The 34 papers which experimentally study the biological roles of both TFs of the PCTFP (Gcn4-Hsf1)
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Simpson CE and Ashe MP (2012) Adaptation to stress in yeast: to translate or not? Biochem Soc Trans 40(4):794-9
Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358
Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Zhang J, et al. (2010) Systems biology of energy homeostasis in yeast. Curr Opin Microbiol 13(3):382-8
Hahn S and Young ET (2011) Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators. Genetics 189(3):705-36
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
Taylor MP, et al. (2012) Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations. Biotechnol J 7(9):1169-81
Mager WH and De Kruijff AJ (1995) Stress-induced transcriptional activation. Microbiol Rev 59(3):506-31
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
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458
Murray DB, et al. (2011) Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta 1810(10):945-58
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7
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
Middendorf M, et al. (2004) Predicting genetic regulatory response using classification. Bioinformatics 20 Suppl 1():i232-40
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
Tsankov AM, et al. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414
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
Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70
Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45
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
Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones ()
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
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
Roider H, et al. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23(2):134-41
Zeng T and Li J (2010) Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways. Nucleic Acids Res 38(1):e1
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