hrab de Angelis, M., Klose, J. and Beckers, J. (2008) An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons. Proteomics, 8, 1165-1169 (Pubitemid 351462922)
    • (2008) Proteomics , vol.8 , Issue.6 , pp. 1165-1169
    • Irmler, M.1    Hartl, D.2    Schmidt, T.3    Schuchhardt, J.4    Lach, C.5    Meyer, H.E.6    De Angelis, M.H.7    Klose, J.8    Beckers, J.9
  • 37
    • 27644455141 scopus 로고    scopus 로고
    • Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals
    • DOI 10.1128/MCB.25.22.10005-10016.2005
    • Underwood, J.G., Boutz, P.L., Dougherty, J.D., Stoilov, P. and Black, D.L. (2005) Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol. Cell. Biol., 25, 10005-10016 (Pubitemid 41572747)
    • (2005) Molecular and Cellular Biology , vol.25 , Issue.22 , pp. 10005-10016
    • Underwood, J.G.1    Boutz, P.L.2    Dougherty, J.D.3    Stoilov, P.4    Black, D.L.5
  • 38
    • 33745899048 scopus 로고    scopus 로고
    • Alternative splicing: New insights from global analyses
    • DOI 10.1016/j.cell.2006.06.023, PII S0092867406008178
    • Blencowe, B.J. (2006) Alternative splicing: new insights from global analyses. Cell, 126, 37-47 (Pubitemid 44040990)
    • (2006) Cell , vol.126 , Issue.1 , pp. 37-47
    • Blencowe, B.J.1
  • 39
    • 34347254621 scopus 로고    scopus 로고
    • A mutant αII-spectrin designed to resist calpain and caspase cleavage questions the functional importance of this process in vivo
    • DOI 10.1074/jbc.M700028200
    • Meary, F., Metral, S., Ferreira, C., Eladari, D., Colin, Y., Lecomte, M.-C. and Nicolas, G. (2007) A mutant alphaII-spectrin designed to resist calpain and caspase cleavage questions the functional importance of this process in vivo. J. Biol. Chem., 282, 14226-14237 (Pubitemid 47100424)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.19 , pp. 14226-14237
    • Meary, F.1    Metral, S.2    Ferreira, C.3    Eladari, D.4    Colin, Y.5    Lecomte, M.-C.6    Nicolas, G.7
  • 40
    • 33847687362 scopus 로고    scopus 로고
    • Role of an alternatively spliced form of αII-spectrin in localization of connexin 43 in cardiomyocytes and regulation by stress-activated protein kinase
    • DOI 10.1016/j.yjmcc.2006.11.018, PII S0022282806010376
    • Ursitti, J.A., Petrich, B.G., Lee, P.C., Resneck, W.G., Ye, X., Yang, J., Randall, W.R., Bloch, R.J. and Wang, Y. (2007) Role of an alternatively spliced form of alphaII-spectrin in localization of connexin 43 in cardiomyocytes and regulation by stress-activated protein kinase. J. Mol. Cell Cardiol., 42, 572-581 (Pubitemid 46357554)
    • (2007) Journal of Molecular and Cellular Cardiology , vol.42 , Issue.3 , pp. 572-581
    • Ursitti, J.A.1    Petrich, B.G.2    Lee, P.C.3    Resneck, W.G.4    Ye, X.5    Yang, J.6    Randall, W.R.7    Bloch, R.J.8    Wang, Y.9
  • 41
    • 4043122640 scopus 로고    scopus 로고
    • Not just a plasma membrane protein: In cardiac muscle cells alpha-II spectrin also shows a close association with myofibrils
    • DOI 10.1023/B:JURE.0000035892.77399.51
    • Bennett, P.M., Baines, A.J., Lecomte, M.-C., Maggs, A.M. and Pinder, J.C. (2004) Not just a plasma membrane protein: in cardiac muscle cells alpha-II spectrin also shows a close association with myofibrils. J. Muscle Res. Cell Motif., 25, 119-126 (Pubitemid 39060886)
    • (2004) Journal of Muscle Research and Cell Motility , vol.25 , Issue.2 , pp. 119-126
    • Bennett, P.M.1    Baines, A.J.2    Lecomte, M.-C.3    Maggs, A.M.4    Pinder, J.C.5
  • 42
    • 79954932575 scopus 로고    scopus 로고
    • Heart failure: Advances through genomics
    • Creemers, E.E., Wilde, A. and Pinto, Y.M. (2011) Heart failure: advances through genomics. Nat. Rev. Genet., 12, 357-362
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 357-362
    • Creemers, E.E.1    Wilde, A.2    Pinto, Y.M.3
  • 43
    • 33749361499 scopus 로고    scopus 로고
    • Gene regulatory networks in the evolution and development of the heart
    • Olson, E.N. (2006) Gene regulatory networks in the evolution and development of the heart. Science, 313, 1922.
    • (2006) Science , vol.313 , pp. 1922
    • Olson, E.N.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.