The 147 papers which experimentally study the biological roles of both TFs of the PCTFP (Mbp1-Swi6)
Dyczkowski J and Vingron M (2005) Comparative analysis of cell cycle regulated genes in eukaryotes. Genome Inform Ser Workshop Genome Inform 16(1):125-31
Igual JC, et al. (1996) Coordinated regulation of gene expression by the cell cycle transcription factor Swi4 and the protein kinase C MAP kinase pathway for yeast cell integrity. EMBO J 15(18):5001-13
Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420
Tahara S, et al. (1998) Functional domains of rep2, a transcriptional activator subunit for Res2-Cdc10, controlling the cell cycle "start". Mol Biol Cell 9(6):1577-88
Shaner L, et al. (2008) The Hsp110 protein chaperone Sse1 is required for yeast cell wall integrity and morphogenesis. Curr Genet 54(1):1-11
Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169
Cross FR, et al. (1994) Role of Swi4 in cell cycle regulation of CLN2 expression. Mol Cell Biol 14(7):4779-87
Ewaskow SP, et al. (1998) Mutation and modeling analysis of the Saccharomyces cerevisiae Swi6 ankyrin repeats. Biochemistry 37(13):4437-50
Lai FJ, et al. (2014) A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol 8 Suppl 4():S9
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6
Zhao Y, et al. (2015) The APSES family proteins in fungi: Characterizations, evolution and functions. Fungal Genet Biol 81():271-80
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414
Mathiasen DP and Lisby M (2014) Cell cycle regulation of homologous recombination in Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):172-84
Dirick L, et al. (1995) Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J 14(19):4803-13
Simmons Kovacs LA, et al. (2012) Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network. Mol Cell 45(5):669-79
Sedgwick SG, et al. (1998) Structural and functional architecture of the yeast cell-cycle transcription factor swi6. J Mol Biol 281(5):763-75
Travesa A, et al. (2013) Repression of G1/S transcription is mediated via interaction of the GTB motifs of Nrm1 and Whi5 with Swi6. Mol Cell Biol 33(8):1476-86
Ferrezuelo F, et al. (2010) The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle. Genome Biol 11(6):R67
Aranda A and Proudfoot N (2001) Transcriptional termination factors for RNA polymerase II in yeast. Mol Cell 7(5):1003-11
Taberner FJ and Igual JC (2010) Yeast karyopherin Kap95 is required for cell cycle progression at Start. BMC Cell Biol 11():47
Ashe M, et al. (2008) The SBF- and MBF-associated Protein Msa1 Is Required for Proper Timing of G1-specific Transcription in Saccharomyces cerevisiae. J Biol Chem 283(10):6040-9
Zhao Y, et al. (2008) Development of a Novel Oligonucleotide Array-Based Transcription Factor Assay Platform for Genome-Wide Active Transcription Factor Profiling in Saccharomyces cerevisiae. J Proteome Res 7(3):1315-1325
Jorgensen P and Tyers M (2004) How cells coordinate growth and division. Curr Biol 14(23):R1014-27
Turner JJ, et al. (2012) Cell size control in yeast. Curr Biol 22(9):R350-9
Lai LC, et al. (2008) Comparison of the transcriptomic "stress response" evoked by antimycin A and oxygen deprivation in saccharomyces cerevisiae. BMC Genomics 9:627
Scrimale T, et al. (2009) The Unfolded Protein Response Is Induced by the Cell Wall Integrity Mitogen-activated Protein Kinase Signaling Cascade and Is Required for Cell Wall Integrity in Saccharomyces cerevisiae. Mol Biol Cell 20(1):164-75
Huang SS and Fraenkel E (2009) Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal 2(81):ra40
Lau KY, et al. (2007) Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network. Phys Rev E Stat Nonlin Soft Matter Phys 75(5 Pt 1):051907
Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8
de Bruin RA, et al. (2008) Stb1 collaborates with other regulators to modulate the G1-specific transcriptional circuit. Mol Cell Biol 28(22):6919-28
Taylor IA, et al. (2000) Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4. Biochemistry 39(14):3943-54
Gong J and Siede W (2009) SBF transcription factor complex positively regulates UV mutagenesis in Saccharomyces cerevisiae. Biochem Biophys Res Commun 379(4):1009-14
Chin SL, et al. (2012) Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators. FEBS J 279(6):1119-30
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708
Tuglus C and van der Laan MJ (2011) Repeated measures semiparametric regression using targeted maximum likelihood methodology with application to transcription factor activity discovery. Stat Appl Genet Mol Biol 10(1):Article2
