The 99 papers which experimentally study the biological roles of both TFs of the PCTFP (Swi5-Ace2)
Doolin MT, et al. (2001) Overlapping and distinct roles of the duplicated yeast transcription factors Ace2p and Swi5p. Mol Microbiol 40(2):422-32
Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420
Yang YL, et al. (2005) Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 6():90
Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87
Parnell EJ, et al. (2014) The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor. J Biol Chem 289(51):35431-7
Syeda-Mahmood T (2003) Clustering time-varying gene expression profiles using scale-space signals. Proc IEEE Comput Soc Bioinform Conf 2():48-56
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6
Parnell EJ and Stillman DJ (2008) Getting a transcription factor to only one nucleus following mitosis. PLoS Biol 6(9):e229
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9
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
Kovacech B, et al. (1996) EGT2 gene transcription is induced predominantly by Swi5 in early G1. Mol Cell Biol 16(7):3264-74
Kellis M, et al. (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428(6983):617-24
Emmert-Streib F and Dehmer M (2009) Predicting cell cycle regulated genes by causal interactions. PLoS One 4(8):e6633
Zhu G, et al. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406(6791):90-4
Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8
Maccallum DM, et al. (2006) Different consequences of ACE2 and SWI5 gene disruptions for virulence of pathogenic and nonpathogenic yeasts. Infect Immun 74(9):5244-8
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
Ye C, et al. (2009) Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol 5(3):e1000311
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708
Althoefer H, et al. (1995) Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae. Mol Cell Biol 15(11):5917-28
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
Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303(5659):808-13
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522
Voth WP, et al. (2007) Forkhead proteins control the outcome of transcription factor binding by antiactivation. EMBO J 26(20):4324-34
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Knapp D, et al. (1996) The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1. Mol Cell Biol 16(10):5701-7
Toyn JH, et al. (1997) The Swi5 transcription factor of Saccharomyces cerevisiae has a role in exit from mitosis through induction of the cdk-inhibitor Sic1 in telophase. Genetics 145(1):85-96
Nguyen Ba AN, et al. (2014) Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS Comput Biol 10(12):e1003977
Yuan S and Li KC (2007) Context-dependent clustering for dynamic cellular state modeling of microarray gene expression. Bioinformatics 23(22):3039-47
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
Stillman DJ, et al. (1994) Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SW15 transcriptional activator. Genetics 136(3):781-8
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
Nachman I, et al. (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 Suppl 1:I248-I256
Dohrmann PR, et al. (1992) Parallel pathways of gene regulation: homologous regulators SWI5 and ACE2 differentially control transcription of HO and chitinase. Genes Dev 6(1):93-104
Sbia M, et al. (2008) Regulation of the yeast Ace2 transcription factor during the cell cycle. J Biol Chem 283(17):11135-45
Postnikoff SD and Harkness TA (2012) Mechanistic insights into aging, cell-cycle progression, and stress response. Front Physiol 3():183
Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64
Zhang DY, et al. (2000) Intramolecular interaction of yeast TFIIB in transcription control. Nucleic Acids Res 28(9):1913-20
Wloka C and Bi E (2012) Mechanisms of cytokinesis in budding yeast. Cytoskeleton (Hoboken) 69(10):710-26
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
de Lichtenberg U, et al. (2005) New weakly expressed cell cycle-regulated genes in yeast. Yeast 22(15):1191-201
Enserink JM and Kolodner RD (2010) An overview of Cdk1-controlled targets and processes. Cell Div 5():11
Chang EJ, et al. (2007) Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One 2(7):e656
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56
O'Conallain C, et al. (1999) Regulated nuclear localisation of the yeast transcription factor Ace2p controls expression of chitinase (CTS1) in Saccharomyces cerevisiae. Mol Gen Genet 262(2):275-82
Kreiman G (2004) Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Res 32(9):2889-900
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
Weiss EL (2012) Mitotic exit and separation of mother and daughter cells. Genetics 192(4):1165-202
Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169
van den Brink J, et al. (2008) New insights into the Saccharomyces cerevisiae fermentation switch: dynamic transcriptional response to anaerobicity and glucose-excess. BMC Genomics 9:100
Pic A, et al. (2000) The forkhead protein Fkh2 is a component of the yeast cell cycle transcription factor SFF. EMBO J 19(14):3750-61
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Bussereau F, et al. (2004) Zinc finger transcriptional activators of yeasts. FEMS Yeast Res 4(4-5):445-58
Gardocki ME, et al. (2005) Genomic analysis of PIS1 gene expression. Eukaryot Cell 4(3):604-14
Measday V, et al. (2000) Interactions between Pho85 cyclin-dependent kinase complexes and the Swi5 transcription factor in budding yeast. Mol Microbiol 35(4):825-34
Gordan R, et al. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 12(12):R125
McBride HJ, et al. (1999) Distinct regions of the Swi5 and Ace2 transcription factors are required for specific gene activation. J Biol Chem 274(30):21029-36
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
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7
Voth WP, et al. (2005) ACE2, CBK1, and BUD4 in budding and cell separation. Eukaryot Cell 4(6):1018-28
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
Seifert M, et al. (2009) Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data. Bioinformatics 25(16):2118-25
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Moses AM, et al. (2007) Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biol 8(2):R23
Dohrmann PR, et al. (1996) Role of negative regulation in promoter specificity of the homologous transcriptional activators Ace2p and Swi5p. Mol Cell Biol 16(4):1746-58
Kelly MT, et al. (2004) The Candida albicans CaACE2 gene affects morphogenesis, adherence and virulence. Mol Microbiol 53(3):969-83
Di Talia S, et al. (2009) Daughter-specific transcription factors regulate cell size control in budding yeast. PLoS Biol 7(10):e1000221
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Chen H, et al. (2014) Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst Biol 8 Suppl 4():S6
Sun W, et al. (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23(17):2290-7
Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet ()
Barberis M (2012) Sic1 as a timer of Clb cyclin waves in the yeast cell cycle--design principle of not just an inhibitor. FEBS J 279(18):3386-410
Zhang Q, et al. (2013) Stochastic expression and epigenetic memory at the yeast HO promoter. Proc Natl Acad Sci U S A 110(34):14012-7
Cantone I, et al. (2009) A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches. Cell 137(1):172-81
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Yalamanchili HK, et al. (2014) DDGni: dynamic delay gene-network inference from high-temporal data using gapped local alignment. Bioinformatics 30(3):377-83
Bohm S, et al. (1997) Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. Nucleic Acids Res 25(12):2464-9
Soria PS, et al. (2014) Functional divergence for every paralog. Mol Biol Evol 31(4):984-92
Xue W, et al. (2004) Enrichment of transcriptional regulatory sites in non-coding genomic region. Bioinformatics 20(4):569-75
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
Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35
Cocklin R, et al. (2011) New insight into the role of the Cdc34 ubiquitin-conjugating enzyme in cell cycle regulation via Ace2 and Sic1. Genetics 187(3):701-15
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
Titz B, et al. (2006) Transcriptional activators in yeast. Nucleic Acids Res 34(3):955-67
Koch C and Nasmyth K (1994) Cell cycle regulated transcription in yeast. Curr Opin Cell Biol 6(3):451-9
Butler G and Thiele DJ (1991) ACE2, an activator of yeast metallothionein expression which is homologous to SWI5. Mol Cell Biol 11(1):476-85
Imoto S, et al. (2003) Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf 2():104-13
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85
Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146
Frenz LM, et al. (2001) Rme1, which controls CLN2 expression in Saccharomyces cerevisiae, is a nuclear protein that is cell cycle regulated. Mol Genet Genomics 266(3):374-84
Varela E, et al. (2010) Mitotic expression of spo13 alters m-phase progression and nucleolar localization of cdc14 in budding yeast. Genetics 185(3):841-54
Asif HM and Sanguinetti G (2013) Simultaneous inference and clustering of transcriptional dynamics in gene regulatory networks. Stat Appl Genet Mol Biol 12(5):545-57
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Tamada Y, et al. (2003) Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics 19 Suppl 2:II227-II236
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94