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Yeast TF dataset

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All files are in TAB-delimited text format and zipped. The following notation is used for TF-gene associations: '.' not significant, 'up' upregulated in del-TF, 'down' downregulated in del-TF, 'b' binding site in promoter, 'b ypd' nucleosome-depleted binding site in promoter (ypd or eth). Combinations of regulatory features are also present, e.g., 'down b eth'. Exceptional systematic gene IDs such as 'YIL082W-A' need to have dash replaced with period.

Dataset details

The TF target compendium for the budding yeast Saccharomyces cerevisiae was compiled using perturbation microarray data, TF-DNA binding profiles and nucleosome positioning measurements [1]. Statistically significant target genes from delta-TF experiments were retrieved from our recent reanalysis [2] of a previously published dataset [3]. High-confidence TF binding site (TFBS) profiles were assembled from earlier chromatin immunoprecipitation [4] and in silico [5,6] analyses as well as more recent refinements with protein-binding microarrays [7]. TFBS profiles were further processed with in vivo nucleosome positioning measurements [8] to distinguish binding sites where lower nucleosome occupancy creates open chromatin structure. Such sites have higher regulatory potential as they become accessible to DNA-binding transcription factors.
These three complementary types of regulatory features were compiled into a compendium of 285 genome-wide regulator profiles that characterize the genome-wide binding preferences and perturbation signatures of these regulators. The profiles contain in total 128,656 gene-TF pairs with statistically significant evidence. The compendium includes 107 profiles with knockout data, 16 profiles with TFBS and 162 profiles with both types of evidence. In addition to 170 confirmed or putative TFs, we included data for cofactors, chromatin modifiers and other regulatory proteins. In accordance with previous observations, the agreement between TF perturbation and DNA-binding targets is sparse, as only 1.5% of all regulator-gene associations constitute differentially expressed targets with TFBS. In all cases, we used clear statistical procedures to distinguish regulatory features from insignificant noise. As a result, our regulator dataset is sparse and comprises statistically meaningful regulatory signals to 7.2% of approximately 1.8 million TF-gene pairs.

References to data sources
[1] J. Reimand, A.Aun, J. Vilo, J. M. Vaquerizas, J. Sedman, N. M. Luscombe, "m:Explorer - multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence", Genome Biol., 2012.
[2] J. Reimand, J. M. Vaquerizas, A. E. Todd, J. Vilo, and N. M. Luscombe, “Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets,” Nucleic Acids Res, 2010.
[3] Z. Hu, P. J. Killion, and V. R. Iyer, “Genetic reconstruction of a functional transcriptional regulatory network,” Nat. Genet. 2007.
[4] C. T. Harbison, D. B. Gordon, T. I. Lee, N. J. Rinaldi, K. D. Macisaac, T. W. Danford, N. M. Hannett, J. B. Tagne, D. B. Reynolds, J. Yoo, E. G. Jennings, J. Zeitlinger, D. K. Pokholok, M. Kellis, P. A. Rolfe, K. T. Takusagawa, E. S. Lander, D. K. Gifford, E. Fraenkel, and R. A. Young, “Transcriptional regulatory code of a eukaryotic genome,” Nature, 2004.
[5] K. D. MacIsaac, T. Wang, D. B. Gordon, D. K. Gifford, G. D. Stormo, and E. Fraenkel, “An improved map of conserved regulatory sites for Saccharomyces cerevisiae,” BMC Bioinformatics, 2006.
[6] I. Erb and E. van Nimwegen, “Statistical features of yeast’s transcriptional regulatory code.,” IEEE Proceedings ICCSB, 2006.
[7] C. Zhu, K. J. Byers, R. P. McCord, Z. Shi, M. F. Berger, D. E. Newburger, K. Saulrieta, Z. Smith, M. V. Shah, M. Radhakrishnan, A. A. Philippakis, Y. Hu, F. De Masi, M. Pacek, A. Rolfs, T. Murthy, J. Labaer, and M. L. Bulyk, “High-resolution DNA-binding specificity analysis of yeast transcription factors,” Genome Res., Apr 2009.
[8] N. Kaplan, I. K. Moore, Y. Fondufe-Mittendorf, A. J. Gossett, D. Tillo, Y. Field, E. M. LeProust, T. R. Hughes, J. D. Lieb, J. Widom, and E. Segal, “The DNA-encoded nucleosome organization of a eukaryotic genome,” Nature, 2009.