Eser U, et al. (2011) Commitment to a Cellular Transition Precedes Genome-wide Transcriptional Change. Mol Cell 43(4):515-27
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522
Tennen RI, et al. (2013) Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level. DNA Repair (Amst) 12(2):97-109
Bean JM, et al. (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(1):49-61
Morgan BA, et al. (1995) A yeast transcription factor bypassing the requirement for SBF and DSC1/MBF in budding yeast has homology to bacterial signal transduction proteins. EMBO J 14(22):5679-89
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Moll T, et al. (1992) SWI6 is a regulatory subunit of two different cell cycle START-dependent transcription factors in Saccharomyces cerevisiae. J Cell Sci Suppl 16:87-96
Moll T, et al. (1993) Transcription factors important for starting the cell cycle in yeast. Philos Trans R Soc Lond B Biol Sci 340(1293):351-60
Cote P, et al. (2009) Transcriptional analysis of the Candida albicans cell cycle. Mol Biol Cell 20(14):3363-73
Stevens SW, et al. (2002) Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol Cell 9(1):31-44
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Queralt E and Igual JC (2005) Functional connection between the Clb5 cyclin, the protein kinase C pathway and the Swi4 transcription factor in Saccharomyces cerevisiae. Genetics 171(4):1485-98
Gormley M, et al. (2011) An integrated framework to model cellular phenotype as a component of biochemical networks. Adv Bioinformatics 2011():608295
Galdieri L, et al. (2016) Reduced histone expression or defect in chromatin assembly induce respiration. Mol Cell Biol ()
Wang G, et al. (2010) Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci U S A 107(23):10478-83
Breeden L (1996) Start-specific transcription in yeast. Curr Top Microbiol Immunol 208():95-127
Artiles K, et al. (2009) The Rts1 regulatory subunit of protein phosphatase 2A is required for control of G1 cyclin transcription and nutrient modulation of cell size. PLoS Genet 5(11):e1000727
Lai LC, et al. (2006) Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell 5(9):1468-89
Flick K, et al. (1998) Regulation of cell size by glucose is exerted via repression of the CLN1 promoter. Mol Cell Biol 18(5):2492-501
Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
Huang SS and Fraenkel E (2012) Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple "-Omics" Datasets. Methods Cell Biol 110():57-80
Harris MR, et al. (2013) Binding specificity of the G1/S transcriptional regulators in budding yeast. PLoS One 8(4):e61059
Chen KC, et al. (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11(1):369-91
Li Y, et al. (2013) Identification of the Molecular Mechanisms for Cell-Fate Selection in Budding Yeast through Mathematical Modeling. Biophys J 104(10):2282-94
Wolfsberg TG, et al. (1999) Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res 9(8):775-92
Iyer VR, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409(6819):533-8
Andrews BJ and Mason SW (1993) Gene expression and the cell cycle: a family affair. Science 261(5128):1543-4
Yu H and Gerstein M (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 103(40):14724-31
Horak CE, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16(23):3017-33
Bertoli C, et al. (2013) Control of cell cycle transcription during G1 and S phases. Nat Rev Mol Cell Biol 14(8):518-28
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56
Wijnen H, et al. (2002) The G(1) cyclin Cln3 promotes cell cycle entry via the transcription factor Swi6. Mol Cell Biol 22(12):4402-18
Piatkowska EM, et al. (2013) Chimeric protein complexes in hybrid species generate novel phenotypes. PLoS Genet 9(10):e1003836
Ho U, et al. (1997) Role of the casein kinase I isoform, Hrr25, and the cell cycle-regulatory transcription factor, SBF, in the transcriptional response to DNA damage in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 94(2):581-6
Alarcon T and Tindall MJ (2007) Modelling cell growth and its modulation of the G1/S transition. Bull Math Biol 69(1):197-214
Wijnen H and Futcher B (1999) Genetic analysis of the shared role of CLN3 and BCK2 at the G(1)-S transition in Saccharomyces cerevisiae. Genetics 153(3):1131-43
Vohradska E and Vohradsky J (2011) Virtual mutagenesis of the yeast cyclins genetic network reveals complex dynamics of transcriptional control networks. PLoS One 6(4):e18827
Haase SB and Wittenberg C (2014) Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics 196(1):65-90
Dionne I, et al. (2013) Cell cycle-dependent transcription factors control the expression of yeast telomerase RNA. RNA 19(7):992-1002
