-
1
-
-
57749121616
-
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
-
Badis,G., Chan,E.T., van Bakel,H., Pena-Castillo,L., Tillo,D., Tsui,K., Carlson,C.D., Gossett,A.J., Hasinoff,M.J., Warren,C.L. 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, 878-887.
-
(2008)
Mol. Cell
, vol.32
, pp. 878-887
-
-
Badis, G.1
Chan, E.T.2
Van Bakel, H.3
Pena-Castillo, L.4
Tillo, D.5
Tsui, K.6
Carlson, C.D.7
Gossett, A.J.8
Hasinoff, M.J.9
Warren, C.L.10
-
2
-
-
38549121792
-
TransfactomeDB: A resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans -acting factors
-
DOI 10.1093/nar/gkm828
-
Foat,B.C., Tepper,R.G. and Bussemaker,H.J. (2008) TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Res., 36, D125-D131. (Pubitemid 351149708)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Foat, B.C.1
Tepper, R.G.2
Bussemaker, H.J.3
-
3
-
-
77956654773
-
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
-
Fordyce,P.M., Gerber,D., Tran,D., Zheng,J., Li,H., DeRisi,J.L. and Quake,S.R. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol., 28, 970-975.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 970-975
-
-
Fordyce, P.M.1
Gerber, D.2
Tran, D.3
Zheng, J.4
Li, H.5
DeRisi, J.L.6
Quake, S.R.7
-
4
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
DOI 10.1038/nature02800
-
Harbison,C.T., Gordon,D.B., Lee,T.I., Rinaldi,N.J., Macisaac,K.D., Danford,T.W., Hannett,N.M., Tagne,J.B., Reynolds,D.B., Yoo,J. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104. (Pubitemid 39215116)
-
(2004)
Nature
, vol.430
, Issue.7004
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldl, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.-B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gilford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
5
-
-
33645769260
-
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
-
MacIsaac,K.D., Wang,T., Gordon,D.B., Gifford,D.K., Stormo,G.D. and Fraenkel,E. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 113
-
-
MacIsaac, K.D.1
Wang, T.2
Gordon, D.B.3
Gifford, D.K.4
Stormo, G.D.5
Fraenkel, E.6
-
7
-
-
33846067980
-
SwissRegulon: A database of genome-wide annotations of regulatory sites
-
DOI 10.1093/nar/gkl857
-
Pachkov,M., Erb,I., Molina,N. and van Nimwegen,E. (2007) SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res., 35, D127-D131. (Pubitemid 46056183)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Pachkov, M.1
Erb, I.2
Molina, N.3
Van Nimwegen, E.4
-
8
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu,C., Byers,K.J., McCord,R.P., Shi,Z., Berger,M.F., Newburger,D.E., Saulrieta,K., Smith,Z., Shah,M.V., Radhakrishnan,M. et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res., 19, 556-566.
-
(2009)
Genome Res.
, vol.19
, pp. 556-566
-
-
Zhu, C.1
Byers, K.J.2
McCord, R.P.3
Shi, Z.4
Berger, M.F.5
Newburger, D.E.6
Saulrieta, K.7
Smith, Z.8
Shah, M.V.9
Radhakrishnan, M.10
-
9
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577. (Pubitemid 29462105)
-
(1999)
Bioinformatics
, vol.15
, Issue.7-8
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
10
-
-
0032861774
-
SCPD: A promoter database of the yeast Saccharomyces cerevisiae
-
Zhu,J. and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611. (Pubitemid 29462109)
-
(1999)
Bioinformatics
, vol.15
, Issue.7-8
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
-
11
-
-
75549083247
-
JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar,E., Thongjuea,S., Kwon,A.T., Arenillas,D., Zhao,X., Valen,E., Yusuf,D., Lenhard,B., Wasserman,W.W. and Sandelin,A. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
12
-
-
59949083631
-
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors
-
Berger,M.F. and Bulyk,M.L. (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature protocols, 4, 393-411.
