The 103 papers which experimentally study the biological roles of both TFs of the PCTFP (Fkh1-Fkh2)
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
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
Kumar R, et al. (2000) Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol 10(15):896-906
Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420
Peace JM, et al. (2016) Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase. Genome Res ()
Yang YL, et al. (2005) Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 6():90
Laoukili J, et al. (2007) FoxM1: At the crossroads of ageing and cancer. Biochim Biophys Acta 1775(1):92-102
Jiao R, et al. (2015) The SNF1 Kinase Ubiquitin-associated Domain Restrains Its Activation, Activity, and the Yeast Life Span. J Biol Chem 290(25):15393-404
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414
Jorgensen P and Tyers M (2000) The fork'ed path to mitosis. Genome Biol 1(3):REVIEWS1022
Knott SR, et al. (2012) Forkhead Transcription Factors Establish Origin Timing and Long-Range Clustering in S. cerevisiae. Cell 148(1-2):99-111
Morillon A, et al. (2003) Regulation of elongating RNA polymerase II by forkhead transcription factors in yeast. Science 300(5618):492-5
Ward LD and Bussemaker HJ (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24(13):i165-71
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
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
Koranda M, et al. (2000) Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406(6791):94-8
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
Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87
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
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708
Bensen ES, et al. (2002) A forkhead transcription factor is important for true hyphal as well as yeast morphogenesis in Candida albicans. Eukaryot Cell 1(5):787-98
Cheng C, et al. (2006) MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics 22(21):2650-7
Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
Pramila T, et al. (2006) The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev 20(16):2266-78
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522
Nguyen T, et al. (2014) Transcription mediated insulation and interference direct gene cluster expression switches. Elife 3():e03635
Voth WP, et al. (2007) Forkhead proteins control the outcome of transcription factor binding by antiactivation. EMBO J 26(20):4324-34
Casey L, et al. (2008) Conversion of a Replication Origin to a Silencer through a Pathway Shared by a Forkhead Transcription Factor and an S Phase Cyclin. Mol Biol Cell 19(2):608-22
Soriano I, et al. (2014) Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae. BMC Genomics 15(1):791
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Jonnalagadda S and Srinivasan R (2008) Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. BMC Bioinformatics 9:267
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Szilagyi Z, et al. (2005) Characterisation of two novel fork-head gene homologues of Schizosaccharomyces pombe: their involvement in cell cycle and sexual differentiation. Gene 348():101-9
Pondugula S, et al. (2009) Coupling phosphate homeostasis to cell cycle-specific transcription: mitotic activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead proteins. Mol Cell Biol 29(18):4891-905
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
Bar-Joseph Z, et al. (2003) Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A 100(18):10146-51
Durocher D and Jackson SP (2002) The FHA domain. FEBS Lett 513(1):58-66
Katoh M and Katoh M (2004) Human FOX gene family (Review). Int J Oncol 25(5):1495-500
Hofmann K and Bucher P (1995) The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem Sci 20(9):347-9
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
Gordan R, et al. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 19(11):2090-100
Postnikoff SD and Harkness TA (2012) Mechanistic insights into aging, cell-cycle progression, and stress response. Front Physiol 3():183
Murakami H, et al. (2010) Regulation of yeast forkhead transcription factors and FoxM1 by cyclin-dependent and polo-like kinases. Cell Cycle 9(16):3233-42
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
Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7
Shapira M, et al. (2004) Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell 15(12):5659-69
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56
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
Futcher B (2000) Microarrays and cell cycle transcription in yeast. Curr Opin Cell Biol 12(6):710-5
Ghosh Dastidar R, et al. (2012) The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Cell Biosci 2(1):30
