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| V |
Gordan R, Murphy K, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol. 2011 Dec 21;12(12):R125. |
2011 |
PBM |
22189060 |
42 |
| V |
Mira NP, Henriques SF, Keller G, Teixeira MC, Matos RG, Arraiano CM, Winge DR, Sá-Correia I. Identification of a DNA-binding site for the transcription factor Haa1, required for Saccharomyces cerevisiae response to acetic acid stress. Nucleic Acids Res. 2011 May 17. [Epub ahead of print] |
2011 |
EMSA, motif finding in co regulated genes |
21586585 |
1 |
| V |
Ghosh S, Pugh BF. Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae. Mol Cell Biol. 2011 Jan;31(1):190-202. Epub 2010 Oct 18. |
2011 |
ChIP-chip |
20956559 |
1 |
| V |
Baker CR, Tuch BB, Johnson AD. Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7493-8. Epub 2011 Apr 15. |
2011 |
Sites found in coregulated genes' promoters, and in orthologous promoters |
21498688 |
1 |
| V |
Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol. 2010 Sep;28(9):970-5. Epub 2010 Aug 29. |
2010 |
MITOMI |
20802496 |
84 |
| V |
Lavoie H, Hogues H, Mallick J, Sellam A, Nantel A, Whiteway M. Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol. 2010 Mar 9;8(3):e1000329. |
2010 |
ChIP-chip |
20231876 |
4 |
| V |
Li D, Dong Y, Jiang Y, Jiang H, Cai J, Wang W. A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand. Cell Res. 2010 Apr;20(4):408-20. Epub 2010 Mar 2. |
2010 |
EMSA |
20195295 |
1 |
| V |
Heise B, van der Felden J, Kern S, Malcher M, Brückner S, Mösch HU. The TEA transcription factor Tec1 confers promoter-specific gene regulation by Ste12-dependent and -independent mechanisms. Eukaryot Cell. 2010 Apr;9(4):514-31. Epub 2010 Jan 29. |
2010 |
EMSA |
20118212 |
1 |
| V |
Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLoS Comput Biol. 2009 Dec;5(12):e1000590. Epub 2009 Dec 4. |
2009 |
PBM |
19997485 |
132 |
| V |
Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009 Apr;19(4):556-66. Epub 2009 Jan 21. |
2009 |
PBM |
19158363 |
89 |
| V |
Bonham AJ, Neumann T, Tirrell M, Reich NO. Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays. Nucleic Acids Res. 2009 Jul;37(13):e94. Epub 2009 May 31. |
2009 |
TIRF-PBM |
19487241 |
5 |
| V |
Foat BC, Tepper RG, Bussemaker HJ. TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Res. 2008 Jan;36(Database issue):D125-31. Epub 2007 Oct 18. |
2008 |
ChIP-chip |
17947326 |
445 |
| V |
Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell. 2008 Dec 26;32(6):878-87. |
2008 |
PBM |
19111667 |
114 |
| V |
Chen X, Guo L, Fan Z, Jiang T. W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. Bioinformatics. 2008 May 1;24(9):1121-8. Epub 2008 Mar 5. |
2008 |
ChIP-chip |
18325926 |
33 |
| V |
Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG. A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2934-9. Epub 2008 Feb 19. |
2008 |
ChIP-chip |
18287073 |
5 |