Maraziotis I, et al. (2005) Gene networks inference from expression data using a recurrent neuro-fuzzy approach. Conf Proc IEEE Eng Med Biol Soc 5:4834-7
Porter SE, et al. (2002) The yeast pafl-rNA polymerase II complex is required for full expression of a subset of cell cycle-regulated genes. Eukaryot Cell 1(5):830-42
Dirick L, et al. (1992) A central role for SWI6 in modulating cell cycle Start-specific transcription in yeast. Nature 357(6378):508-13
Banerjee N and Zhang MQ (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31(23):7024-31
Chen T and Li F (2009) Identifying cell cycle regulators and combinatorial interactions among transcription factors with microarray data and ChIP-chip data. Int J Bioinform Res Appl 5(6):625-46
Toone WM, et al. (1997) Getting started: regulating the initiation of DNA replication in yeast. Annu Rev Microbiol 51:125-49
Ho Y, et al. (1999) Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol Cell Biol 19(8):5267-78
Siegmund RF and Nasmyth KA (1996) The Saccharomyces cerevisiae Start-specific transcription factor Swi4 interacts through the ankyrin repeats with the mitotic Clb2/Cdc28 kinase and through its conserved carboxy terminus with Swi6. Mol Cell Biol 16(6):2647
Koch C, et al. (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261(5128):1551-7
Hart CE, et al. (2005) A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data. Nucleic Acids Res 33(8):2580-94
Tanaka K and Okayama H (2000) A pcl-like cyclin activates the Res2p-Cdc10p cell cycle "start" transcriptional factor complex in fission yeast. Mol Biol Cell 11(9):2845-62
Manioudaki ME and Poirazi P (2013) Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response. Front Genet 4():110
To CC and Vohradsky J (2010) Measurement variation determines the gene network topology reconstructed from experimental data: a case study of the yeast cyclin network. FASEB J 24(9):3468-78
Stillman DJ (2013) Dancing the cell cycle two-step: regulation of yeast G1-cell-cycle genes by chromatin structure. Trends Biochem Sci 38(9):467-75
de Bruin RA, et al. (2004) Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. Cell 117(7):887-98
Moriya H, et al. (2011) Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico. Mol Syst Biol 7():556
Gallo CA, et al. (2011) Discovering Time-Lagged Rules from Microarray Data using Gene Profile Classifiers. BMC Bioinformatics 12(1):123
Laman H, et al. (1995) Disturbance of normal cell cycle progression enhances the establishment of transcriptional silencing in Saccharomyces cerevisiae. Mol Cell Biol 15(7):3608-17
Smolka MB, et al. (2006) An FHA domain-mediated protein interaction network of Rad53 reveals its role in polarized cell growth. J Cell Biol 175(5):743-53
Liu N, et al. (2013) The transcription cofactor FgSwi6 plays a role in growth and development, carbendazim sensitivity, cellulose utilization, lithium tolerance, deoxynivalenol production and virulence in the filamentous fungus Fusarium graminearum. Funga
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Kumar A and Snyder M (2001) Emerging technologies in yeast genomics. Nat Rev Genet 2(4):302-12
Chen H, et al. (2014) Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst Biol 8 Suppl 4():S6
Wang RS, et al. (2007) Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics 23(22):3056-3064
Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet ()
Ho SW, et al. (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci U S A 103(26):9940-5
Ozonov EA and van Nimwegen E (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Comput Biol 9(8):e1003181
Sassi HE, et al. (2009) Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating the Cell Cycle in Saccharomyces cerevisiae. Methods Mol Biol 548:55-73
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Contador CA, et al. (2011) Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae. Biotechnol Prog 27(4):925-36
Alberghina L, et al. (2009) Molecular networks and system-level properties. J Biotechnol 144(3):224-33
Millar JB (2002) A genomic approach to studying cell-size homeostasis in yeast. Genome Biol 3(10):REVIEWS1028
Costanzo M, et al. (2003) G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol 23(14):5064-77
Queralt E and Igual JC (2003) Cell cycle activation of the Swi6p transcription factor is linked to nucleocytoplasmic shuttling. Mol Cell Biol 23(9):3126-40
Hess D and Winston F (2005) Evidence that Spt10 and Spt21 of Saccharomyces cerevisiae play distinct roles in vivo and functionally interact with MCB-binding factor, SCB-binding factor and Snf1. Genetics 170(1):87-94
