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Volumn 10, Issue 1-2, 2010, Pages 89-123

Exhaustive analysis of the modular structure of the spliceosomal assembly network: A Petri net approach

Author keywords

Alternative splicing; MCTS; Pathway analysis; Petri net theory; Regulated splicing; Signal transduction networks; Spliceosome; T clusters; T invariants

Indexed keywords

FUNGAL PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RNA;

EID: 77952035086     PISSN: 14343207     EISSN: None     Source Type: Journal    
DOI: 10.3233/ISB-2010-0419     Document Type: Article
Times cited : (7)

References (112)
  • 1
    • 0030911051 scopus 로고    scopus 로고
    • Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals
    • Abovich, N. and Rosbash, M. (1997). Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89, 403-412.
    • (1997) Cell , vol.89 , pp. 403-412
    • Abovich, N.1    Rosbash, M.2
  • 3
    • 18344396487 scopus 로고    scopus 로고
    • Lsm proteins and RNA processing
    • Beggs, J. D. (2005). Lsm proteins and RNA processing. Biochem. Soc. Trans. 33, 433-438.
    • (2005) Biochem. Soc. Trans. , vol.33 , pp. 433-438
    • Beggs, J.D.1
  • 4
    • 33748173310 scopus 로고    scopus 로고
    • Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta-snRNP
    • Behzadnia, N., Hartmuth, K., Will, C. L. and Lührmann, R. (2006). Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta-snRNP. RNA 12, 1738-1746.
    • (2006) RNA , vol.12 , pp. 1738-1746
    • Behzadnia, N.1    Hartmuth, K.2    Will, C.L.3    Lührmann, R.4
  • 5
    • 0036591882 scopus 로고    scopus 로고
    • The mrna assembly line: Transcription and processing machines in the same factory
    • Bentley, D. (2002). The mrna assembly line: transcription and processing machines in the same factory. Curr. Opin. Cell. Biol. 14, 336-342.
    • (2002) Curr. Opin. Cell. Biol. , vol.14 , pp. 336-342
    • Bentley, D.1
  • 6
    • 0032521186 scopus 로고    scopus 로고
    • A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition
    • Berglund, J. A., Abovich, N. and Rosbash, M. (1998). A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes Dev. 12, 858-867.
    • (1998) Genes Dev. , vol.12 , pp. 858-867
    • Berglund, J.A.1    Abovich, N.2    Rosbash, M.3
  • 8
    • 44949091262 scopus 로고    scopus 로고
    • Comparative analysis of sequence features involved in the recognition of tandem splice sites
    • Bortfeldt, R., Schindler, S., Szafranski, K., Schuster, S. and Holste, D. (2008). Comparative analysis of sequence features involved in the recognition of tandem splice sites. BMC Genomics 9, 202.
    • (2008) BMC Genomics , vol.9 , pp. 202
    • Bortfeldt, R.1    Schindler, S.2    Szafranski, K.3    Schuster, S.4    Holste, D.5
  • 10
    • 0036948420 scopus 로고    scopus 로고
    • Allosteric cascade of spliceosome activation
    • Brow, D. A. (2002). Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36, 333-360.
    • (2002) Annu. Rev. Genet. , vol.36 , pp. 333-360
    • Brow, D.A.1
  • 11
    • 0027287852 scopus 로고
    • A mechanism to enhance mRNA splicing fidelity: The RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates
    • Burgess, S. M. and Guthrie, C. (1993). A mechanism to enhance mRNA splicing fidelity: the RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates. Cell 73, 1377-1391.
    • (1993) Cell , vol.73 , pp. 1377-1391
    • Burgess, S.M.1    Guthrie, C.2
  • 12
    • 0032493734 scopus 로고    scopus 로고
    • A serine/arginine-rich domain in the human U1 70k protein is necessary and sufficient for ASF/SF2 binding
    • Cao, W. and Garcia-Blanco, M. A. (1998). A serine/arginine-rich domain in the human U1 70k protein is necessary and sufficient for ASF/SF2 binding. J. Biol. Chem. 273, 20629-20635.
    • (1998) J. Biol. Chem. , vol.273 , pp. 20629-20635
    • Cao, W.1    Garcia-Blanco, M.A.2
  • 13
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • Chaouiya, C. (2007). Petri net modelling of biological networks. Brief. Bioinform. 8, 210-219.
    • (2007) Brief. Bioinform. , vol.8 , pp. 210-219
    • Chaouiya, C.1
  • 14
    • 0035105921 scopus 로고    scopus 로고
    • Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor
    • Chen, J. Y.-F., Stands, L., Staley, J. P., Jackups, R. R., Latus, L. J. and Chang, T.-H. (2001). Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol. Cell. 7, 227-232.
