메뉴 건너뛰기




Volumn 6, Issue SUPPL.1, 2012, Pages

Integrating many co-splicing networks to reconstruct splicing regulatory modules

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; BIOLOGY; CLUSTER ANALYSIS; EPIGENETICS; EXON; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ANALYSIS;

EID: 84875808464     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-S1-S17     Document Type: Article
Times cited : (14)

References (41)
  • 2
    • 18344364099 scopus 로고    scopus 로고
    • Understanding alternative splicing: towards a cellular code
    • 10.1038/nrm1645, 15956978
    • Matlin AJ, Clark F, Smith CWJ. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005, 6(5):386-398. 10.1038/nrm1645, 15956978.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , Issue.5 , pp. 386-398
    • Matlin, A.J.1    Clark, F.2    Smith, C.W.J.3
  • 3
    • 70350569286 scopus 로고    scopus 로고
    • Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
    • 2958924, 19773805
    • Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 2009, 10(11):741-754. 2958924, 19773805.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , Issue.11 , pp. 741-754
    • Chen, M.1    Manley, J.L.2
  • 4
    • 0024294339 scopus 로고
    • The control of alternative splicing at genes regulating sexual differentiation in D. melanogaster
    • 10.1016/0092-8674(88)90384-4, 3129196
    • Nagoshi R, McKeown M, Burtis K, Belote J, Baker B. The control of alternative splicing at genes regulating sexual differentiation in D. melanogaster. Cell 1988, 53(2):229-236. 10.1016/0092-8674(88)90384-4, 3129196.
    • (1988) Cell , vol.53 , Issue.2 , pp. 229-236
    • Nagoshi, R.1    McKeown, M.2    Burtis, K.3    Belote, J.4    Baker, B.5
  • 5
    • 0025745243 scopus 로고
    • Sex-specific splicing and polyadenylation of dsx pre-mRNA requires a sequence that binds specifically to tra-2 protein in vitro
    • 10.1016/0092-8674(91)90090-L, 1674449
    • Hedley M, Maniatis T. Sex-specific splicing and polyadenylation of dsx pre-mRNA requires a sequence that binds specifically to tra-2 protein in vitro. Cell 1991, 65(4):579-586. 10.1016/0092-8674(91)90090-L, 1674449.
    • (1991) Cell , vol.65 , Issue.4 , pp. 579-586
    • Hedley, M.1    Maniatis, T.2
  • 7
    • 0029758487 scopus 로고    scopus 로고
    • Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress
    • 10.1073/pnas.93.16.8175, 38642, 8710843
    • Hentze M, Kuhn L. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proceedings of the National Academy of Sciences of the United States of America 1996, 93(16):8175-82. 10.1073/pnas.93.16.8175, 38642, 8710843.
    • (1996) Proceedings of the National Academy of Sciences of the United States of America , vol.93 , Issue.16 , pp. 8175-8182
    • Hentze, M.1    Kuhn, L.2
  • 8
    • 51949111100 scopus 로고    scopus 로고
    • Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2
    • 10.1101/gad.1703108, 3355274, 22639738
    • Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer A, Zhang M. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes & Development 2008, 22(18):2550-2563. 10.1101/gad.1703108, 3355274, 22639738.
    • (2008) Genes & Development , vol.22 , Issue.18 , pp. 2550-2563
    • Zhang, C.1    Zhang, Z.2    Castle, J.3    Sun, S.4    Johnson, J.5    Krainer, A.6    Zhang, M.7
  • 9
    • 77955662560 scopus 로고    scopus 로고
    • An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis
    • 10.1016/j.cell.2010.07.019, 2924962, 20705336
    • Moore M, Wang Q, Kennedy C, Silver P. An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis. Cell 2010, 142(4):625-636. 10.1016/j.cell.2010.07.019, 2924962, 20705336.
    • (2010) Cell , vol.142 , Issue.4 , pp. 625-636
    • Moore, M.1    Wang, Q.2    Kennedy, C.3    Silver, P.4
  • 10
    • 60849112260 scopus 로고    scopus 로고
    • Studying alternative splicing regulatory networks through partial correlation analysis
    • 10.1186/gb-2009-10-1-r3, 2687791, 19133160
    • Chen L, Zheng S. Studying alternative splicing regulatory networks through partial correlation analysis. Genome biology 2009, 10:R3. 10.1186/gb-2009-10-1-r3, 2687791, 19133160.