-
(2009)
Nature Protocols
, vol.4
, pp. 393-411
-
-
Berger, M.F.1
Bulyk, M.L.2
-
13
-
-
77955817629
-
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets
-
Reimand,J., Vaquerizas,J.M., Todd,A.E., Vilo,J. and Luscombe,N.M. (2010) Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res., 38, 4768-4777.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 4768-4777
-
-
Reimand, J.1
Vaquerizas, J.M.2
Todd, A.E.3
Vilo, J.4
Luscombe, N.M.5
-
14
-
-
79958115193
-
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
-
Zhao,Y. and Stormo,G.D. (2011) Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat. Biotechnol., 29, 480-483.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 480-483
-
-
Zhao, Y.1
Stormo, G.D.2
-
15
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
DOI 10.1093/nar/gkg108
-
Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378. (Pubitemid 36150406)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.-U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Munch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
16
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis,G., Berger,M.F., Philippakis,A.A., Talukder,S., Gehrke,A.R., Jaeger,S.A., Chan,E.T., Metzler,G., Vedenko,A., Chen,X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
17
-
-
75549087626
-
Saccharomyces Genome Database provides mutant phenotype data
-
Engel,S.R., Balakrishnan,R., Binkley,G., Christie,K.R., Costanzo,M.C., Dwight,S.S., Fisk,D.G., Hirschman,J.E., Hitz,B.C., Hong,E.L. et al. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res., 38, D433-D436.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Engel, S.R.1
Balakrishnan, R.2
Binkley, G.3
Christie, K.R.4
Costanzo, M.C.5
Dwight, S.S.6
Fisk, D.G.7
Hirschman, J.E.8
Hitz, B.C.9
Hong, E.L.10
-
18
-
-
0036677662
-
TFBS: Computational framework for transcription factor binding site analysis
-
Lenhard,B. and Wasserman,W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics, 18, 1135-1136. (Pubitemid 34919236)
-
(2002)
Bioinformatics
, vol.18
, Issue.8
, pp. 1135-1136
-
-
Lenhard, B.1
Wasserman, W.W.2
-
19
-
-
46049107540
-
Asap: A framework for over-representation statistics for transcription factor binding sites
-
Marstrand,T.T., Frellsen,J., Moltke,I., Thiim,M., Valen,E., Retelska,D. and Krogh,A. (2008) Asap: a framework for over-representation statistics for transcription factor binding sites. PLoS One, 3, e1623.
-
(2008)
PLoS One
, vol.3
-
-
Marstrand, T.T.1
Frellsen, J.2
Moltke, I.3
Thiim, M.4
Valen, E.5
Retelska, D.6
Krogh, A.7
-
20
-
-
2342479179
-
Transcriptional Activation of Metalloid Tolerance Genes in Saccharomyces cerevisiae Requires the AP-1-like Proteins Yap1p and Yap8p
-
DOI 10.1091/mbc.E03-04-0236
-
Wysocki,R., Fortier,P.K., Maciaszczyk,E., Thorsen,M., Leduc,A., Odhagen,A., Owsianik,G., Ulaszewski,S., Ramotar,D. and Tamas,M.J. (2004) Transcriptional activation of metalloid tolerance genes in Saccharomyces cerevisiae requires the AP-1-like proteins Yap1p and Yap8p. Mol. Biol. Cell, 15, 2049-2060. (Pubitemid 38580627)
-
(2004)
Molecular Biology of the Cell
, vol.15
, Issue.5
, pp. 2049-2060
-
-
Wysocki, R.1
Fortier, P.-K.2
Maciaszczyk, E.3
Thorsen, M.4
Leduc, A.5
Odhagen, A.6
Owsianik, G.7
Ulaszewski, S.8
Ramotar, D.9