    • (2001) Mol. Cell. , vol.7 , pp. 227-232
    • Chen, J.Y.-F.1    Stands, L.2    Staley, J.P.3    Jackups, R.R.4    Latus, L.J.5    Chang, T.-H.6
  • 15
    • 34547647038 scopus 로고    scopus 로고
    • Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors
    • Chen, Y.-I. G., Moore, R. E., Ge, H. Y., Young, M. K., Lee, T. D. and Stevens, S. W. (2007). Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Nucleic Acids Res. 35, 3928-3944.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3928-3944
    • Chen, Y.-I.G.1    Moore, R.E.2    Ge, H.Y.3    Young, M.K.4    Lee, T.D.5    Stevens, S.W.6
  • 16
    • 0000490505 scopus 로고
    • A review of classification
    • Cormack, R. M. (1971). A review of classification. J. R. Stat. Soc. 134, 321-367.
    • (1971) J. R. Stat. Soc. , vol.134 , pp. 321-367
    • Cormack, R.M.1
  • 17
    • 0029089334 scopus 로고
    • A U6 snRNA:pre-mRNA interaction can be rate-limiting for U1-independent splicing
    • Crispino, J. D. and Sharp, P. A. (1995). A U6 snRNA:pre-mRNA interaction can be rate-limiting for U1-independent splicing. Genes Dev. 9, 2314-2323.
    • (1995) Genes Dev. , vol.9 , pp. 2314-2323
    • Crispino, J.D.1    Sharp, P.A.2
  • 18
    • 0029949594 scopus 로고    scopus 로고
    • Cis-acting elements distinct from the 5' splice site promote U1-independent pre-mRNA splicing
    • Crispino, J. D., Mermoud, J. E., Lamond, A. I. and Sharp, P. A. (1996). Cis-acting elements distinct from the 5' splice site promote U1-independent pre-mRNA splicing. RNA 2, 664-673.
    • (1996) RNA , vol.2 , pp. 664-673
    • Crispino, J.D.1    Mermoud, J.E.2    Lamond, A.I.3    Sharp, P.A.4
  • 19
    • 0033636518 scopus 로고    scopus 로고
    • Functional association of U2 snRNP with the ATP-independent spliceosomal complex e
    • Das, R., Zhou, Z. and Reed, R. (2000). Functional association of U2 snRNP with the ATP-independent spliceosomal complex E. Mol. Cell. 5, 779-787.
    • (2000) Mol. Cell. , vol.5 , pp. 779-787
    • Das, R.1    Zhou, Z.2    Reed, R.3
  • 20
    • 0033838148 scopus 로고    scopus 로고
    • The RNA-binding protein TIA-1 is a novel mammalian splicing regulator acting through intron sequences adjacent to a 5' splice site
    • Del Gatto-Konczak, F., Bourgeois, C. F., Le Guiner, C., Kister, L., Gesnel, M.-C., St Évenin, J. and Breathnach, R. (2000). The RNA-binding protein TIA-1 is a novel mammalian splicing regulator acting through intron sequences adjacent to a 5' splice site. Mol. Cell. Biol. 20, 6287-6299
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 6287-6299
    • Del Gatto-Konczak, F.1    Bourgeois, C.F.2    Le Guiner, C.3    Kister, L.4    Gesnel, M.-C.5    St Évenin, J.6    Breathnach, R.7
  • 21
    • 33846665912 scopus 로고    scopus 로고
    • The 5' end of U2 snRNA is in close proximity to U1 and functional sites of the pre-mRNA in early spliceosomal complexes
    • Dönmez, G., Hartmuth, K., Kastner, B., Will, C. L. and Lührmann, R. (2007). The 5' end of U2 snRNA is in close proximity to U1 and functional sites of the pre-mRNA in early spliceosomal complexes. Mol. Cell. 25, 399-411.
    • (2007) Mol. Cell. , vol.25 , pp. 399-411
    • Dönmez, G.1    Hartmuth, K.2    Kastner, B.3    Will, C.L.4    Lührmann, R.5
  • 22
    • 0037026523 scopus 로고    scopus 로고
    • The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairing
    • Du, H. and Rosbash, M. (2002). The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairing. Nature 419, 86-90.
    • (2002) Nature , vol.419 , pp. 86-90
    • Du, H.1    Rosbash, M.2
  • 23
    • 33645212088 scopus 로고    scopus 로고
    • U2 snRNA-protein contacts in purified human 17S U2 snRNPs and in spliceosomal A and B complexes
    • Dybkov, O., Will, C. L., Deckert, J., Behzadnia, N., Hartmuth, K. and Lührmann, R. (2006). U2 snRNA-protein contacts in purified human 17S U2 snRNPs and in spliceosomal A and B complexes. Mol. Cell. Biol. 26, 2803-2816.
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 2803-2816
    • Dybkov, O.1    Will, C.L.2    Deckert, J.3    Behzadnia, N.4    Hartmuth, K.5    Lührmann, R.6
  • 24
    • 0030611640 scopus 로고    scopus 로고
    • U2AF65 recruits a novel human DEAD box protein required for the U2 snRNPbranchpoint interaction
    • Fleckner, J., Zhang, M., Valcárcel, J. and Green, M. R. (1997). U2AF65 recruits a novel human DEAD box protein required for the U2 snRNPbranchpoint interaction. Genes Dev. 11, 1864-1872.
