메뉴 건너뛰기




Volumn 9, Issue 11, 2012, Pages 1339-1343

Splooce: A new portal for the analysis of human splicing variants

Author keywords

Alternative splicing; Bioinformatics; Combined alternative splicing events; Database; Method of analysis; Next generation sequencing; Regular expressions

Indexed keywords

ALTERNATIVE RNA SPLICING; ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; COMPLEX FORMATION; COMPUTATIONAL FLUID DYNAMICS; CONTROLLED STUDY; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; INFORMATION RETRIEVAL; RNA ANALYSIS; SPLOOCE; WEB BROWSER;

EID: 84875125164     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.22182     Document Type: Article
Times cited : (8)

References (34)
  • 2
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • PMID:18978789
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008; 40:1413-5; PMID:18978789; http://dx.doi.org/10.1038/ ng.259.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 3
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • PMID:11753382
    • Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002; 30:13-9; PMID:11753382; http://dx.doi.org/10.1038/ng0102-13.
    • (2002) Nat Genet , vol.30 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 4
    • 1942533477 scopus 로고    scopus 로고
    • Detection and evaluation of intron retention events in the human transcriptome
    • DOI 10.1261/rna.5123504
    • Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ. Detection and evaluation of intron retention events in the human transcriptome. RNA 2004; 10:757-65; PMID:15100430; http://dx.doi.org/10.1261/rna.5123504. (Pubitemid 38529738)
    • (2004) RNA , vol.10 , Issue.5 , pp. 757-765
    • Galante, P.A.F.1    Sakabe, N.J.2    Kirschbaum-Slager, N.3    De Souza, S.J.4
  • 5
    • 34548758543 scopus 로고    scopus 로고
    • Splicing in disease: Disruption of the splicing code and the decoding machinery
    • DOI 10.1038/nrg2164, PII NRG2164
    • Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007; 8:749-61; PMID:17726481; http://dx.doi.org/10.1038/nrg2164. (Pubitemid 47429207)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.10 , pp. 749-761
    • Wang, G.-S.1    Cooper, T.A.2
  • 6
    • 7444220147 scopus 로고    scopus 로고
    • Aberrant and alternative splicing in cancer
    • DOI 10.1158/0008-5472.CAN-04-1910
    • Venables J P. Aberrant and alternative splicing in cancer. Cancer Res 2004; 64:7647-54; PMID:15520162; http://dx.doi.org/10.1158/0008-5472.CAN-04- 1910. (Pubitemid 39446889)
    • (2004) Cancer Research , vol.64 , Issue.21 , pp. 7647-7654
    • Venables, J.P.1
  • 7
    • 21244470351 scopus 로고    scopus 로고
    • Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data
    • DOI 10.1152/physiolgenomics.00237.2004
    • Kirschbaum-Slager N, Parmigiani RB, Camargo AA, de Souza SJ. Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data. Physiol Genomics 2005; 21:423-32; PMID:15784694; http://dx.doi.org/10.1152/physiol-genomics.00237.2004. (Pubitemid 40898503)
    • (2005) Physiological Genomics , vol.21 , pp. 423-432
    • Kirschbaum-Slager, N.1    Parmigiani, R.B.2    Camargo, A.A.3    De Souza, S.J.4
  • 8
    • 0037101633 scopus 로고    scopus 로고
    • Ischemia induces a translocation of the splicing factor tra2-beta1 and changes alternative splicing patterns in the brain
    • Daoud R, Mies G, Smialowska A, Oláh L, Hossmann KA, Stamm S. Ischemia induces a translocation of the splicing factor tra2-beta 1 and changes alternative splicing patterns in the brain. J Neurosci 2002; 22:5889-99; PMID:12122051. (Pubitemid 35387633)
    • (2002) Journal of Neuroscience , vol.22 , Issue.14 , pp. 5889-5899
    • Daoud, R.1    Mies, G.2    Smialowska, A.3    Olah, L.4    Hossmann, K.-A.5    Stamm, S.6
  • 9
    • 2342450548 scopus 로고    scopus 로고
    • Alternative splicing in disease and therapy
    • DOI 10.1038/nbt964
    • Garcia-Blanco MA, Baraniak A P, Lasda EL. Alternative splicing in disease and therapy. Nat Biotechnol 2004; 22:535-46; PMID:15122293; http://dx.doi.org/10.1038/nbt964. (Pubitemid 38585905)
    • (2004) Nature Biotechnology , vol.22 , Issue.5 , pp. 535-546
    • Garcia-Blanco, M.A.1    Baraniak, A.P.2    Lasda, E.L.3
  • 10
    • 67650299463 scopus 로고    scopus 로고
    • Control of alternative splicing through siRNA-mediated transcriptional gene silencing
    • PMID:19543290
    • Alló M, Buggiano V, Fededa J P, Petrillo E, Schor I, de la Mata M, et al. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol 2009; 16:717-24; PMID:19543290; http://dx.doi.org/10.1038/nsmb.1620.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 717-724