Goh WS, et al. (2010) Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6(1):e1000649
Wright J, et al. (2013) A growing role for hypertrophy in senescence. FEMS Yeast Res 13(1):2-6
Wagner A (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Res 25(18):3594-604
Lyu S (2009) Combining boolean method with delay times for determining behaviors of biological networks. Conf Proc IEEE Eng Med Biol Soc 1():4884-7
Manderson EN, et al. (2008) A Novel Genetic Screen Implicates Elm1 in the Inactivation of the Yeast Transcription Factor SBF. PLoS One 3(1):e1500
Busnelli S, et al. (2013) Snf1/AMPK promotes SBF and MBF-dependent transcription in budding yeast. Biochim Biophys Acta 1833(12):3254-64
Yu X, et al. (2006) Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res 34(3):917-27
Busti S, et al. (2010) Glucose signaling-mediated coordination of cell growth and cell cycle in Saccharomyces cerevisiae. Sensors (Basel) 10(6):6195-240
Alter O and Golub GH (2004) Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci U S A 101(47):16577-82
Leem SH, et al. (1998) Meiotic role of SWI6 in Saccharomyces cerevisiae. Nucleic Acids Res 26(13):3154-8
Machado AK, et al. (1997) Thioredoxin reductase-dependent inhibition of MCB cell cycle box activity in Saccharomyces cerevisiae. J Biol Chem 272(27):17045-54
Eriksson PR, et al. (2012) Regulation of histone gene expression in budding yeast. Genetics 191(1):7-20
Hansen L, et al. (2012) Differences in local genomic context of bound and unbound motifs. Gene 506(1):125-34
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85
O'Donnell AF, et al. (2009) New mutant versions of yeast FACT subunit Spt16 affect cell integrity. Mol Genet Genomics 282(5):487-502
Braunewell S and Bornholdt S (2007) Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity. J Theor Biol 245(4):638-43
Morano KA, et al. (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190(4):1157-95
Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146
Partridge JF, et al. (1997) Cell cycle-dependent transcription of CLN1 involves swi4 binding to MCB-like elements. J Biol Chem 272(14):9071-7
Dynlacht BD (1997) Regulation of transcription by proteins that control the cell cycle. Nature 389(6647):149-52
Enserink JM and Kolodner RD (2012) What makes the engine hum: Rad6, a cell cycle supercharger. Cell Cycle 11(2):249-52
Malagon F and Jensen TH (2008) The T body, a new cytoplasmic RNA granule in Saccharomyces cerevisiae. Mol Cell Biol 28(19):6022-32
Raithatha SA and Stuart DT (2005) Meiosis-specific regulation of the Saccharomyces cerevisiae S-phase cyclin CLB5 is dependent on MluI cell cycle box (MCB) elements in its promoter but is independent of MCB-binding factor activity. Genetics 169(3):1329-42
Tirosh I, et al. (2008) On the relation between promoter divergence and gene expression evolution. Mol Syst Biol 4():159
Aucher W, et al. (2010) A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data. Mol Cell Proteomics 9(12):2745-59
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Costanzo M, et al. (2004) CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell 117(7):899-913
Shohat-Tal A and Eshel D (2011) Cell cycle regulators interact with pathways that modulate microtubule stability in Saccharomyces cerevisiae. Eukaryot Cell 10(12):1705-13
Ofir A, et al. (2012) Role of a Candida albicans Nrm1/Whi5 homologue in cell cycle gene expression and DNA replication stress response. Mol Microbiol 84(4):778-94
Hussein B, et al. (2011) G1/S Transcription Factor Orthologues Swi4p and Swi6p Are Important but Not Essential for Cell Proliferation and Influence Hyphal Development in the Fungal Pathogen Candida albicans. Eukaryot Cell 10(3):384-97
Johnston LH and Johnson AL (1995) The DNA repair genes RAD54 and UNG1 are cell cycle regulated in budding yeast but MCB promoter elements have no essential role in the DNA damage response. Nucleic Acids Res 23(12):2147-52
Moriya H, et al. (2006) In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet 2(7):e111
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94
Verdicchio MP and Kim S (2011) Identifying targets for intervention by analyzing basins of attraction. Pac Symp Biocomput ():350-61
Ear PH and Michnick SW (2009) A general life-death selection strategy for dissecting protein functions. Nat Methods 6(11):813-6
de Bruin RA, et al. (2006) Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Mol Cell 23(4):483-96
Galdieri L, et al. (2014) Protein acetylation and acetyl coenzyme a metabolism in budding yeast. Eukaryot Cell 13(12):1472-83