    • (1997) Genes Dev. , vol.11 , pp. 1864-1872
    • Fleckner, J.1    Zhang, M.2    Valcárcel, J.3    Green, M.R.4
  • 25
    • 0037121924 scopus 로고    scopus 로고
    • The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5′ splice sites
    • Förch, P., Puig, O., Marténez, C., Séraphin, B. and Valcárcel, J. (2002). The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5′ splice sites. EMBO J. 21, 6882-6892.
    • (2002) EMBO J. , vol.21 , pp. 6882-6892
    • Förch, P.1    Puig, O.2    Marténez, C.3    Séraphin, B.4    Valcárcel, J.5
  • 27
    • 0035161659 scopus 로고    scopus 로고
    • The yeast U5 snrnp coisolated with the U1 snrnp has an unexpected protein composition and includes the splicing factor Aar2p
    • Gottschalk, A., Kastner, B., Lührmann, R. and Fabrizio, P. (2001). The yeast U5 snrnp coisolated with the U1 snrnp has an unexpected protein composition and includes the splicing factor Aar2p. RNA 7, 1554-1565.
    • (2001) RNA , vol.7 , pp. 1554-1565
    • Gottschalk, A.1    Kastner, B.2    Lührmann, R.3    Fabrizio, P.4
  • 28
    • 0031878108 scopus 로고    scopus 로고
    • A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site
    • Gozani, O., Potashkin, J. and Reed, R. (1998). A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol. Cell. Biol. 18, 4752-4760.
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 4752-4760
    • Gozani, O.1    Potashkin, J.2    Reed, R.3
  • 30
    • 0035252410 scopus 로고    scopus 로고
    • Alternative splicing: Increasing diversity in the proteomic world
    • Graveley, B. R. (2001). Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 17, 100-107.
    • (2001) Trends Genet. , vol.17 , pp. 100-107
    • Graveley, B.R.1
  • 31
    • 21244493903 scopus 로고    scopus 로고
    • Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex
    • Görnemann, J., Kotovic, K. M., Hujer, K. and Neugebauer, K. M. (2005). Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol. Cell. 19, 53-63.
    • (2005) Mol. Cell. , vol.19 , pp. 53-63
    • Görnemann, J.1    Kotovic, K.M.2    Hujer, K.3    Neugebauer, K.M.4
  • 32
    • 41549085829 scopus 로고    scopus 로고
    • Petri net modelling of gene regulation of the Duchenne muscular dystrophy
    • Grunwald, S., Speer, A., Ackermann, J. and Koch, I. (2008). Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Biosystems 92, 189-205.
    • (2008) Biosystems , vol.92 , pp. 189-205
    • Grunwald, S.1    Speer, A.2    Ackermann, J.3    Koch, I.4
  • 33
    • 0036029247 scopus 로고    scopus 로고
    • Cytokines and related receptor-mediated signaling pathways
    • Haddad, J. J. (2002). Cytokines and related receptor-mediated signaling pathways. Biochem. Biophys. Res. Commun. 297, 700-713.
    • (2002) Biochem. Biophys. Res. Commun. , vol.297 , pp. 700-713
    • Haddad, J.J.1
  • 34
    • 3042699469 scopus 로고    scopus 로고
    • Model validation of biological pathways using Petri nets-demonstrated for apoptosis
    • Heiner, M., Koch, I. and Will, J. (2004). Model validation of biological pathways using Petri nets-demonstrated for apoptosis. Biosystems 75, 15-28.
    • (2004) Biosystems , vol.75 , pp. 15-28
    • Heiner, M.1    Koch, I.2    Will, J.3
  • 35
    • 9644278038 scopus 로고    scopus 로고
    • Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    • Hiller, M., Huse, K., Szafranski, K., Jahn, N., Hampe, J., Schreiber, S., Backofen, R. and Platzer, M. (2004). Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat. Genet. 36, 1255-1257.
    • (2004) Nat. Genet. , vol.36 , pp. 1255-1257
    • Hiller, M.1    Huse, K.2    Szafranski, K.3    Jahn, N.4    Hampe, J.5    Schreiber, S.6    Backofen, R.7    Platzer, M.8
  • 38
    • 0032229446 scopus 로고    scopus 로고
    • Quantitative modeling of biochemical networks
    • Hofestädt, R. and Thelen, S. (1998). Quantitative modeling of biochemical networks. In Silico Biol. 1, 0006.
    • (1998) Silico Biol. , vol.1 , pp. 0006
    • Hofestädt, R.1    Thelen, S.2
  • 39
    • 38349138834 scopus 로고    scopus 로고
    • Regulation of alternative splicing: More than just the ABCs
    • House, A. E. and Lynch, K. W. (2007). Regulation of alternative splicing: More than just the ABCs. J. Biol. Chem. 283, 1217-1221.
    • (2007) J. Biol. Chem. , vol.283 , pp. 1217-1221
    • House, A.E.1    Lynch, K.W.2
  • 40
    • 25144489068 scopus 로고    scopus 로고
    • Overview of cell death signaling pathways
    • Jin, Z. and El-Deiry, W. S. (2005). Overview of cell death signaling pathways. Cancer Biol. Ther. 4, 139-163.