    • (2009) Genome biology , vol.10
    • Chen, L.1    Zheng, S.2
  • 11
    • 34547852219 scopus 로고    scopus 로고
    • A graph-based approach to systematically reconstruct human transcriptional regulatory modules
    • 10.1093/bioinformatics/btm227, 17646346
    • Yan X, Mehan M, Huang Y, Waterman M, Yu P, Zhou X. A graph-based approach to systematically reconstruct human transcriptional regulatory modules. Bioinformatics 2007, 23(13):i577. 10.1093/bioinformatics/btm227, 17646346.
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Yan, X.1    Mehan, M.2    Huang, Y.3    Waterman, M.4    Yu, P.5    Zhou, X.6
  • 12
    • 79959834606 scopus 로고    scopus 로고
    • Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation
    • 3116899, 21698123
    • Li W, Liu CC, Zhang T, Li H, Waterman MS, Zhou XJ. Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation. PLoS Comput Biol 2011, 7(6):e1001106. 3116899, 21698123.
    • (2011) PLoS Comput Biol , vol.7 , Issue.6
    • Li, W.1    Liu, C.C.2    Zhang, T.3    Li, H.4    Waterman, M.S.5    Zhou, X.J.6
  • 13
    • 0020118274 scopus 로고
    • Neural networks and physical systems with emergent collective computational abilities
    • 10.1073/pnas.79.8.2554, 346238, 6953413
    • Hopfield JJ. Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci USA 1982, 79(8):2554-2558. 10.1073/pnas.79.8.2554, 346238, 6953413.
    • (1982) Proc Natl Acad Sci USA , vol.79 , Issue.8 , pp. 2554-2558
    • Hopfield, J.J.1
  • 14
    • 0000230999 scopus 로고
    • Maxima for Graphs and a New Proof of a Theorem of Turán
    • Motzkin TS, Straus EG. Maxima for Graphs and a New Proof of a Theorem of Turán. Canadian Journal of Mathematics 1965, 17(4):533-540.
    • (1965) Canadian Journal of Mathematics , vol.17 , Issue.4 , pp. 533-540
    • Motzkin, T.S.1    Straus, E.G.2
  • 15
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 16
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 3146043, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28(5):511-515. 10.1038/nbt.1621, 3146043, 20436464.
    • (2010) Nature Biotechnology , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 18
    • 64549119707 scopus 로고    scopus 로고
    • Statistical inferences for isoform expression in RNA-Seq
    • 10.1093/bioinformatics/btp113, 2666817, 19244387
    • Jiang H, Wong WH. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 2009, 25(8):1026-1032. 10.1093/bioinformatics/btp113, 2666817, 19244387.
    • (2009) Bioinformatics , vol.25 , Issue.8 , pp. 1026-1032
    • Jiang, H.1    Wong, W.H.2
  • 20
    • 84857687714 scopus 로고    scopus 로고
    • SpliceAid 2: A database of human splicing factors expression data and RNA target motifs
    • 10.1002/humu.21609, 21922594
    • Piva F, Giulietti M, Burini AB, Principato G. SpliceAid 2: A database of human splicing factors expression data and RNA target motifs. Hum Mutat 2012, 33:81-85. 10.1002/humu.21609, 21922594.
    • (2012) Hum Mutat , vol.33 , pp. 81-85
    • Piva, F.1    Giulietti, M.2    Burini, A.B.3    Principato, G.4
  • 21
    • 23844471326 scopus 로고    scopus 로고
    • HnRNP L represses exon splicing via a regulated exonic splicing silencer
    • 10.1038/sj.emboj.7600745, 1182240, 16001081
    • Rothrock CR, House AE, Lynch KW. HnRNP L represses exon splicing via a regulated exonic splicing silencer. The EMBO Journal 2005, 24(15):2792-2802. 10.1038/sj.emboj.7600745, 1182240, 16001081.
    • (2005) The EMBO Journal , vol.24 , Issue.15 , pp. 2792-2802
    • Rothrock, C.R.1    House, A.E.2    Lynch, K.W.3
  • 22
    • 33847342492 scopus 로고    scopus 로고
    • HnRNP-U directly interacts with WT1 and modulates WT1 transcriptional activation
    • 10.1038/sj.onc.1209922, 16924231
    • Spraggon L, Dudnakova T, Slight J, Lustig-Yariv O, Cotterell J, Hastie N, Miles C. hnRNP-U directly interacts with WT1 and modulates WT1 transcriptional activation. Oncogene 2007, 26(10):1484-1491. 10.1038/sj.onc.1209922, 16924231.
