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Volumn 2, Issue 12, 2006, Pages 1592-1607

Connectivity in the yeast cell cycle transcription network: Inferences from neural networks

Author keywords

[No Author keywords available]

Indexed keywords

NEURAL NETWORKS; TRANSCRIPTION; YEAST;

EID: 33846013249     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020169     Document Type: Article
Times cited : (13)

References (48)
  • 1
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
    • (1998) Mol Biol Cell , vol.9 , pp. 3273-3297
    • Spellman, P.T.1    Sherlock, G.2    Zhang, M.Q.3    Iyer, V.R.4    Anders, K.5
  • 3
    • 3543042493 scopus 로고    scopus 로고
    • Periodic gene expression program of the fission yeast cell cycle
    • Rustici G, Mata J, Kivinen K, Lio P, Penkett CJ, et al. (2004) Periodic gene expression program of the fission yeast cell cycle. Nat Genet 8: 809-817.
    • (2004) Nat Genet , vol.8 , pp. 809-817
    • Rustici, G.1    Mata, J.2    Kivinen, K.3    Lio, P.4    Penkett, C.J.5
  • 4
    • 20044366888 scopus 로고    scopus 로고
    • Identification of cell cycle-regulated genes in fission yeast
    • Peng X, Karuturi RK, Miller LD, Lin K, Jia Y, et al. (2005) Identification of cell cycle-regulated genes in fission yeast. Mol Biol Cell 16: 1026-1042.
    • (2005) Mol Biol Cell , vol.16 , pp. 1026-1042
    • Peng, X.1    Karuturi, R.K.2    Miller, L.D.3    Lin, K.4    Jia, Y.5
  • 5
    • 22744437234 scopus 로고    scopus 로고
    • The cell cycle-regulated genes of Schizosaccharomyces pombe
    • Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H, et al. (2005) The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol 3 (7): e225.
    • (2005) PLoS Biol , vol.3 , Issue.7
    • Oliva, A.1    Rosebrock, A.2    Ferrezuelo, F.3    Pyne, S.4    Chen, H.5
  • 6
    • 0032863227 scopus 로고    scopus 로고
    • Zhang MQ (1999) Large-scale gene expression data analysis: A new challenge to computational biologists [published erratum appears in Genome Res 9: 1156]. Genome Res 9: 681-688.
    • Zhang MQ (1999) Large-scale gene expression data analysis: A new challenge to computational biologists [published erratum appears in Genome Res 9: 1156]. Genome Res 9: 681-688.
  • 7
    • 0034710620 scopus 로고    scopus 로고
    • Cyclin transcription: Timing is everything
    • Breeden LL (2000) Cyclin transcription: Timing is everything. Curr Biol 10: R586-R588.
    • (2000) Curr Biol , vol.10
    • Breeden, L.L.1
  • 8
    • 0037425623 scopus 로고    scopus 로고
    • Periodic transcription: A cycle within a cycle
    • Breeden LL (2003) Periodic transcription: A cycle within a cycle. Curr Biol 13: R31-R38.
    • (2003) Curr Biol , vol.13
    • Breeden, L.L.1
  • 9
    • 19444387865 scopus 로고    scopus 로고
    • A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data
    • Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, et al. (2005) A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data. Nucleic Acids Res 33: 2580-2594.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2580-2594
    • Hart, C.E.1    Sharenbroich, L.2    Bornstein, B.J.3    Trout, D.4    King, B.5
  • 10
    • 0035163845 scopus 로고    scopus 로고
    • Transcriptional regulation and function during the human cell cycle
    • Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, et al. (2001) Transcriptional regulation and function during the human cell cycle. Nat Genet 27: 48-54.
    • (2001) Nat Genet , vol.27 , pp. 48-54
    • Cho, R.J.1    Huang, M.2    Campbell, M.J.3    Dong, H.4    Steinmetz, L.5
  • 11
    • 0035985177 scopus 로고    scopus 로고
    • Identification of genes periodically expressed in the human cell cycle and their expression in tumors
    • Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13: 1977-2000.
    • (2002) Mol Biol Cell , vol.13 , pp. 1977-2000
    • Whitfield, M.L.1    Sherlock, G.2    Saldanha, A.J.3    Murray, J.I.4    Ball, C.A.5
  • 12
    • 1342266280 scopus 로고    scopus 로고
    • Genome-wide gene expression in an Arabidopsis cell suspension
    • Menges M, Hennig L, Gruissem W, Murray JA (2003) Genome-wide gene expression in an Arabidopsis cell suspension. Plant Mol Biol 53: 423-442.
    • (2003) Plant Mol Biol , vol.53 , pp. 423-442
    • Menges, M.1    Hennig, L.2    Gruissem, W.3    Murray, J.A.4
  • 13
    • 29444455715 scopus 로고    scopus 로고
    • Cell-cycle control of gene expression in budding and fission yeast
    • Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39: 69-94.
    • (2005) Annu Rev Genet , vol.39 , pp. 69-94
    • Bahler, J.1