    • (2005) Cancer Biol. Ther. , vol.4 , pp. 139-163
    • Jin, Z.1    El-Deiry, W.S.2
  • 42
    • 0042671357 scopus 로고    scopus 로고
    • Pre-mRNA splicing: Awash in a sea of proteins
    • Jurica, M. S. and Moore, M. J. (2003). Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell. 12, 5-14.
    • (2003) Mol. Cell. , vol.12 , pp. 5-14
    • Jurica, M.S.1    Moore, M.J.2
  • 45
    • 57849130707 scopus 로고    scopus 로고
    • Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
    • Kielbassa, J., Bortfeldt, R., Schuster, S. and Koch, I. (2008). Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Comput. Biol. Chem. 33, 46-61.
    • (2008) Comput. Biol. Chem. , vol.33 , pp. 46-61
    • Kielbassa, J.1    Bortfeldt, R.2    Schuster, S.3    Koch, I.4
  • 46
    • 67651223375 scopus 로고    scopus 로고
    • Petri nets in analysis of biological networks
    • Junker, B. H. and Schreiber, F. (eds.), Pan, Y. and Zomaya, A. Y. (series eds.), Wiley
    • Koch, I. and Heiner, M. (2008). Petri nets in analysis of biological networks. In: Wiley Book Series in Bioinformatics, Junker, B. H. and Schreiber, F. (eds.), Pan, Y. and Zomaya, A. Y. (series eds.), Wiley, pp. 139-180.
    • (2008) Wiley Book Series in Bioinformatics , pp. 139-180
    • Koch, I.1    Heiner, M.2
  • 47
    • 16344381707 scopus 로고    scopus 로고
    • Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
    • Koch, I., Junker, B. H. and Heiner, M. (2005). Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21, 1219-1226.
    • (2005) Bioinformatics , vol.21 , pp. 1219-1226
    • Koch, I.1    Junker, B.H.2    Heiner, M.3
  • 48
    • 25844443478 scopus 로고    scopus 로고
    • Insights into the mechanisms of splicing: More lessons from the ribosome
    • Konarska, M. M. and Query, C. C. (2005). Insights into the mechanisms of splicing: more lessons from the ribosome. Genes Dev. 19, 2255-2260.
    • (2005) Genes Dev. , vol.19 , pp. 2255-2260
    • Konarska, M.M.1    Query, C.C.2
  • 51
    • 0032515969 scopus 로고    scopus 로고
    • The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro
    • Laggerbauer, B., Achsel, T. and Lührmann, R. (1998). The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Proc. Natl. Acad. Sci. USA 95, 4188-4192.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 4188-4192
    • Laggerbauer, B.1    Achsel, T.2    Lührmann, R.3
  • 52
    • 33745613530 scopus 로고    scopus 로고
    • The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP
    • Liu, S., Rauhut, R., Vornlocher, H.-P. and Lührmann, R. (2006). The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. RNA 12, 1418-1430.
    • (2006) RNA , vol.12 , pp. 1418-1430
    • Liu, S.1    Rauhut, R.2    Vornlocher, H.-P.3    Lührmann, R.4
  • 53
    • 0032908071 scopus 로고    scopus 로고
    • Elevated levels of a U4/U6.U5 snRNP-associated protein, Spp381p, rescue a mutant defective in spliceosome maturation
    • Lybarger, S., Beickman, K., Brown, V., Dembla-Rajpal, N., Morey, K., Seipelt, R. and Rymond, B. C. (1999). Elevated levels of a U4/U6.U5 snRNP-associated protein, Spp381p, rescue a mutant defective in spliceosome maturation. Mol. Cell. Biol. 19, 577-584.
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 577-584
    • Lybarger, S.1    Beickman, K.2    Brown, V.3    Dembla-Rajpal, N.4    Morey, K.5    Seipelt, R.6    Rymond, B.C.7
  • 55
    • 0037073946 scopus 로고    scopus 로고
    • Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome
    • Makarov, E. M., Makarova, O. V., Urlaub, H., Gentzel, M.,Will, C. L.,Wilm, M. and Lührmann, R. (2002). Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science 298, 2205-2208.
    • (2002) Science , vol.298 , pp. 2205-2208
    • Makarov, E.M.1    Makarova, O.V.2    Urlaub, H.3    Gentzel, M.4    Will, C.L.5    Wilm, M.6    Lührmann, R.7
  • 56
    • 3242737496 scopus 로고    scopus 로고
    • A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing
    • Makarova, O. V., Makarov, E. M., Urlaub, H., Will, C. L., Gentzel, M., Wilm, M. and Lührmann, R. (2004). A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing. EMBO J. 23, 2381-2391.