    • Alló, M.1    Buggiano, V.2    Fededa, J.P.3    Petrillo, E.4    Schor, I.5    De La Mata, M.6
  • 11
    • 63149192174 scopus 로고    scopus 로고
    • Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing
    • PMID:19251664
    • Schor IE, Rascovan N, Pelisch F, Alló M, Kornblihtt AR. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc Natl Acad Sci USA 2009; 106:4325-30; PMID:19251664; http://dx.doi.org/10.1073/pnas.0810666106.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 4325-4330
    • Schor, I.E.1    Rascovan, N.2    Pelisch, F.3    Alló, M.4    Kornblihtt, A.R.5
  • 12
    • 65549147264 scopus 로고    scopus 로고
    • DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation
    • PMID:19450518
    • Muñoz MJ, Pérez Santangelo MS, Paronetto M P, de la Mata M, Pelisch F, Boireau S, et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 2009; 137:708-20; PMID:19450518; http://dx.doi.org/10.1016/j.cell.2009.03.010.
    • (2009) Cell , vol.137 , pp. 708-720
    • Muñoz, M.J.1    Pérez Santangelo, M.S.2    Paronetto, M.P.3    De La Mata, M.4    Pelisch, F.5    Boireau, S.6
  • 13
    • 79952266577 scopus 로고    scopus 로고
    • Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
    • PMID:21163941
    • Ip JY, Schmidt D, Pan Q, Ramani AK, Fraser AG, Odom D T, et al. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res 2011; 21:390-401; PMID:21163941; http://dx.doi.org/10. 1101/gr.111070.110.
    • (2011) Genome Res , vol.21 , pp. 390-401
    • Ip, J.Y.1    Schmidt, D.2    Pan, Q.3    Ramani, A.K.4    Fraser, A.G.5    Odom, D.T.6
  • 14
    • 77149175671 scopus 로고    scopus 로고
    • Regulation of alternative splicing by histone modifications
    • PMID:20133523
    • Luco R F, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science 2010; 327:996-1000; PMID:20133523; http://dx.doi.org/10.1126/science.1184208.
    • (2010) Science , vol.327 , pp. 996-1000
    • Luco, R.F.1    Pan, Q.2    Tominaga, K.3    Blencowe, B.J.4    Pereira-Smith, O.M.5    Misteli, T.6
  • 15
    • 30044441988 scopus 로고    scopus 로고
    • The human SWI/SNF subunit Brm is a regulator of alternative splicing
    • DOI 10.1038/nsmb1030
    • Batsché E, Yaniv M, Muchardt C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol 2006; 13:22-9; PMID:16341228; http://dx.doi.org/10.1038/nsmb1030. (Pubitemid 43049398)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.1 , pp. 22-29
    • Batsche, E.1    Yaniv, M.2    Muchardt, C.3
  • 16
    • 79952364016 scopus 로고    scopus 로고
    • Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons
    • PMID:21358630
    • Saint-André V, Batsché E, Rachez C, Muchardt C. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat Struct Mol Biol 2011; 18:337-44; PMID:21358630; http://dx.doi.org/10.1038/nsmb. 1995.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 337-344
    • Saint-André, V.1    Batsché, E.2    Rachez, C.3    Muchardt, C.4
  • 17
    • 33947653234 scopus 로고    scopus 로고
    • Sequence features responsible for intron retention in human
    • PMID:17324281
    • Sakabe NJ, de Souza SJ. Sequence features responsible for intron retention in human. BMC Genomics 2007; 8:59; PMID:17324281; http://dx.doi.org/ 10.1186/1471-2164-8-59.
    • (2007) BMC Genomics , vol.8 , pp. 59
    • Sakabe, N.J.1    De Souza, S.J.2
  • 18
    • 79960283905 scopus 로고    scopus 로고
    • Alternative splicing and genetic diversity: Silencers are more frequently modified by SNVs associated with alternative exon/intron borders
    • PMID:21398627
    • de Souza JES, Ramalho RF, Galante PAF, Meyer D, de Souza SJ. Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders. Nucleic Acids Res 2011; 39:4942-8; PMID:21398627; http://dx.doi.org/10.1093/nar/gkr081.
    • (2011) Nucleic Acids Res , vol.39 , pp. 4942-4948
    • De Souza Jes1    Ramalho, R.F.2    Paf, G.3    Meyer, D.4    De Souza, S.J.5
  • 19
    • 0034625260 scopus 로고    scopus 로고
    • Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity
    • PMID:10892653
    • Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 2000; 101:671-84; PMID:10892653; http://dx.doi.org/10.1016/ S0092-8674(00)80878-8.
    • (2000) Cell , vol.101 , pp. 671-684
    • Schmucker, D.1    Clemens, J.C.2    Shu, H.3    Worby, C.A.4    Xiao, J.5    Muda, M.6
  • 20
    • 10444263171 scopus 로고    scopus 로고
    • Molecular mechanisms regulating the tumor-targeting potential of splice-activated gene expression
