| Patton EE, et al. (2000) SCF(Met30)-mediated control of the transcriptional activator Met4 is required for the G(1)-S transition. EMBO J 19(7):1613-24 |
| Dormer UH, et al. (2000) Cadmium-inducible expression of the yeast GSH1 gene requires a functional sulfur-amino acid regulatory network. J Biol Chem 275(42):32611-6 |
| Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420 |
| Gertz J and Cohen BA (2009) Environment-specific combinatorial cis-regulation in synthetic promoters. Mol Syst Biol 5:244 |
| 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 |
| Cormier L, et al. (2010) Transcriptional plasticity through differential assembly of a multiprotein activation complex. Nucleic Acids Res 38(15):4998-5014 |
| Carreto L, et al. (2011) Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains. BMC Genomics 12(1):201 |
| 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 |
| Ouni I, et al. (2010) A transcriptional activator is part of an SCF ubiquitin ligase to control degradation of its cofactors. Mol Cell 40(6):954-64 |
| 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 |
| Moxley JF, et al. (2009) Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A 106(16):6477-82 |
| Moler EJ, et al. (2000) Integrating naive Bayes models and external knowledge to examine copper and iron homeostasis in S. cerevisiae. Physiol Genomics 4(2):127-135 |
| Bussereau F, et al. (2004) Zinc finger transcriptional activators of yeasts. FEMS Yeast Res 4(4-5):445-58 |
| McIsaac RS, et al. (2011) Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Mol Biol Cell 22(22):4447-59 |
| Futcher B (2000) Microarrays and cell cycle transcription in yeast. Curr Opin Cell Biol 12(6):710-5 |
| Blaiseau PL, et al. (1997) Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism. Mol Cell Biol 17(7):3640-8 |
| Baudouin-Cornu P, et al. (2001) Molecular evolution of protein atomic composition. Science 293(5528):297-300 |
| 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 |
| Siggers T, et al. (2011) Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol Syst Biol 7():555 |
| 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 |
| Aranda A and del Olmo ML (2004) Exposure of Saccharomyces cerevisiae to acetaldehyde induces sulfur amino acid metabolism and polyamine transporter genes, which depend on Met4p and Haa1p transcription factors, respectively. Appl Environ Microbiol 70(4):19 |
| Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35 |
| Carrillo E, et al. (2012) Characterizing the roles of Met31 and Met32 in coordinating Met4-activated transcription in the absence of Met30. Mol Biol Cell 23(10):1928-42 |
| Ouni I, et al. (2011) Ubiquitin and transcription: The SCF/Met4 pathway, a (protein-) complex issue. Transcription 2(3):135-139 |
| De Nicola R, et al. (2007) Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures. Appl Environ Microbiol 73(23):7680-92 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| McIsaac RS, et al. (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell 23(15):2993-3007 |
| Lee TA, et al. (2010) Dissection of combinatorial control by the met4 transcriptional complex. Mol Biol Cell 21(3):456-69 |
| 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 |
| 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 |
| Chiang DY, et al. (2006) Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol 7():16 |
| Thomas D and Surdin-Kerjan Y (1997) Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61(4):503-32 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Rouillon A, et al. (2000) Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCF(Met30 )complex. EMBO J 19(2):282-94 |
| Hansen J, et al. (2002) The level of MXR1 gene expression in brewing yeast during beer fermentation is a major determinant for the concentration of dimethyl sulfide in beer. FEMS Yeast Res 2(2):137-49 |
| 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 |
| Rossouw D and Bauer FF (2009) Comparing the transcriptomes of wine yeast strains: toward understanding the interaction between environment and transcriptome during fermentation. Appl Microbiol Biotechnol 84(5):937-54 |
| Pereira Y, et al. (2008) Chromate causes sulfur starvation in yeast. Toxicol Sci 106(2):400-12 |
| Linder T (2012) Genomics of alternative sulfur utilization in ascomycetous yeasts. Microbiology 158(Pt 10):2585-97 |
| 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 |
| Petti AA, et al. (2011) Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc Natl Acad Sci U S A 108(45):E1089-98 |
| Ljungdahl PO and Daignan-Fornier B (2012) Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae. Genetics 190(3):885-929 |
| Su NY, et al. (2008) A Dominant Suppressor Mutation of the met30 Cell Cycle Defect Suggests Regulation of the Saccharomyces cerevisiae Met4-Cbf1 Transcription Complex by Met32. J Biol Chem 283(17):11615-24 |
| Kasavi C, et al. (2014) A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. BMC Syst Biol 8(1):90 |
| Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58 |
| Hebert A, et al. (2011) Biodiversity in sulfur metabolism in hemiascomycetous yeasts. FEMS Yeast Res 11(4):366-78 |
| Siddharthan R, et al. (2005) PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol 1(7):e67 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Gonze D, et al. (2005) Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics 21(17):3490-500 |
| Blaiseau PL and Thomas D (1998) Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J 17(21):6327-36 |
| Craig KL and Tyers M (1999) The F-box: a new motif for ubiquitin dependent proteolysis in cell cycle regulation and signal transduction. Prog Biophys Mol Biol 72(3):299-328 |
| Fordyce PM, et al. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol 28(9):970-5 |
| Petti AA, et al. (2012) Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell 23(15):3008-24 |
| Haugen AC, et al. (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol 5(12):R95 |