    • (2004) EMBO J. , vol.23 , pp. 2381-2391
    • Makarova, O.V.1    Makarov, E.M.2    Urlaub, H.3    Will, C.L.4    Gentzel, M.5    Wilm, M.6    Lührmann, R.7
  • 57
    • 0037627610 scopus 로고    scopus 로고
    • The U1 snRNP base pairs with the 5' splice site within a penta-snRNP complex
    • Malca, H., Shomron, N. and Ast, G. (2003). The U1 snRNP base pairs with the 5' splice site within a penta-snRNP complex. Mol. Cell. Biol. 23, 3442-3455.
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 3442-3455
    • Malca, H.1    Shomron, N.2    Ast, G.3
  • 58
    • 0033648431 scopus 로고    scopus 로고
    • Hybrid Petri net representation of gene regulatory network
    • Matsuno, H., Doi, A., Nagasaki, M. and Miyano, S. (2000). Hybrid Petri net representation of gene regulatory network. Pac. Symp. Biocomput. 5, 338-349.
    • (2000) Pac. Symp. Biocomput. , vol.5 , pp. 338-349
    • Matsuno, H.1    Doi, A.2    Nagasaki, M.3    Miyano, S.4
  • 59
    • 33645299531 scopus 로고    scopus 로고
    • A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals
    • Matsuno, H., Inouye, S.-I. T., Okitsu, Y., Fujii, Y. and Miyano, S. (2006). A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. J. Bioinform. Comput. Biol. 4, 139-153.
    • (2006) J. Bioinform. Comput. Biol. , vol.4 , pp. 139-153
    • Matsuno, H.1    Inouye, S.-I.T.2    Okitsu, Y.3    Fujii, Y.4    Miyano, S.5
  • 60
    • 33744937919 scopus 로고    scopus 로고
    • Exon ligation is proofread by the DExD/H-box ATPase Prp22p
    • Mayas, R. M., Maita, H. and Staley, J. P. (2006). Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat. Struct. Mol. Biol. 13, 482-490.
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 482-490
    • Mayas, R.M.1    Maita, H.2    Staley, J.P.3
  • 61
    • 0035393343 scopus 로고    scopus 로고
    • Genome-wide detection of alternative splicing in expressed sequences of human genes
    • Modrek, B., Resch, A., Grasso, C. and Lee, C. (2001). Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29, 2850-2859.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2850-2859
    • Modrek, B.1    Resch, A.2    Grasso, C.3    Lee, C.4
  • 62
    • 0037107418 scopus 로고    scopus 로고
    • Hierarchical, clustered protein interactions with U4/U6 snRNA: A biochemical role for U4/U6 proteins
    • Nottrott, S., Urlaub, H. and Lührmann, R. (2002). Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins. EMBO J. 21, 5527-5538.
    • (2002) EMBO J. , vol.21 , pp. 5527-5538
    • Nottrott, S.1    Urlaub, H.2    Lührmann, R.3
  • 63
    • 33748766359 scopus 로고    scopus 로고
    • Inhibition of a spliceosome turnover pathway suppresses splicing defects
    • Pandit, S., Lynn, B. and Rymond, B. C. (2006). Inhibition of a spliceosome turnover pathway suppresses splicing defects. Proc. Natl. Acad. Sci. USA 103, 13700-13705.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 13700-13705
    • Pandit, S.1    Lynn, B.2    Rymond, B.C.3
  • 65
    • 8644278829 scopus 로고    scopus 로고
    • Identification of alternative splicing regulators by RNA interference in Drosophila
    • Park, J. W., Parisky, K., Celotto, A. M., Reenan, R. A. and Graveley, B. R. (2004). Identification of alternative splicing regulators by RNA interference in Drosophila. Proc. Natl. Acad. Sci. USA 101, 15974-15979.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 15974-15979
    • Park, J.W.1    Parisky, K.2    Celotto, A.M.3    Reenan, R.A.4    Graveley, B.R.5
  • 66
    • 0034193568 scopus 로고    scopus 로고
    • Protein-protein interactions define specificity in signal transduction
    • Pawson, T. and Nash, P. (2000). Protein-protein interactions define specificity in signal transduction. Genes Dev. 14, 1027-1047.
    • (2000) Genes Dev. , vol.14 , pp. 1027-1047
    • Pawson, T.1    Nash, P.2
  • 67
    • 0345564842 scopus 로고    scopus 로고
    • ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA
    • Perriman, R., Barta, I., Voeltz, G. K., Abelson, J. and Ares, M. jr. (2003). ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA. Proc. Natl. Acad. Sci. USA 100, 13857-13862.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13857-13862
    • Perriman, R.1    Barta, I.2    Voeltz, G.K.3    Abelson, J.4    Ares Jr., M.5
  • 69
    • 33747853260 scopus 로고    scopus 로고
    • APID: Agile Protein Interaction DataAnalyzer
    • Prieto, C. and De Las Rivas, J. (2006). APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res. 34, W298-W302.
    • (2006) Nucleic Acids Res. , vol.34
    • Prieto, C.1    De Las Rivas, J.2
  • 70
    • 0033105003 scopus 로고    scopus 로고
    • Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection
    • Puig, O., Gottschalk, A., Fabrizio, P. and Séraphin, B. (1999). Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection. Genes Dev. 13, 569-580.
