The 36 papers which experimentally study the biological roles of both TFs of the PCTFP (Sfp1-Rap1)
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
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
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
Carreto L, et al. (2011) Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains. BMC Genomics 12(1):201
Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92
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
Chua G, et al. (2006) Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A 103(32):12045-50
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
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
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
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
Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74
Teixeira MC, et al. (2007) Environmental genomics: mechanistic insights into toxicity of and resistance to the herbicide 2,4-D. Trends Biotechnol 25(8):363-70
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
Reja R, et al. (2015) Molecular mechanisms of ribosomal protein gene coregulation. Genes Dev 29(18):1942-54
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
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
Jimenez-Marti E and Del Olmo ML (2008) Addition of ammonia or amino acids to a nitrogen-depleted medium affects gene expression patterns in yeast cells during alcoholic fermentation. FEMS Yeast Res 8(2):245-56
Gomez-Herreros F, et al. (2012) TFIIS is required for the balanced expression of the genes encoding ribosomal components under transcriptional stress. Nucleic Acids Res 40(14):6508-19
Meyer P, et al. (2013) Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Res 23(11):1928-37
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
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
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
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
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
de Virgilio C (2012) The essence of yeast quiescence. FEMS Microbiol Rev 36(2):306-39
Conrad M, et al. (2014) Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):254-99
Morris RT, et al. (2010) Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. Bioinformatics 26(2):168-74
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