Tamas, M.J.10
-
21
-
-
0033105051
-
The DNA-binding specificity of SOX9 and other SOX proteins
-
DOI 10.1093/nar/27.5.1359
-
Mertin,S., McDowall,S.G. and Harley,V.R. (1999) The DNA-binding specificity of SOX9 and other SOX proteins. Nucleic Acids Res., 27, 1359-1364. (Pubitemid 29206447)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.5
, pp. 1359-1364
-
-
Mertin, S.1
McDowall, S.G.2
Harley, V.R.3
-
22
-
-
0027493475
-
The Rox1 repressor of the Saccharomyces cerevisiae hypoxic genes is a specific DNA-binding protein with a high-mobility-group motif
-
Balasubramanian,B., Lowry,C.V. and Zitomer,R.S. (1993) The Rox1 repressor of the Saccharomyces cerevisiae hypoxic genes is a specific DNA-binding protein with a high-mobility-group motif. Mol. Cell Biol., 13, 6071-6078. (Pubitemid 23292602)
-
(1993)
Molecular and Cellular Biology
, vol.13
, Issue.10
, pp. 6071-6078
-
-
Balasubramanian, B.1
Lowry, C.V.2
Zitomer, R.S.3
-
23
-
-
70350731108
-
Distinguishing direct versus indirect transcription factor-DNA interactions
-
Gordan,R., Hartemink,A.J. and Bulyk,M.L. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res., 19, 2090-2100.
-
(2009)
Genome Res.
, vol.19
, pp. 2090-2100
-
-
Gordan, R.1
Hartemink, A.J.2
Bulyk, M.L.3
-
24
-
-
0036896774
-
Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle
-
DOI 10.1101/gad.1034302
-
Pramila,T., Miles,S., GuhaThakurta,D., Jemiolo,D. and Breeden,L.L. (2002) Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev., 16, 3034-3045. (Pubitemid 35424191)
-
(2002)
Genes and Development
, vol.16
, Issue.23
, pp. 3034-3045
-
-
Pramila, T.1
Miles, S.2
GuhaThakurta, D.3
Jemiolo, D.4
Breeden, L.L.5
-
25
-
-
75849158230
-
The Gene Ontology in 2010: Extensions and refinements
-
Gene Ontology Consortium
-
Gene Ontology Consortium. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res., 38, D331-D335.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
-
26
-
-
0344906814
-
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
-
DOI 10.1093/bioinformatics/btg329
-
Wang,T. and Stormo,G.D. (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics, 19, 2369-2380. (Pubitemid 38016636)
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2369-2380
-
-
Wang, T.1
Stormo, G.D.2
-
27
-
-
0023403099
-
GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA
-
Hope,I.A. and Struhl,K. (1987) GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA. EMBO J., 6, 2781-2784.
-
(1987)
EMBO J.
, vol.6
, pp. 2781-2784
-
-
Hope, I.A.1
Struhl, K.2
-
28
-
-
0032192502
-
Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor Spt3 (SUPT3H)
-
DOI 10.1006/geno.1998.5500
-
Yu,J., Madison,J.M., Mundlos,S., Winston,F. and Olsen,B.R. (1998) Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor spt3 (SUPT3H). Genomics, 53, 90-96. (Pubitemid 28489649)
-
(1998)
Genomics
, vol.53
, Issue.1
, pp. 90-96
-
-
Yu, J.1
Madison, J.M.2
Mundlos, S.3
Winston, F.4
Olsen, B.R.5
-
29
-
-
0024281389
-
A yeast and a human CCAAT-binding protein have heterologous subunits that are functionally interchangeable
-
Chodosh,L.A., Olesen,J., Hahn,S., Baldwin,A.S., Guarente,L. and Sharp,P.A. (1988) A yeast and a human CCAAT-binding protein have heterologous subunits that are functionally interchangeable. Cell, 53, 25-35.