    • (1999) Genes Dev. , vol.13 , pp. 569-580
    • Puig, O.1    Gottschalk, A.2    Fabrizio, P.3    Séraphin, B.4
  • 71
    • 28444445926 scopus 로고    scopus 로고
    • The R Development Core Team. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
    • The R Development Core Team (2005). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
    • (2005) R: A Language and Environment for Statistical Computing
  • 74
    • 77951956151 scopus 로고    scopus 로고
    • Snoopy - A unifying petri net framework to investigate biomolecular networks
    • published ahead of print
    • Rohr, C., Marwan, W. and Heiner, M. (2010). Snoopy - a unifying petri net framework to investigate biomolecular networks. Bioinformatics 26, published ahead of print.
    • (2010) Bioinformatics , vol.26
    • Rohr, C.1    Marwan, W.2    Heiner, M.3
  • 75
    • 33845417184 scopus 로고    scopus 로고
    • Application of Petri net based analysis techniques to signal transduction pathways
    • Sackmann, A., Heiner, M. and Koch, I. (2006). Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics 7, 482.
    • (2006) BMC Bioinformatics , vol.7 , pp. 482
    • Sackmann, A.1    Heiner, M.2    Koch, I.3
  • 77
    • 4143124637 scopus 로고    scopus 로고
    • RNAi knockdown of hPrp31 leads to an accumulation of 36 U4/U6 di-snRNPs in Cajal bodies
    • Schaffert, N., Hossbach, M., Heintzmann, R., Achsel, T. and Lührmann, R. (2004). RNAi knockdown of hPrp31 leads to an accumulation of 36 U4/U6 di-snRNPs in Cajal bodies. EMBO J. 23, 3000-3009.
    • (2004) EMBO J. , vol.23 , pp. 3000-3009
    • Schaffert, N.1    Hossbach, M.2    Heintzmann, R.3    Achsel, T.4    Lührmann, R.5
  • 78
    • 0033136116 scopus 로고    scopus 로고
    • Toward metabolic phenomics: Analysis of genomic data using flux balances
    • Schilling, C. H., Edwards, J. S. and Palsson, B. O. (1999). Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol. Prog. 15, 288-295.
    • (1999) Biotechnol. Prog. , vol.15 , pp. 288-295
    • Schilling, C.H.1    Edwards, J.S.2    Palsson, B.O.3
  • 79
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster, S. and Hilgetag, C. (1994). On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 2, 165-182.
    • (1994) J. Biol. Syst. , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 80
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • Schuster, S., Dandekar, T. and Fell, D. A. (1999). Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17, 53-60.
    • (1999) Trends Biotechnol. , vol.17 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 82
    • 37649001073 scopus 로고    scopus 로고
    • Understanding the roadmap of metabolism by pathway analysis
    • Schuster, S., von Kamp, A. and Pachkov, M. (2007). Understanding the roadmap of metabolism by pathway analysis. Methods Mol. Biol. 358, 199-226.
    • (2007) Methods Mol. Biol. , vol.358 , pp. 199-226
    • Schuster, S.1    Von Kamp, A.2    Pachkov, M.3
  • 83
    • 0026019713 scopus 로고
    • PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome
    • Schwer, B. and Guthrie, C. (1991). PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349, 494-499.
    • (1991) Nature , vol.349 , pp. 494-499
    • Schwer, B.1    Guthrie, C.2
  • 84
    • 8644268780 scopus 로고    scopus 로고
    • A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly
    • Shen, H. and Green, M. R. (2004). A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol. Cell. 16, 363-373.
    • (2004) Mol. Cell. , vol.16 , pp. 363-373
    • Shen, H.1    Green, M.R.2
  • 85
    • 34547931108 scopus 로고    scopus 로고
    • Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor
    • Shen, J., Zhang, L. and Zhao, R. (2007). Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor. J. Biol. Chem. 282, 22544-22550.
    • (2007) J. Biol. Chem. , vol.282 , pp. 22544-22550
    • Shen, J.1    Zhang, L.2    Zhao, R.3
  • 86
    • 27544501653 scopus 로고    scopus 로고
    • Qualitative modelling of regulated metabolic pathways: Application to the tryptophan biosynthesis in E. coli
    • Simão, E., Remy, E., Thieffry, D. and Chaouiya, C. (2005). Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E. coli. Bioinformatics 21 Suppl. 2, ii190-ii196.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Simão, E.1    Remy, E.2    Thieffry, D.3    Chaouiya, C.4
  • 87
    • 33746441457 scopus 로고    scopus 로고
    • The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase
    • Small, E. C., Leggett, S. R.,Winans, A. A. and Staley, J. P. (2006). The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol. Cell. 23, 389-399.
    • (2006) Mol. Cell. , vol.23 , pp. 389-399
    • Small, E.C.1    Leggett, S.R.2    Winans, A.A.3    Staley, J.P.4
  • 88
    • 33344463111 scopus 로고    scopus 로고
    • Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing
    • Spadaccini, R., Reidt, U., Dybkov, O., Will, C., Frank, R., Stier, G., Corsini, L., Wahl, M. C., L ührmann, R. and Sattler, M. (2006). Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing. RNA 12, 410-425.
