Reference | Year | Description | PMID | #Motifs in DB |
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Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE. The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13431-6. Epub 2002 Oct 7. | 2002 | alignments of various sites under same control | 12370439 | 1 |
Spode I, Maiwald D, Hollenberg CP, Suckow M. ATF/CREB sites present in sub-telomeric regions of Saccharomyces cerevisiae chromosomes are part of promoters and act as UAS/URS of highly conserved COS genes. J Mol Biol. 2002 May 31;319(2):407-20. | 2002 | alignments of various sites under same control | 12051917 | 2 |
Kim TS, Kim HY, Yoon JH, Kang HS. Recruitment of the Swi/Snf complex by Ste12-Tec1 promotes Flo8-Mss11-mediated activation of STA1 expression. Mol Cell Biol. 2004 Nov;24(21):9542-56. | 2004 | analysis of two binding sites | 15485921 | 2 |
Kent NA, Eibert SM, Mellor J. Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast. J Biol Chem. 2004 Jun 25;279(26):27116-23. Epub 2004 Apr 24. | 2004 | ChIP | 15111622 | 1 |
Eriksson PR, Mendiratta G, McLaughlin NB, Wolfsberg TG, Mariño-Ramírez L, Pompa TA, Jainerin M, Landsman D, Shen CH, Clark DJ. Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements. Mol Cell Biol. 2005 Oct;25(20):9127-37. | 2005 | ChIP, EMSA | 16199888 | 1 |
Wysocki R, Fortier PK, Maciaszczyk E, Thorsen M, Leduc A, Odhagen A, Owsianik G, Ulaszewski S, Ramotar D, Tamás MJ. Transcriptional activation of metalloid tolerance genes in Saccharomyces cerevisiae requires the AP-1-like proteins Yap1p and Yap8p. Mol Biol Cell. 2004 May;15(5):2049-60. Epub 2004 Feb 20. | 2004 | ChIP, expression enrichment | 14978214 | 1 |
Hikkel I, Lucau-Danila A, Delaveau T, Marc P, Devaux F, Jacq C. A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast. J Biol Chem. 2003 Mar 28;278(13):11427-32. Epub 2003 Jan 14. | 2003 | ChIP, microarray Enrichment | 12529331 | 1 |
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Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001 Jan 25;409(6819):533-8. | 2001 | ChIP-chip | 11206552 | 2 |
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 |
Moqtaderi Z, Struhl K. Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol. 2004 May;24(10):4118-27. | 2004 | ChIP-chip | 15121834 | 1 |
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Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events. Nat Biotechnol. 2006 Aug;24(8):963-70. | 2006 | ChIP-chip | 16900145 | 2 |
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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 |
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 |
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 |
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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 |
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 |
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Huang M, Zhou Z, Elledge SJ. The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell. 1998 Sep 4;94(5):595-605. | 1998 | EMSA | 9741624 | 1 |
Proft M, Serrano R. Repressors and upstream repressing sequences of the stress-regulated ENA1 gene in Saccharomyces cerevisiae: bZIP protein Sko1p confers HOG-dependent osmotic regulation. Mol Cell Biol. 1999 Jan;19(1):537-46. | 1999 | EMSA | 9858577 | 1 |
Mendizabal I, Pascual-Ahuir A, Serrano R, de Larrinoa IF. Promoter sequences regulated by the calcineurin-activated transcription factor Crz1 in the yeast ENA1 gene. Mol Genet Genomics. 2001 Jul;265(5):801-11. | 2001 | EMSA | 11523797 | 2 |
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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 |
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Newcomb LL, Hall DD, Heideman W. AZF1 is a glucose-dependent positive regulator of CLN3 transcription in Saccharomyces cerevisiae. Mol Cell Biol. 2002 Mar;22(5):1607-14. | 2002 | EMSA, ChIP, single binding site | 11839825 | 1 |
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Park SH, Koh SS, Chun JH, Hwang HJ, Kang HS. Nrg1 is a transcriptional repressor for glucose repression of STA1 gene expression in Saccharomyces cerevisiae. Mol Cell Biol. 1999 Mar;19(3):2044-50. | 1999 | EMSA, DNase protection | 10022891 | 1 |
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