-
(1988)
Cell
, vol.53
, pp. 25-35
-
-
Chodosh, L.A.1
Olesen, J.2
Hahn, S.3
Baldwin, A.S.4
Guarente, L.5
Sharp, P.A.6
-
30
-
-
21344451200
-
Multiple cis-regulatory elements and the yeast sulphur regulatory network are required for the regulation of the yeast glutathione transporter, Hgt1p
-
DOI 10.1007/s00294-005-0571-7
-
Srikanth,C.V., Vats,P., Bourbouloux,A., Delrot,S. and Bachhawat,A.K. (2005) Multiple cis-regulatory elements and the yeast sulphur regulatory network are required for the regulation of the yeast glutathione transporter, Hgt1p. Current genetics, 47, 345-358. (Pubitemid 40909173)
-
(2005)
Current Genetics
, vol.47
, Issue.6
, pp. 345-358
-
-
Srikanth, C.V.1
Vats, P.2
Bourbouloux, A.3
Delrot, S.4
Bachhawat, A.K.5
-
31
-
-
0033976523
-
Discovery and modeling of transcriptional regulatory regions
-
DOI 10.1016/S0958-1669(99)00049-X
-
Fickett,J.W. and Wasserman,W.W. (2000) Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol., 11, 19-24. (Pubitemid 30099033)
-
(2000)
Current Opinion in Biotechnology
, vol.11
, Issue.1
, pp. 19-24
-
-
Fickett, J.W.1
Wasserman, W.W.2
-
32
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
DOI 10.1038/ng724
-
Pilpel,Y., Sudarsanam,P. and Church,G.M. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet., 29, 153-159. (Pubitemid 32952651)
-
(2001)
Nature Genetics
, vol.29
, Issue.2
, pp. 153-159
-
-
Pilpel, Y.1
Sudarsanam, P.2
Church, G.M.3
-
33
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch,B.B., Galgoczy,D.J., Hernday,A.D., Li,H. and Johnson,A.D. (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol., 6, e38.
-
(2008)
PLoS Biol.
, vol.6
-
-
Tuch, B.B.1
Galgoczy, D.J.2
Hernday, A.D.3
Li, H.4
Johnson, A.D.5
-
34
-
-
77950349095
-
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
-
Singh,L.N. and Hannenhalli,S. (2010) Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Res., 38, 738-749.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 738-749
-
-
Singh, L.N.1
Hannenhalli, S.2
-
35
-
-
33747379083
-
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle
-
Pramila,T., Wu,W., Miles,S., Noble,W.S. and Breeden,L.L. (2006) The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev., 20, 2266-2278.
-
(2006)
Genes Dev.
, vol.20
, pp. 2266-2278
-
-
Pramila, T.1
Wu, W.2
Miles, S.3
Noble, W.S.4
Breeden, L.L.5
-
36
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch,A.P., Spellman,P.T., Kao,C.M., Carmel-Harel,O., Eisen,M.B., Storz,G., Botstein,D. and Brown,P.O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
37
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes,T.R., Marton,M.J., Jones,A.R., Roberts,C.J., Stoughton,R., Armour,C.D., Bennett,H.A., Coffey,E., Dai,H., He,Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
-
38
-
-
29444455715
-
Cell-cycle control of gene expression in budding and fission yeast
-
Bahler,J. (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet., 39, 69-94.
-
(2005)
Annu. Rev. Genet.
, vol.39
, pp. 69-94
-
-
Bahler, J.1
-
39
-
-
34547461293
-
Emerging principles of regulatory evolution
-
DOI 10.1073/pnas.0700488104
-
Prud'homme,B., Gompel,N. and Carroll,S.B. (2007) Emerging principles of regulatory evolution. Proc. Natl Acad. Sci. USA, 104(Suppl. 1), 8605-8612. (Pubitemid 47175453)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.SUPPL. 1
, pp. 8605-8612
-
-
Prud'homme, B.1
Gompel, N.2
Carroll, S.B.3
|