The 54 papers which experimentally study the biological roles of both TFs of the PCTFP (Hsf1-Yap1)
Verghese J, et al. (2012) Biology of the Heat Shock Response and Protein Chaperones: Budding Yeast (Saccharomyces cerevisiae) as a Model System. Microbiol Mol Biol Rev 76(2):115-58
Costa V and Moradas-Ferreira P (2001) Oxidative stress and signal transduction in Saccharomyces cerevisiae: insights into ageing, apoptosis and diseases. Mol Aspects Med 22(4-5):217-46
Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45
Kim IS, et al. (2013) Saccharomyces cerevisiae KNU5377 stress response during high-temperature ethanol fermentation. Mol Cells 35(3):210-8
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
Wu WS and Li WH (2008) Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics 9:439
Engelberg D, et al. (2014) Transmembrane signaling in Saccharomyces cerevisiae as a model for signaling in metazoans: state of the art after 25 years. Cell Signal 26(12):2865-78
Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358
Saxena A and Sitaraman R (2014) Osmoregulation and the human mycobiome. Front Microbiol 5():167
Estruch F (2000) Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiol Rev 24(4):469-86
Trott A, et al. (2008) Activation of Heat Shock and Antioxidant Responses by the Natural Product Celastrol: Transcriptional Signatures of a Thiol-targeted Molecule. Mol Biol Cell 19(3):1104-12
Yazgan O and Krebs JE (2012) Mitochondrial and nuclear genomic integrity after oxidative damage in Saccharomyces cerevisiae. Front Biosci 17():1079-93
Lelandais G and Devaux F (2010) Comparative functional genomics of stress responses in yeasts. OMICS 14(5):501-15
Morano KA, et al. (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190(4):1157-95
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
Teixeira MC, et al. (2011) A genome-wide perspective on the response and tolerance to food-relevant stresses in Saccharomyces cerevisiae. Curr Opin Biotechnol 22(2):150-156
Mager WH and De Kruijff AJ (1995) Stress-induced transcriptional activation. Microbiol Rev 59(3):506-31
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Mazumder A, et al. (2013) Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Res 41(20):9310-24
Wang YC and Chen BS (2010) Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol 4():20
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
Hahn JS, et al. (2006) A stress regulatory network for co-ordinated activation of proteasome expression mediated by yeast heat shock transcription factor. Mol Microbiol 60(1):240-51
Dohmen RJ, et al. (2007) Biting the hand that feeds: Rpn4-dependent feedback regulation of proteasome function. Biochim Biophys Acta 1773(11):1599-604
Caspeta L, et al. (2015) Modifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes. Front Bioeng Biotechnol 3():184
Murray DB, et al. (2011) Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta 1810(10):945-58
Alejandro-Osorio AL, et al. (2009) The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol 10(5):R57
Nussbaum I, et al. (2014) Deteriorated stress response in stationary-phase yeast: sir2 and yap1 are essential for hsf1 activation by heat shock and oxidative stress, respectively. PLoS One 9(10):e111505
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
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
Hong SY, et al. (2013) Oxidative stress-related transcription factors in the regulation of secondary metabolism. Toxins (Basel) 5(4):683-702
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
Haugen AC, et al. (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol 5(12):R95
Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70
Ma M and Liu ZL (2010) Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae. BMC Microbiol 10():169
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 ()
Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7
Kim IS, et al. (2011) Decarbonylated cyclophilin A Cpr1 protein protects Saccharomyces cerevisiae KNU5377Y when exposed to stress induced by menadione. Cell Stress Chaperones 16(1):1-14
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
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458
Liu ZL (2011) Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates. Appl Microbiol Biotechnol 90(3):809-25
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
Hosiner D, et al. (2009) Arsenic toxicity to Saccharomyces cerevisiae is a consequence of inhibition of the TORC1 kinase combined with a chronic stress response. Mol Biol Cell 20(3):1048-57
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
Kundaje A, et al. (2006) A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics 7 Suppl 1():S5