  • 14
    • 0037168519 scopus 로고    scopus 로고
    • A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
    • Wang W, Cherry JM, Botstein D, Li H (2002) A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 99: 16893-16898.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 16893-16898
    • Wang, W.1    Cherry, J.M.2    Botstein, D.3    Li, H.4
  • 16
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe NM, Madan Babu M, Yu H, Snyder M, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Madan Babu, M.2    Yu, H.3    Snyder, M.4
  • 17
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117: 185-198.
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 18
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • Lee I, Date SV, Adai AT, Marcotte EM (2004) A probabilistic functional network of yeast genes. Science 306: 1555-1558.
    • (2004) Science , vol.306 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 19
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    • Gao F, Foat BC, Bussemaker HJ (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5: 31.
    • (2004) BMC Bioinformatics , vol.5 , pp. 31
    • Gao, F.1    Foat, B.C.2    Bussemaker, H.J.3
  • 22
    • 0036894656 scopus 로고    scopus 로고
    • Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
    • Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16: 3017-3033.
    • (2002) Genes Dev , vol.16 , pp. 3017-3033
    • Horak, C.E.1    Luscombe, N.M.2    Qian, J.3    Bertone, P.4    Piccirrillo, S.5
  • 23
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5
  • 24
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1    Rinaldi, N.J.2    Robert, F.3    Odom, D.T.4    Bar-Joseph, Z.5
  • 25
    • 2442446708 scopus 로고    scopus 로고
    • Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
    • Segal E, Yelensky R, Koller D (2003) Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 19 (Supplement 1): i273-282.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL.EMENT 1
    • Segal, E.1    Yelensky, R.2    Koller, D.3
  • 26
    • 26444501081 scopus 로고    scopus 로고
    • Statistical methods for identifying yeast cell cycle transcription factors
    • Tsai HK, Lu HH, Li WH (2005) Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci U S A 102: 13532-13537.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13532-13537
    • Tsai, H.K.1    Lu, H.H.2    Li, W.H.3
  • 30
    • 0035965273 scopus 로고    scopus 로고
    • Neural model of genetic network
    • Vohradsky J (2001) Neural model of genetic network. J Biol Chem 276: 36168-36173.
    • (2001) J Biol Chem , vol.276 , pp. 36168-36173
    • Vohradsky, J.1
  • 31
    • 33744501241 scopus 로고    scopus 로고
    • Bayesian error analysis model for reconstructing transcriptional regulatory networks
    • Sun N, Carroll RJ, Zhao H (2006) Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc Natl Acad Sci U S A 103: 7988-7993.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 7988-7993
    • Sun, N.1    Carroll, R.J.2    Zhao, H.3
  • 32
    • 33646748283 scopus 로고    scopus 로고
    • A systems approach to mapping DNA damage response pathways
    • Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312: 1054-1059.
    • (2006) Science , vol.312 , pp. 1054-1059
    • Workman, C.T.1    Mak, H.C.2    McCuine, S.3    Tagne, J.B.4    Agarwal, M.5
  • 33
    • 0029107149 scopus 로고
    • Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback
    • Reinitz J, Mjolsness E, Sharp DH (1995) Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback. J Exp Zool 271: 47-56.
    • (1995) J Exp Zool , vol.271 , pp. 47-56
    • Reinitz, J.1    Mjolsness, E.2    Sharp, D.H.3
  • 34
    • 0027501142 scopus 로고
    • A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase
    • Koch C, Moll T, Neuberg M, Ahorn H, Nasmyth K (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261: 1551-1557.
    • (1993) Science , vol.261 , pp. 1551-1557
    • Koch, C.1    Moll, T.2    Neuberg, M.3    Ahorn, H.4    Nasmyth, K.5
  • 35
    • 0038110950 scopus 로고    scopus 로고
    • G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1
    • Costanzo M, Schub O, Andrews B (2003) G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol 23: 5064-5077.
    • (2003) Mol Cell Biol , vol.23 , pp. 5064-5077
    • Costanzo, M.1    Schub, O.2    Andrews, B.3
  • 36
    • 0034612501 scopus 로고    scopus 로고
    • Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters
    • Koranda M, Schleiffer A, Endler L, Ammerer G (2000) Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406: 94-98.