    • (2007) Oncogene , vol.26 , Issue.10 , pp. 1484-1491
    • Spraggon, L.1    Dudnakova, T.2    Slight, J.3    Lustig-Yariv, O.4    Cotterell, J.5    Hastie, N.6    Miles, C.7
  • 23
    • 0028338991 scopus 로고
    • Characterization and cloning of the human splicing factor 9G8: a novel 35 kDa factor of the serine/arginine protein family
    • 395138, 8013463
    • Cavaloc Y, Popielarz M, Fuchs JP, Gattoni R, Stévenin J. Characterization and cloning of the human splicing factor 9G8: a novel 35 kDa factor of the serine/arginine protein family. The EMBO Journal 1994, 13(11):2639-2649. 395138, 8013463.
    • (1994) The EMBO Journal , vol.13 , Issue.11 , pp. 2639-2649
    • Cavaloc, Y.1    Popielarz, M.2    Fuchs, J.P.3    Gattoni, R.4    Stévenin, J.5
  • 24
    • 77955416143 scopus 로고    scopus 로고
    • Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells
    • 10.1038/nsmb.1862, 22637702
    • Ankö M, Morales L, Henry I, Beyer A, Neugebauer KM. Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nature Structural & Molecular Biology 2010, 17(8):962-970. 10.1038/nsmb.1862, 22637702.
    • (2010) Nature Structural & Molecular Biology , vol.17 , Issue.8 , pp. 962-970
    • Ankö, M.1    Morales, L.2    Henry, I.3    Beyer, A.4    Neugebauer, K.M.5
  • 25
    • 0036261810 scopus 로고    scopus 로고
    • SRp30c is a repressor of 3' splice site utilization
    • 10.1128/MCB.22.12.4001-4010.2002, 133842, 12024014
    • Simard MJ, Chabot B. SRp30c is a repressor of 3' splice site utilization. Molecular and Cellular Biology 2002, 22(12):4001-4010. 10.1128/MCB.22.12.4001-4010.2002, 133842, 12024014.
    • (2002) Molecular and Cellular Biology , vol.22 , Issue.12 , pp. 4001-4010
    • Simard, M.J.1    Chabot, B.2
  • 29
    • 0742306875 scopus 로고    scopus 로고
    • GA-binding protein transcription factor: a review of GABP as an integrator of intracellular signaling and protein-protein interactions
    • 10.1016/j.bcmd.2003.09.005, 22639170
    • Rosmarin AG, Resendes KK, Yang Z, McMillan JN, Fleming SL. GA-binding protein transcription factor: a review of GABP as an integrator of intracellular signaling and protein-protein interactions. Blood Cells Mol Dis 2004, 32:143-154. 10.1016/j.bcmd.2003.09.005, 22639170.
    • (2004) Blood Cells Mol Dis , vol.32 , pp. 143-154
    • Rosmarin, A.G.1    Resendes, K.K.2    Yang, Z.3    McMillan, J.N.4    Fleming, S.L.5
  • 30
    • 0032191915 scopus 로고    scopus 로고
    • C-Fos as a transcription factor: a stressful (re)view from a functional map
    • 10.1016/S0197-0186(98)00023-0, 9840219
    • Kovács KJ. c-Fos as a transcription factor: a stressful (re)view from a functional map. Neurochemistry International 1998, 33(4):287-297. 10.1016/S0197-0186(98)00023-0, 9840219.
    • (1998) Neurochemistry International , vol.33 , Issue.4 , pp. 287-297
    • Kovács, K.J.1
  • 31
    • 79952854016 scopus 로고    scopus 로고
    • NF-Y recruits Ash2L to impart H3K4 trimethylation on CCAAT promoters
    • 10.1371/journal.pone.0017220, 3061855, 21445285
    • Fossati A, Dolfini D, Donati G, Mantovani R. NF-Y recruits Ash2L to impart H3K4 trimethylation on CCAAT promoters. PloS One 2011, 6(3):e17220. 10.1371/journal.pone.0017220, 3061855, 21445285.