    • (2006) RNA , vol.12 , pp. 410-425
    • Spadaccini, R.1    Reidt, U.2    Dybkov, O.3    Will, C.4    Frank, R.5    Stier, G.6    Corsini, L.7    Wahl, M.C.8    Lührmann, R.9    Sattler, M.10
  • 89
    • 0032489021 scopus 로고    scopus 로고
    • Mechanical devices of the spliceosome: Motors, clocks, springs, and things
    • Staley, J. P. and Guthrie, C. (1998). Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315-326.
    • (1998) Cell , vol.92 , pp. 315-326
    • Staley, J.P.1    Guthrie, C.2
  • 90
    • 0036798006 scopus 로고    scopus 로고
    • Signals and their transduction pathways regulating alternative splicing: A new dimension of the human genome
    • Stamm, S. (2002). Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Hum. Mol. Genet. 11, 2409-2416.
    • (2002) Hum. Mol. Genet. , vol.11 , pp. 2409-2416
    • Stamm, S.1
  • 91
    • 0003953265 scopus 로고    scopus 로고
    • Berlin. HU Berlin, Dept. of CS
    • Starke, P. (1998). INA - Integrated Net Analyzer Manual, Berlin. HU Berlin, Dept. of CS, www2.informatik.huberlin. de/lehrstuehle/automaten/ina/.
    • (1998) INA - Integrated Net Analyzer Manual
    • Starke, P.1
  • 92
    • 0035161567 scopus 로고    scopus 로고
    • Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae
    • Stevens, S. W., Barta, I., Ge, H. Y., Moore, R. E., Young, M. K., Lee, T. D. and Abelson, J. (2001). Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae. RNA 7, 1543-1553.
    • (2001) RNA , vol.7 , pp. 1543-1553
    • Stevens, S.W.1    Barta, I.2    Ge, H.Y.3    Moore, R.E.4    Young, M.K.5    Lee, T.D.6    Abelson, J.7
  • 93
    • 0036158942 scopus 로고    scopus 로고
    • Composition and functional characterization of the yeast spliceosomal penta-snRNP
    • Stevens, S. W., Ryan, D. E., Ge, H. Y., Moore, R. E., Young, M. K., Lee, T. D. and Abelson, J. (2002). Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol. Cell. 9, 31-44.
    • (2002) Mol. Cell. , vol.9 , pp. 31-44
    • Stevens, S.W.1    Ryan, D.E.2    Ge, H.Y.3    Moore, R.E.4    Young, M.K.5    Lee, T.D.6    Abelson, J.7
  • 94
    • 33244484374 scopus 로고    scopus 로고
    • Ontology based standardization of Petri net modeling for signaling pathways
    • Takai-Igarashi, T. (2005). Ontology based standardization of Petri net modeling for signaling pathways. In Silico Biol. 5, 0047.
    • (2005) Silico Biol. , vol.5 , pp. 0047
    • Takai-Igarashi, T.1
  • 95
    • 0028072388 scopus 로고
    • SR proteins can compensate for the loss of U1 snRNP functions in vitro
    • Tarn, W.-Y. and Steitz, J. A. (1994). SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes Dev. 8, 2704-2717.
    • (1994) Genes Dev. , vol.8 , pp. 2704-2717
    • Tarn, W.-Y.1    Steitz, J.A.2
  • 97
    • 84891561223 scopus 로고    scopus 로고
    • TInA (T-invariant analysis) - A tool box for exploring pathways in biochemical systems at steady state
    • Grosse I., Neumann, S., Posch, S., Schreiber, F. and Stadler, P. (eds.), Halle
    • Thormann, A., Rudolph, K. and Koch, I. (2009). TInA (T-invariant analysis) - a tool box for exploring pathways in biochemical systems at steady state. In: German Conference on Bioinformatics 2009, Short Papers and Abstracts, Grosse, I., Neumann, S., Posch, S., Schreiber, F. and Stadler, P. (eds.), Halle, pp. 157-158.
    • (2009) German Conference on Bioinformatics 2009, Short Papers and Abstracts , pp. 157-158
    • Thormann, A.1    Rudolph, K.2    Koch, I.3
  • 99
    • 36248936068 scopus 로고    scopus 로고
    • Protein-free spliceosomal snRNAs catalyze a reaction that resembles the first step of splicing
    • Valadkhan, S., Mohammadi, A., Wachtel, C. and Manley, J. L. (2007). Protein-free spliceosomal snRNAs catalyze a reaction that resembles the first step of splicing. RNA 13, 2300-2311.
    • (2007) RNA , vol.13 , pp. 2300-2311
    • Valadkhan, S.1    Mohammadi, A.2    Wachtel, C.3    Manley, J.L.4
  • 100
    • 0035053295 scopus 로고    scopus 로고
    • Functional contacts with a range of splicing proteins suggest a central role for Brr2p in the dynamic control of the order of events in spliceosomes of Saccharomyces cerevisiae
    • van Nues, R. W. and Beggs, J. D. (2001). Functional contacts with a range of splicing proteins suggest a central role for Brr2p in the dynamic control of the order of events in spliceosomes of Saccharomyces cerevisiae. Genetics 157, 1451-1467.