    • (2000) Nature , vol.406 , pp. 94-98
    • Koranda, M.1    Schleiffer, A.2    Endler, L.3    Ammerer, G.4
  • 37
    • 0038246285 scopus 로고    scopus 로고
    • Polyphosphate loss promotes SNF/SWI- and Gcn5-dependent mitotic induction of PHO5
    • Neef DW, Kladde MP (2003) Polyphosphate loss promotes SNF/SWI- and Gcn5-dependent mitotic induction of PHO5. Mol Cell Biol 23: 3788-3797.
    • (2003) Mol Cell Biol , vol.23 , pp. 3788-3797
    • Neef, D.W.1    Kladde, M.P.2
  • 38
    • 0036468361 scopus 로고    scopus 로고
    • Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4
    • Gaudet J, Mango SE (2002) Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295: 821-825.
    • (2002) Science , vol.295 , pp. 821-825
    • Gaudet, J.1    Mango, S.E.2
  • 39
    • 0029939202 scopus 로고    scopus 로고
    • Role of negative regulation in promoter specificity of the homologous transcriptional activators Ace2p and Swi5p
    • Dohrmann PR, Voth WP, Stillman DJ (1996) Role of negative regulation in promoter specificity of the homologous transcriptional activators Ace2p and Swi5p. Mol Cell Biol 16: 1746-1758.
    • (1996) Mol Cell Biol , vol.16 , pp. 1746-1758
    • Dohrmann, P.R.1    Voth, W.P.2    Stillman, D.J.3
  • 40
    • 0035028716 scopus 로고    scopus 로고
    • Overlapping and distinct roles of the duplicated yeast transcription factors Ace2p and Swi5p
    • Doolin MT, Johnson AL, Johnston LH, Butler G (2001) Overlapping and distinct roles of the duplicated yeast transcription factors Ace2p and Swi5p. Mol Microbiol 40: 422-432.
    • (2001) Mol Microbiol , vol.40 , pp. 422-432
    • Doolin, M.T.1    Johnson, A.L.2    Johnston, L.H.3    Butler, G.4
  • 41
    • 0342868306 scopus 로고    scopus 로고
    • Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth
    • Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, et al. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406: 90-94.
    • (2000) Nature , vol.406 , pp. 90-94
    • Zhu, G.1    Spellman, P.T.2    Volpe, T.3    Brown, P.O.4    Botstein, D.5
  • 42
    • 0034111824 scopus 로고    scopus 로고
    • Forkhead genes in transcriptional silencing, cell morphology and the cell cycle. Overlapping and distinct functions for FKH1 and FKH2 in Saccharomyces cerevisiae
    • Hollenhorst PC, Bose ME, Mielke MR, Muller U, Fox CA (2000) Forkhead genes in transcriptional silencing, cell morphology and the cell cycle. Overlapping and distinct functions for FKH1 and FKH2 in Saccharomyces cerevisiae. Genetics 154: 1533-1548.
    • (2000) Genetics , vol.154 , pp. 1533-1548
    • Hollenhorst, P.C.1    Bose, M.E.2    Mielke, M.R.3    Muller, U.4    Fox, C.A.5
  • 43
    • 0036896774 scopus 로고    scopus 로고
    • Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle
    • Pramila T, Miles S, GuhaThakurta D, Jemiolo D, Breeden LL (2002) Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev 16: 3034-3045.
    • (2002) Genes Dev , vol.16 , pp. 3034-3045
    • Pramila, T.1    Miles, S.2    GuhaThakurta, D.3    Jemiolo, D.4    Breeden, L.L.5
  • 44
    • 0024854493 scopus 로고
    • The yeast SWI4 protein contains a motif present in developmental regulators and is part of a complex involved in cell-cycle-dependent transcription
    • Andrews BJ, Herskowitz I (1989) The yeast SWI4 protein contains a motif present in developmental regulators and is part of a complex involved in cell-cycle-dependent transcription. Nature 342: 830-833.
    • (1989) Nature , vol.342 , pp. 830-833
    • Andrews, B.J.1    Herskowitz, I.2
  • 45
    • 26444467253 scopus 로고    scopus 로고
    • High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae
    • Bean JM, Siggia ED, Cross FR (2005) High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae. Genetics 171: 49-61.
    • (2005) Genetics , vol.171 , pp. 49-61
    • Bean, J.M.1    Siggia, E.D.2    Cross, F.R.3
  • 46
  • 47
    • 33845996775 scopus 로고    scopus 로고
    • Maclin R, Opitz D, Shavlik JW (1992) University of Wisconsin-Madison Backpropagation (UWBP). Madison (Wisconsin); Computer Sciences Department, University of Wisconsin Madison.
    • Maclin R, Opitz D, Shavlik JW (1992) University of Wisconsin-Madison Backpropagation (UWBP). Madison (Wisconsin); Computer Sciences Department, University of Wisconsin Madison.
  • 48
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm
    • Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J Roy Stat Soc B 39: 1-38.
    • (1977) J Roy Stat Soc B , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3


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