Haase SB and Wittenberg C (2014) Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics 196(1):65-90
Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169
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
Ostrow AZ, et al. (2014) Fkh1 and Fkh2 Bind Multiple Chromosomal Elements in the S. cerevisiae Genome with Distinct Specificities and Cell Cycle Dynamics. PLoS One 9(2):e87647
Pohlmann R and Philippsen P (1996) Sequencing a cosmid clone of Saccharomyces cerevisiae chromosome XIV reveals 12 new open reading frames (ORFs) and an ancient duplication of six ORFs. Yeast 12(4):391-402
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92
Gerber S, et al. (2010) Graphical analysis and experimental evaluation of Saccharomyces cerevisiae p(trk(1|2)) and p(bmh(1|2)) promoter region. Genome Inform 22(1):11-20
Erb I and van Nimwegen E (2011) Transcription factor binding site positioning in yeast: proximal promoter motifs characterize tata-less promoters. PLoS One 6(9):e24279
Selth LA, et al. (2009) An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics. Mol Cell Biol 29(15):4220-34
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
Dwyer DS, et al. (2011) Role of the evolutionarily conserved starvation response in anorexia nervosa. Mol Psychiatry 16(6):595-603
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7
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
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
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
Wang M, et al. (2009) Evolutionary selection pressure of forkhead domain and functional divergence. Gene 432(1-2):19-25
Hollenhorst PC, et al. (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(4):1533-48
Moreno D, et al. (2013) A fluorescent reporter for mapping cellular protein-protein interactions in time and space. Mol Syst Biol 9():647
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Huang M and Elledge SJ (2000) The FHA domain, a phosphoamino acid binding domain involved in the DNA damage response pathway. Cold Spring Harb Symp Quant Biol 65():413-21
Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet ()
Morozov AV and Siggia ED (2007) Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A 104(17):7068-73
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
Wang JJ, et al. (2015) Transcriptional control of fungal cell cycle and cellular events by Fkh2, a forkhead transcription factor in an insect pathogen. Sci Rep 5():10108
Zhu G and Davis TN (1998) The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the yeast spindle pole body. Biochim Biophys Acta 1448(2):236-44
Rodriguez-Colman MJ, et al. (2010) The forkhead transcription factor hcm1 promotes mitochondrial biogenesis and stress resistance in yeast. J Biol Chem 285(47):37092-101
Lee E and Bussemaker HJ (2010) Identifying the genetic determinants of transcription factor activity. Mol Syst Biol 6():412
Mechali M, et al. (2013) Genetic and epigenetic determinants of DNA replication origins, position and activation. Curr Opin Genet Dev 23(2):124-31
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
Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001
Carlsson P and Mahlapuu M (2002) Forkhead transcription factors: key players in development and metabolism. Dev Biol 250(1):1-23
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
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458
Hollenhorst PC, et al. (2001) Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation. Genes Dev 15(18):2445-56
Haber JE (2012) Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae. Genetics 191(1):33-64
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
Linke C, et al. (2013) Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions. Front Physiol 4():173
Sun K, et al. (2002) Saccharomyces forkhead protein Fkh1 regulates donor preference during mating-type switching through the recombination enhancer. Genes Dev 16(16):2085-96
de Lichtenberg U, et al. (2003) Protein feature based identification of cell cycle regulated proteins in yeast. J Mol Biol 329(4):663-74
Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58
Zhu Z, et al. (2002) Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol 318(1):71-81
Sherriff JA, et al. (2007) The Isw2 chromatin-remodeling ATPase cooperates with the Fkh2 transcription factor to repress transcription of the B-type cyclin gene CLB2. Mol Cell Biol 27(8):2848-60
Postnikoff SD, et al. (2012) The yeast forkhead transcription factors fkh1 and fkh2 regulate lifespan and stress response together with the anaphase-promoting complex. PLoS Genet 8(3):e1002583
Breeden LL (2000) Cyclin transcription: Timing is everything. Curr Biol 10(16):R586-8
Maoz N, et al. (2015) The Yeast Forkhead HCM1 Controls Life Span Independent of Calorie Restriction. J Gerontol A Biol Sci Med Sci 70(4):444-53