    • (2001) Genetics , vol.157 , pp. 1451-1467
    • Van Nues, R.W.1    Beggs, J.D.2
  • 101
    • 7444220147 scopus 로고    scopus 로고
    • Aberrant and alternative splicing in cancer
    • Venables, J. P. (2004). Aberrant and alternative splicing in cancer. Cancer Res. 64, 7647-7654.
    • (2004) Cancer Res. , vol.64 , pp. 7647-7654
    • Venables, J.P.1
  • 102
    • 23944469448 scopus 로고    scopus 로고
    • The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing
    • Villa, T. and Guthrie, C. (2005). The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev. 19, 1894-1904.
    • (2005) Genes Dev. , vol.19 , pp. 1894-1904
    • Villa, T.1    Guthrie, C.2
  • 104
    • 0035370526 scopus 로고    scopus 로고
    • Spliceosomal UsnRNP biogenesis, structure and function
    • Will, C. L. and Lührmann, R. (2001). Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol. 13, 290-301.
    • (2001) Curr. Opin. Cell Biol. , vol.13 , pp. 290-301
    • Will, C.L.1    Lührmann, R.2
  • 105
    • 26844431946 scopus 로고    scopus 로고
    • Splicing of a rare class of introns by the U12-dependent spliceosome
    • Will, C. L. and Lührmann, R. (2005). Splicing of a rare class of introns by the U12-dependent spliceosome. Biol. Chem. 386, 713-724.
    • (2005) Biol. Chem. , vol.386 , pp. 713-724
    • Will, C.L.1    Lührmann, R.2
  • 106
    • 0037119975 scopus 로고    scopus 로고
    • Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein
    • Will, C. L., Urlaub, H., Achsel, T., Gentzel, M., Wilm, M. and Lührmann, R. (2002). Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. EMBO J. 21, 4978-4988.
    • (2002) EMBO J. , vol.21 , pp. 4978-4988
    • Will, C.L.1    Urlaub, H.2    Achsel, T.3    Gentzel, M.4    Wilm, M.5    Lührmann, R.6
  • 107
    • 0032525135 scopus 로고    scopus 로고
    • Progression through the spliceosome cycle requires Prp38p function for U4/U6 snRNA dissociation
    • Xie, J., Beickman, K., Otte, E. and Rymond, B. C. (1998). Progression through the spliceosome cycle requires Prp38p function for U4/U6 snRNA dissociation. EMBO J. 17, 2938-2946.
    • (1998) EMBO J. , vol.17 , pp. 2938-2946
    • Xie, J.1    Beickman, K.2    Otte, E.3    Rymond, B.C.4
  • 108
    • 4544276777 scopus 로고    scopus 로고
    • Network-based regulatory pathways analysis
    • Xiong, M., Zhao, J. and Xiong, H. (2004). Network-based regulatory pathways analysis. Bioinformatics 20, 2056-2066.
    • (2004) Bioinformatics , vol.20 , pp. 2056-2066
    • Xiong, M.1    Zhao, J.2    Xiong, H.3
  • 109
    • 1542380571 scopus 로고    scopus 로고
    • Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA
    • Xu, Y.-Z., Newnham, C. M., Kameoka, S., Huang, T., Konarska, M. M. and Query, C. C. (2004). Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA. EMBO J. 23, 376-385.
    • (2004) EMBO J. , vol.23 , pp. 376-385
    • Xu, Y.-Z.1    Newnham, C.M.2    Kameoka, S.3    Huang, T.4    Konarska, M.M.5    Query, C.C.6
  • 110
    • 0345602990 scopus 로고    scopus 로고
    • Topological analysis of metabolic networks based on Petri net theory
    • Zevedei-Oancea, I. and Schuster, S. (2003). Topological analysis of metabolic networks based on Petri net theory. In Silico Biol. 3, 0029.
    • (2003) Silico Biol. , vol.3 , pp. 0029
    • Zevedei-Oancea, I.1    Schuster, S.2
  • 111
    • 34548407017 scopus 로고    scopus 로고
    • Discovering functions and revealing mechanisms at molecular level from biological networks
    • Zhang, S., Jin, G., Zhang, X.-S. and Chen, L. (2007). Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 7, 2856-2869.
    • (2007) Proteomics , vol.7 , pp. 2856-2869
    • Zhang, S.1    Jin, G.2    Zhang, X.-S.3    Chen, L.4
  • 112
    • 0037068447 scopus 로고    scopus 로고
    • Comprehensive proteomic analysis of the human spliceosome
    • Zhou, Z., Licklider, L. J., Gygi, S. P. and Reed, R. (2002). Comprehensive proteomic analysis of the human spliceosome. Nature 419, 182-185.
    • (2002) Nature , vol.419 , pp. 182-185
    • Zhou, Z.1    Licklider, L.J.2    Gygi, S.P.3    Reed, R.4


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