메뉴 건너뛰기




Volumn 4, Issue 3, 2008, Pages

Entropy measures quantify global splicing disorders in cancer

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROLIFERATION; DISEASES; HISTOLOGY; MAMMALS; TISSUE; TRANSCRIPTION; UNCERTAINTY ANALYSIS;

EID: 41849110528     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000011     Document Type: Article
Times cited : (48)

References (38)
  • 1
  • 3
    • 0038349624 scopus 로고    scopus 로고
    • Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
    • Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, et al. (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 13: 1290-1300.
    • (2003) Genome Res , vol.13 , pp. 1290-1300
    • Zavolan, M.1    Kondo, S.2    Schonbach, C.3    Adachi, J.4    Hume, D.A.5
  • 4
    • 0347623371 scopus 로고    scopus 로고
    • Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays
    • Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, et al. (2003) Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays. Science 302: 2141-2144.
    • (2003) Science , vol.302 , pp. 2141-2144
    • Johnson, J.M.1    Castle, J.2    Garrett-Engele, P.3    Kan, Z.4    Loerch, P.M.5
  • 5
    • 19944365069 scopus 로고    scopus 로고
    • Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
    • Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, et al. (2004) Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 16: 929-941.
    • (2004) Mol Cell , vol.16 , pp. 929-941
    • Pan, Q.1    Shai, O.2    Misquitta, C.3    Zhang, W.4    Saltzman, A.L.5
  • 6
    • 0036712421 scopus 로고    scopus 로고
    • Genome-wide detection of tissue-specific alternative splicing in the human transcriptome
    • Xu Q, Modrek B, Lee C (2002) Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucl Acids Res 30: 3754-3766.
    • (2002) Nucl Acids Res , vol.30 , pp. 3754-3766
    • Xu, Q.1    Modrek, B.2    Lee, C.3
  • 7
    • 33646950851 scopus 로고    scopus 로고
    • Biased alternative polyadenylation in human tissues
    • Zhang H, Lee J, Tian B (2005) Biased alternative polyadenylation in human tissues. Genome Biology 6: R100.
    • (2005) Genome Biology , vol.6
    • Zhang, H.1    Lee, J.2    Tian, B.3
  • 8
    • 7444240909 scopus 로고    scopus 로고
    • VEGF165b, an Inhibitory Vascular Endothelial Growth Factor Splice Variant: Mechanism of Action, In vivo Effect On Angiogenesis and Endogenous Protein Expression
    • Woolard J, Wang W-Y, Bevan HS, Qiu Y, Morbidelli L, et al. (2004) VEGF165b, an Inhibitory Vascular Endothelial Growth Factor Splice Variant: Mechanism of Action, In vivo Effect On Angiogenesis and Endogenous Protein Expression. Cancer Res 64: 7822-7835.
    • (2004) Cancer Res , vol.64 , pp. 7822-7835
    • Woolard, J.1    Wang, W.-Y.2    Bevan, H.S.3    Qiu, Y.4    Morbidelli, L.5
  • 9
    • 0242329770 scopus 로고    scopus 로고
    • FGFR3IIIS: A novel soluble FGFR3 spliced variant that modulates growth is frequently expressed in tumour cells
    • Sturla LM, Merrick AE, Burchill SA (2003) FGFR3IIIS: a novel soluble FGFR3 spliced variant that modulates growth is frequently expressed in tumour cells. Br J Cancer 89: 1276-1284.
    • (2003) Br J Cancer , vol.89 , pp. 1276-1284
    • Sturla, L.M.1    Merrick, A.E.2    Burchill, S.A.3
  • 10
    • 11244313840 scopus 로고    scopus 로고
    • Rac1b, a tumor associated, constitutively active Rac1 splice variant, promotes cellular transformation
    • Singh A, Karnoub AE, Palmby TR, Lengyel E, Sondek J, et al. (2004) Rac1b, a tumor associated, constitutively active Rac1 splice variant, promotes cellular transformation. Oncogene 23: 9369-9380.
    • (2004) Oncogene , vol.23 , pp. 9369-9380
    • Singh, A.1    Karnoub, A.E.2    Palmby, T.R.3    Lengyel, E.4    Sondek, J.5
  • 11
    • 33746927884 scopus 로고    scopus 로고
    • The connection between splicing and cancer
    • Srebrow A, Kornblihtt AR (2006) The connection between splicing and cancer. J Cell Sci 119: 2635-2641.
    • (2006) J Cell Sci , vol.119 , pp. 2635-2641
    • Srebrow, A.1    Kornblihtt, A.R.2
  • 12
    • 7444220147 scopus 로고    scopus 로고
    • Aberrant and alternative splicing in cancer
