The 35 papers which experimentally study the biological roles of both TFs of the PCTFP (Swi4-Skn7)
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420
Cui Z, et al. (2002) Cdc4 is involved in the transcriptional control of OCH1, a gene encoding alpha-1,6-mannosyltransferase in Saccharomyces cerevisiae. Yeast 19(1):69-77
Morgan BA, et al. (1995) A yeast transcription factor bypassing the requirement for SBF and DSC1/MBF in budding yeast has homology to bacterial signal transduction proteins. EMBO J 14(22):5679-89
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
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358
Zhao XM, et al. (2008) Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 36(9):e48
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
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92
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
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
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
Sopko R, et al. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21(3):319-30
Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7
Lai LC, et al. (2006) Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell 5(9):1468-89
Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Ear PH and Michnick SW (2009) A general life-death selection strategy for dissecting protein functions. Nat Methods 6(11):813-6
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
Banerjee N and Zhang MQ (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31(23):7024-31
Ye C, et al. (2009) Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol 5(3):e1000311
Levin DE (2011) Regulation of Cell Wall Biogenesis in Saccharomyces cerevisiae: The Cell Wall Integrity Signaling Pathway. Genetics 189(4):1145-75
Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
Arino J (2010) Integrative Responses to High pH Stress in S. cerevisiae. OMICS 14(5):517-23
Hansen L, et al. (2012) Differences in local genomic context of bound and unbound motifs. Gene 506(1):125-34
Roberts Iii GG and Hudson AP (2009) Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S. cerevisiae. Yeast 26(2):95-110
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