    • DOI 10.1038/sj.cgt.7700759
    • Hayes GM, Dougherty ST, Davis PD, Dougherty GJ. Molecular mechanisms regulating the tumor-targeting potential of splice-activated gene expression. Cancer Gene Ther 2004; 11:797-807; PMID:15359288; http://dx.doi.org/10.1038/sj. cgt.7700759. (Pubitemid 39636347)
    • (2004) Cancer Gene Therapy , vol.11 , Issue.12 , pp. 797-807
    • Hayes, G.M.1    Dougherty, S.T.2    Davis, P.D.3    Dougherty, G.J.4
  • 22
    • 0037134764 scopus 로고    scopus 로고
    • A hMLH1 genomic mutation and associated novel mRNA defects in a hereditary non-polyposis colorectal cancer family
    • DOI 10.1016/S0027-5107(02)00031-3, PII S0027510702000313
    • Tanko Q, Franklin B, Lynch H, Knezetic J. A hMLH1 genomic mutation and associated novel mRNA defects in a hereditary non-polyposis colorectal cancer family. Mutat Res 2002; 503:37-42; PMID:12052501; http://dx.doi.org/10.1016/ S0027-5107(02)00031-3. (Pubitemid 34607600)
    • (2002) Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis , vol.503 , Issue.1-2 , pp. 37-42
    • Tanko, Q.1    Franklin, B.2    Lynch, H.3    Knezetic, J.4
  • 23
    • 33645833000 scopus 로고    scopus 로고
    • Unbalanced alternative splicing and its significance in cancer
    • PMID:16547952
    • Venables J P. Unbalanced alternative splicing and its significance in cancer. Bioessays 2006; 28:378-86; PMID:16547952; http://dx.doi.org/10.1002/ bies.20390.
    • (2006) Bioessays , vol.28 , pp. 378-386
    • Venables, J.P.1
  • 25
    • 33646866597 scopus 로고    scopus 로고
    • Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns
    • DOI 10.1093/bioinformatics/btl067
    • Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O. Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics 2006; 22:1211-6; PMID:16500940; http://dx.doi.org/10.1093/bioinformatics/btl067. (Pubitemid 43779013)
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1211-1216
    • Nagasaki, H.1    Arita, M.2    Nishizawa, T.3    Suwa, M.4    Gotoh, O.5
  • 26
    • 33645521073 scopus 로고    scopus 로고
    • Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes
    • PMID:16520458
    • Malko DB, Makeev VJ, Mironov AA, Gelfand MS. Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res 2006; 16:505-9; PMID:16520458; http://dx.doi.org/10.1101/gr.4236606.
    • (2006) Genome Res , vol.16 , pp. 505-509
    • Malko, D.B.1    Makeev, V.J.2    Mironov, A.A.3    Gelfand, M.S.4
  • 27
    • 50949105626 scopus 로고    scopus 로고
    • A general definition and nomenclature for alternative splicing events
    • PMID:18688268
    • Sammeth M, Foissac S, Guigó R. A general definition and nomenclature for alternative splicing events. PLoS Comput Biol 2008; 4:e1000147; PMID:18688268; http://dx.doi.org/10.1371/journal.pcbi.1000147.
    • (2008) PLoS Comput Biol , vol.4
    • Sammeth, M.1    Foissac, S.2    Guigó, R.3
  • 28
    • 34250212945 scopus 로고    scopus 로고
    • Sense-antisense pairs in mammals: Functional and evolutionary considerations
    • PMID:17371592
    • Galante PAF, Vidal DO, de Souza JE, Camargo AA, de Souza SJ. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol 2007; 8:R40; PMID:17371592; http://dx.doi.org/10.1186/gb-2007-8-3- r40.
    • (2007) Genome Biol , vol.8
    • Paf, G.1    Vidal, D.O.2    De Souza, J.E.3    Camargo, A.A.4    De Souza, S.J.5
  • 29
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • PMID:11932250
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002; 12:656-64; PMID:11932250.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 30
    • 0031732094 scopus 로고    scopus 로고
    • A computer program for aligning a cDNA sequence with a genomic DNA sequence
    • Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998; 8:967-74; PMID:9750195. (Pubitemid 28495448)
    • (1998) Genome Research , vol.8 , Issue.9 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.M.4    Miller, W.5
  • 31
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • PMID:19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-11; PMID:19289445; http://dx.doi.org/10.1093/bioinformatics/btp120.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 32
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • PMID:20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511-5; PMID:20436464; http://dx.doi.org/10.1038/nbt.1621.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.M.4    Kwan, G.5    Van Baren, M.J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.