    • Venables JP (2004) Aberrant and alternative splicing in cancer. Cancer Res 64: 7647-7654.
    • (2004) Cancer Res , vol.64 , pp. 7647-7654
    • Venables, J.P.1
  • 14
    • 33645220093 scopus 로고    scopus 로고
    • Regulation of CD44 alternative splicing by SRm160 and its potential role in tumor cell invasion
    • Cheng C, Sharp PA (2006) Regulation of CD44 alternative splicing by SRm160 and its potential role in tumor cell invasion. Mol Cell Biol 26: 362-370.
    • (2006) Mol Cell Biol , vol.26 , pp. 362-370
    • Cheng, C.1    Sharp, P.A.2
  • 15
    • 1542359466 scopus 로고    scopus 로고
    • Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA
    • Stoilov P, Daoud R, Nayler O, Stamm S (2004) Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA. Hum Mol Genet 13: 509-524.
    • (2004) Hum Mol Genet , vol.13 , pp. 509-524
    • Stoilov, P.1    Daoud, R.2    Nayler, O.3    Stamm, S.4
  • 16
    • 33646426385 scopus 로고    scopus 로고
    • Splicing factor Tra2-beta1 is specifically induced in breast cancer and regulates alternative splicing of the CD44 gene
    • Watermann DO, Tang Y, Zur Hausen A, Jager M, Stamm S, et al. (2006) Splicing factor Tra2-beta1 is specifically induced in breast cancer and regulates alternative splicing of the CD44 gene. Cancer Res 66: 4774-4780.
    • (2006) Cancer Res , vol.66 , pp. 4774-4780
    • Watermann, D.O.1    Tang, Y.2    Zur Hausen, A.3    Jager, M.4    Stamm, S.5
  • 17
    • 29144447982 scopus 로고    scopus 로고
    • Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene
    • Ghigna C, Giordano S, Shen H, Benvenuto F, Castiglioni F, et al. (2005) Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol Cell 20: 881-890.
    • (2005) Mol Cell , vol.20 , pp. 881-890
    • Ghigna, C.1    Giordano, S.2    Shen, H.3    Benvenuto, F.4    Castiglioni, F.5
  • 18
  • 19
    • 0033380257 scopus 로고    scopus 로고
    • Differential expression of the splicing regulatory factor genes during two-step chemical transformation in a BALB/3T3-derived cell line, MT-5
    • Maeda T, Hiranuma H, Jikko A (1999) Differential expression of the splicing regulatory factor genes during two-step chemical transformation in a BALB/3T3-derived cell line, MT-5. Carcinogenesis 20: 2341-2344.
    • (1999) Carcinogenesis , vol.20 , pp. 2341-2344
    • Maeda, T.1    Hiranuma, H.2    Jikko, A.3
  • 20
    • 9244221107 scopus 로고    scopus 로고
    • Relative amounts of antagonistic splicing factors, hnRNP A1 and ASF/SF2, change during neoplastic lung growth: Implications for pre-mRNA processing
    • Zerbe LK, Pino I, Pio R, Cosper PF, Dwyer-Nield LD, et al. (2004) Relative amounts of antagonistic splicing factors, hnRNP A1 and ASF/SF2, change during neoplastic lung growth: implications for pre-mRNA processing. Mol Carcinog 41: 187-196.
    • (2004) Mol Carcinog , vol.41 , pp. 187-196
    • Zerbe, L.K.1    Pino, I.2    Pio, R.3    Cosper, P.F.4    Dwyer-Nield, L.D.5
  • 21
    • 24944494948 scopus 로고    scopus 로고
    • Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms
    • Roy M, Xu Q, Lee C (2005) Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. Nucleic Acids Res 33: 5026-5033.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5026-5033
    • Roy, M.1    Xu, Q.2    Lee, C.3
  • 22
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 23
    • 0038817774 scopus 로고    scopus 로고
    • eVOC: A controlled vocabulary for unifying gene expression data
    • Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, et al. (2003) eVOC: a controlled vocabulary for unifying gene expression data. Genome Res 13: 1222-1230.
    • (2003) Genome Res , vol.13 , pp. 1222-1230
    • Kelso, J.1    Visagie, J.2    Theiler, G.3    Christoffels, A.4    Bardien, S.5
  • 24
    • 1642473041 scopus 로고    scopus 로고
    • How prevalent is functional alternative splicing in the human genome?
    • Sorek R, Shamir R, Ast G (2004) How prevalent is functional alternative splicing in the human genome? Trends Genet 20: 68-71.
    • (2004) Trends Genet , vol.20 , pp. 68-71
    • Sorek, R.1    Shamir, R.2    Ast, G.3
  • 25
    • 33645808501 scopus 로고    scopus 로고
    • AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
    • Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, et al. (2006) AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics 7: 169.
    • (2006) BMC Bioinformatics , vol.7 , pp. 169
    • Le Texier, V.1    Riethoven, J.J.2    Kumanduri, V.3    Gopalakrishnan, C.4    Lopez, F.5
  • 26
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 27
    • 8444224184 scopus 로고    scopus 로고
    • A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models
    • Puthier D, Joly F, Irla M, Saade M, Victorero G, et al. (2004) A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models. J Immunol 173: 6109-6118.
    • (2004) J Immunol , vol.173 , pp. 6109-6118
    • Puthier, D.1    Joly, F.2    Irla, M.3    Saade, M.4    Victorero, G.5
  • 28
    • 0030850812 scopus 로고    scopus 로고
    • The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation
    • Jumaa H, Nielsen PJ (1997) The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation. Embo J 16: 5077-5085.
    • (1997) Embo J , vol.16 , pp. 5077-5085
    • Jumaa, H.1    Nielsen, P.J.2
  • 29
    • 0141974926 scopus 로고    scopus 로고
    • Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences
    • Xu Q, Lee C (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res 31: 5635-5643.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5635-5643
    • Xu, Q.1    Lee, C.2
  • 31
    • 0033578006 scopus 로고    scopus 로고
    • Stage-specific changes in SR splicing factors and alternative splicing in mammary tumorigenesis
    • Stickeler E, Kittrell F, Medina D, Berget SM (1999) Stage-specific changes in SR splicing factors and alternative splicing in mammary tumorigenesis. Oncogene 18: 3574-3582.
    • (1999) Oncogene , vol.18 , pp. 3574-3582
    • Stickeler, E.1    Kittrell, F.2    Medina, D.3    Berget, S.M.4
  • 32
    • 34247330971 scopus 로고    scopus 로고
    • Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
    • Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE (2007) Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446: 926-929.
    • (2007) Nature , vol.446 , pp. 926-929
    • Lareau, L.F.1    Inada, M.2    Green, R.E.3    Wengrod, J.C.4    Brenner, S.E.5
  • 33
    • 33947305594 scopus 로고    scopus 로고
    • Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
    • Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, et al. (2007) Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 21: 708-718.
    • (2007) Genes Dev , vol.21 , pp. 708-718
    • Ni, J.Z.1    Grate, L.2    Donohue, J.P.3    Preston, C.4    Nobida, N.5
  • 35
    • 33645746620 scopus 로고    scopus 로고
    • Targeting the RNA splicing machinery as a novel treatment strategy for pancreatic carcinoma
    • Hayes GM, Carrigan PE, Beck AM, Miller LJ (2006) Targeting the RNA splicing machinery as a novel treatment strategy for pancreatic carcinoma. Cancer Res 66: 3819-3827.
    • (2006) Cancer Res , vol.66 , pp. 3819-3827
    • Hayes, G.M.1    Carrigan, P.E.2    Beck, A.M.3    Miller, L.J.4
  • 36
    • 0035884180 scopus 로고    scopus 로고
    • Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-506
    • Pilch B, Allemand E, Facompre M, Bailly C, Riou JF, et al. (2001) Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-506. Cancer Res 61: 6876-6884.
    • (2001) Cancer Res , vol.61 , pp. 6876-6884
    • Pilch, B.1    Allemand, E.2    Facompre, M.3    Bailly, C.4    Riou, J.F.5
  • 37
    • 33846870354 scopus 로고    scopus 로고
    • Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing
    • Tian B, Pan Z, Lee JY (2007) Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res 17: 156-165.
    • (2007) Genome Res , vol.17 , pp. 156-165
    • Tian, B.1    Pan, Z.2    Lee, J.Y.3
  • 38
    • 20444365683 scopus 로고    scopus 로고
    • GOToolBox: Functional analysis of gene datasets based on Gene Ontology
    • Martin D, Brun C, Remy E, Mouren P, Thieffry D, et al. (2004) GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 5: R101.
    • (2004) Genome Biol , vol.5
    • Martin, D.1    Brun, C.2    Remy, E.3    Mouren, P.4    Thieffry, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.