The 69 papers which experimentally study the biological roles of both TFs of the PCTFP (Rap1-Fhl1)
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
Bosio MC, et al. (2011) Promoter architectures in the yeast ribosomal expression program. Transcription 2(2):71-77
Wade JT, et al. (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432(7020):1054-8
Schawalder SB, et al. (2004) Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 432(7020):1058-61
Breslow DK, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods 5(8):711-8
Chen X, et al. (2010) A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics 26(12):i334-42
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
Choi JK and Kim YJ (2008) Epigenetic regulation and the variability of gene expression. Nat Genet 40(2):141-7
Kresnowati MT, et al. (2006) When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Mol Syst Biol 2():49
Lavoie H, et al. (2010) Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol 8(3):e1000329
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
Fazio A, et al. (2008) Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. BMC Genomics 9:341
Shah AN, et al. (2011) Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance. Physiol Genomics 43(14):855-72
Kasahara K, et al. (2007) Assembly of Regulatory Factors on rRNA and Ribosomal Protein Genes in Saccharomyces cerevisiae. Mol Cell Biol 27(19):6686-6705
Badis G, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87
Taylor MP, et al. (2012) Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations. Biotechnol J 7(9):1169-81
Hogues H, et al. (2008) Transcription factor substitution during the evolution of fungal ribosome regulation. Mol Cell 29(5):552-62
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414
Reja R, et al. (2015) Molecular mechanisms of ribosomal protein gene coregulation. Genes Dev 29(18):1942-54
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
Garbett KA, et al. (2007) Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol Cell Biol 27(1):297-311
Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001
Boender LG, et al. (2011) Extreme calorie restriction and energy source starvation in Saccharomyces cerevisiae represent distinct physiological states. Biochim Biophys Acta 1813(12):2133-44
Slavov N, et al. (2014) Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis. Cell Rep 7(3):705-14
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
Gordan R, et al. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 19(11):2090-100
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7
Knight B, et al. (2014) Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes Dev 28(15):1695-709
Muller D and Stelling J (2009) Precise regulation of gene expression dynamics favors complex promoter architectures. PLoS Comput Biol 5(1):e1000279
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74
Ma M and Liu ZL (2010) Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae. BMC G
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
Ye Y, et al. (2009) Gaining insight into the response logic of Saccharomyces cerevisiae to heat shock by combining expression profiles with metabolic pathways. Biochem Biophys Res Commun 385(3):357-62
Tsankov AM, et al. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414
Leyfer D and Weng Z (2005) Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics 21 Suppl 2():ii197-203
Ho YH and Gasch AP (2015) Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Curr Genet 61(4):503-11
Sharon E, et al. (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.LID - 10.1038/nbt.2205 [doi] Nat Biotechnol ()
Bernstein BE, et al. (2004) Global nucleosome occupancy in yeast. Genome Biol 5(9):R62
Zeevi D, et al. (2011) Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res 21(12):2114-28
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Geijer C, et al. (2012) Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response. BMC Genomics 13(1):554
Holloway DT, et al. (2007) Machine learning for regulatory analysis and transcription factor target prediction in yeast. Syst Synth Biol 1(1):25-46
Guo X, et al. (2006) Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics 22(4):392-9
Wu WS and Lai FJ (2015) Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. BMC Genomics 16 Suppl 12():S10
Ganapathi M, et al. (2011) Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res 39(6):2032-44
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
Meyer P, et al. (2013) Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Res 23(11):1928-37
Shi L and Tu BP (2013) Acetyl-CoA induces transcription of the key G1 cyclin CLN3 to promote entry into the cell division cycle in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 110(18):7318-23
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
Xiao L and Grove A (2009) Coordination of Ribosomal Protein and Ribosomal RNA Gene Expression in Response to TOR Signaling. Curr Genomics 10(3):198-205
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
Hvidsten TR, et al. (2005) Discovering regulatory binding-site modules using rule-based learning. Genome Res 15(6):856-66
Kamei Y, et al. (2015) Transcription factor genes essential for cell proliferation and replicative lifespan in budding yeast. Biochem Biophys Res Commun 463(3):351-6
Zhao Y, et al. (2006) Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol 26(13):4853-62
Lavoie H, et al. (2009) Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi. Curr Opin Microbiol 12(6):655-63
Joshi A, et al. (2011) Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. Nucleic Acids Res 39(21):9108-17
Hesselberth JR, et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6(4):283-9
Joo YJ, et al. (2009) Determination of the core promoter regions of the Saccharomyces cerevisiae RPS3 gene. Biochim Biophys Acta 1789(11-12):741-50
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
Rudra D, et al. (2007) Potential interface between ribosomal protein production and pre-rRNA processing. Mol Cell Biol 27(13):4815-24
de Virgilio C (2012) The essence of yeast quiescence. FEMS Microbiol Rev 36(2):306-39
Hall DB, et al. (2006) An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol 26(9):3672-9
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
Conrad M, et al. (2014) Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):254-99
Miller C, et al. (2012) Mediator phosphorylation prevents stress response transcription during non-stress conditions. J Biol Chem 287(53):44017-26
Mallick J and Whiteway M (2013) The Evolutionary Rewiring of the Ribosomal Protein Transcription Pathway Modifies the Interaction of Transcription Factor Heteromer Ifh1-Fhl1 (Interacts with Forkhead 1-Forkhead-like 1) with the DNA-binding Specificity Elem
Dahlquist KD, et al. (2015) Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bull Math Biol 77(8):1457-92
Ratnakumar S, et al. (2011) Phenomic and transcriptomic analyses reveal that autophagy plays a major role in desiccation tolerance in Saccharomyces cerevisiae. Mol Biosyst 7(1):139-49