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|
|
|
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| 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 |
Reddy TE, DeLisi C, Shakhnovich BE. Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10. |
2006 |
ChIP-chip |
17500587 |
261 |
| 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 |
MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics. 2006 Mar 7;7:113. |
2006 |
ChIP-chip |
16522208 |
125 |
| 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 |
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25;298(5594):799-804. |
2002 |
ChIP-chip |
12399584 |
100 |
| 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 |
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 |
Pachkov M, Erb I, Molina N, van Nimwegen E. SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 2007 Jan;35(Database issue):D127-31. Epub 2006 Nov 27. |
2007 |
ChIP-chip, conservation, combination of existing motifs |
17130146 |
81 |
| V |
Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73. Epub 2007 Apr 16. |
2007 |
ChIP-chip, structural prior |
17438293 |
79 |
| V |
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004 Sep 2;431(7004):99-104. |
2004 |
ChIP-chip |
15343339 |
65 |
| 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 |
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. |
2003 |
Conservation |
12748633 |
41 |
| 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 |
Zhu J, Zhang MQ. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics. 1999 Jul-Aug;15(7-8):607-11. |
1999 |
alignments of various mapped sites |
10487868 |
20 |
