The 33 papers which experimentally study the biological roles of both TFs of the PCTFP (Ume6-Abf1)
Ozonov EA and van Nimwegen E (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Comput Biol 9(8):e1003181
Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169
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
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
Choi JK and Kim YJ (2008) Epigenetic regulation and the variability of gene expression. Nat Genet 40(2):141-7
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
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Park HD, et al. (1999) Synergistic operation of the CAR2 (Ornithine transaminase) promoter elements in Saccharomyces cerevisiae. J Bacteriol 181(22):7052-64
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
On T, et al. (2010) The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 78(9):2075-89
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
Badis G, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87
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
Kratzer S and Schuller HJ (1997) Transcriptional control of the yeast acetyl-CoA synthetase gene, ACS1, by the positive regulators CAT8 and ADR1 and the pleiotropic repressor UME6. Mol Microbiol 26(4):631-41
Henikoff JG, et al. (2011) Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A 108(45):18318-23
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
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
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Schlecht U and Primig M (2003) Mining meiosis and gametogenesis with DNA microarrays. Reproduction 125(4):447-56
Einerhand AW, et al. (1995) The upstream region of the FOX3 gene encoding peroxisomal 3-oxoacyl-coenzyme A thiolase in Saccharomyces cerevisiae contains ABF1- and replication protein A-binding sites that participate in its regulation by glucose repression
Holloway DT, et al. (2007) Machine learning for regulatory analysis and transcription factor target prediction in yeast. Syst Synth Biol 1(1):25-46
Guo X, et al. (2006) Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics 22(4):392-9
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7
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
Shimizu M, et al. (2003) Yeast Ume6p repressor permits activator binding but restricts TBP binding at the HOP1 promoter. Nucleic Acids Res 31(12):3033-7
Tevzadze GG, et al. (2007) Genetic evidence for a SPO1-dependent signaling pathway controlling meiotic progression in yeast. Genetics 175(3):1213-27
Dubois E and Messenguy F (1997) Integration of the multiple controls regulating the expression of the arginase gene CAR1 of Saccharomyces cerevisiae in response to differentnitrogen signals: role of Gln3p, ArgRp-Mcm1p, and Ume6p. Mol Gen Genet 253(5):568-
Tabancay AP Jr and Forsburg SL (2006) Eukaryotic DNA replication in a chromatin context. Curr Top Dev Biol 76():129-84
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
Woo DK, et al. (2009) Multiple pathways of mitochondrial-nuclear communication in yeast: Intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation. Biochim Biophys Acta 1789(2):135-45