    • (2011) PloS One , vol.6 , Issue.3
    • Fossati, A.1    Dolfini, D.2    Donati, G.3    Mantovani, R.4
  • 35
    • 0026569419 scopus 로고
    • D-E-A-D protein family of putative RNA helicases
    • 10.1111/j.1365-2958.1992.tb01470.x, 1552844
    • Schmid SR, Linder P. D-E-A-D protein family of putative RNA helicases. Molecular Microbiology 1992, 6(3):283-291. 10.1111/j.1365-2958.1992.tb01470.x, 1552844.
    • (1992) Molecular Microbiology , vol.6 , Issue.3 , pp. 283-291
    • Schmid, S.R.1    Linder, P.2
  • 36
    • 0030967951 scopus 로고    scopus 로고
    • RNA helicase A mediates association of CBP with RNA polymerase II
    • 10.1016/S0092-8674(00)80376-1, 9323138
    • Nakajima T, Uchida C, Anderson SF, Lee CG, Hurwitz J, Parvin JD, Montminy M. RNA helicase A mediates association of CBP with RNA polymerase II. Cell 1997, 90(6):1107-1112. 10.1016/S0092-8674(00)80376-1, 9323138.
    • (1997) Cell , vol.90 , Issue.6 , pp. 1107-1112
    • Nakajima, T.1    Uchida, C.2    Anderson, S.F.3    Lee, C.G.4    Hurwitz, J.5    Parvin, J.D.6    Montminy, M.7
  • 37
    • 1242264341 scopus 로고    scopus 로고
    • DNA-dependent protein kinase (DNA-PK) phosphorylates nuclear DNA helicase II/RNA helicase A and hnRNP proteins in an RNA-dependent manner
    • 10.1093/nar/gkg933, 373260, 14704337
    • Zhang S, Schlott B, Görlach M, Grosse F. DNA-dependent protein kinase (DNA-PK) phosphorylates nuclear DNA helicase II/RNA helicase A and hnRNP proteins in an RNA-dependent manner. Nucleic Acids Research 2004, 32:1-10. 10.1093/nar/gkg933, 373260, 14704337.
    • (2004) Nucleic Acids Research , vol.32 , pp. 1-10
    • Zhang, S.1    Schlott, B.2    Görlach, M.3    Grosse, F.4
  • 38
    • 84880317039 scopus 로고    scopus 로고
    • A role for TREX components in the release of spliced mRNA from nuclear speckle domains
    • 10.1038/ncomms1103, 20981025
    • Dias AP, Dufu K, Lei H, Reed R. A role for TREX components in the release of spliced mRNA from nuclear speckle domains. Nature Communications 2010, 1:97. 10.1038/ncomms1103, 20981025.
    • (2010) Nature Communications , vol.1 , pp. 97
    • Dias, A.P.1    Dufu, K.2    Lei, H.3    Reed, R.4
  • 39
    • 51249115622 scopus 로고    scopus 로고
    • Alternative splicing in the NF-kappaB signaling pathway
    • 10.1016/j.gene.2008.07.015, 2624576, 18718859
    • Leeman JR, Gilmore TD. Alternative splicing in the NF-kappaB signaling pathway. Gene 2008, 423(2):97-107. 10.1016/j.gene.2008.07.015, 2624576, 18718859.
    • (2008) Gene , vol.423 , Issue.2 , pp. 97-107
    • Leeman, J.R.1    Gilmore, T.D.2
  • 40
    • 33645677012 scopus 로고    scopus 로고
    • Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors
    • 10.1021/bi052387u, 16584190
    • Conte MR, Kelly G, Babon J, Sanfelice D, Youell J, Smerdon SJ, Proud CG. Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors. Biochemistry 2006, 45(14):4550-4558. 10.1021/bi052387u, 16584190.
    • (2006) Biochemistry , vol.45 , Issue.14 , pp. 4550-4558
    • Conte, M.R.1    Kelly, G.2    Babon, J.3    Sanfelice, D.4    Youell, J.5    Smerdon, S.J.6    Proud, C.G.7
  • 41
    • 77951191949 scopus 로고    scopus 로고
    • Analysis of Multi-stage Convex Relaxation for Sparse Regularization
    • Zhang T. Analysis of Multi-stage Convex Relaxation for Sparse Regularization. J Mach Learn Res 2010, 11:1081-1107.
    • (2010) J Mach Learn Res , vol.11 , pp. 1081-1107
    • Zhang, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.