-
1
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
The Gene Ontology Consortium
-
Ashburner M et al. (2000). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
2
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37, W202-W208.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
3
-
-
0025370208
-
Isolation of the gene encoding the Saccharomyces cerevisiae centromere-binding protein CP1
-
Baker RE, Masison DC (1990). Isolation of the gene encoding the Saccharomyces cerevisiae centromere-binding protein CP1. Mol Cell Biol 10, 2458-2467.
-
(1990)
Mol Cell Biol
, vol.10
, pp. 2458-2467
-
-
Baker, R.E.1
Masison, D.C.2
-
4
-
-
0024356738
-
Purification of the yeast centromere binding protein CP1 and a mutational analysis of its binding site
-
Baker RE, Fitzgerald-Hayes M, O'Brien TC (1989). Purification of the yeast centromere binding protein CP1 and a mutational analysis of its binding site. J Biol Chem 264, 10843-10850.
-
(1989)
J Biol Chem
, vol.264
, pp. 10843-10850
-
-
Baker, R.E.1
Fitzgerald-Hayes, M.2
O'Brien, T.C.3
-
5
-
-
0032476584
-
Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA
-
Blaiseau PL, Thomas D (1998). Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J 17, 6327-6336.
-
(1998)
EMBO J
, vol.17
, pp. 6327-6336
-
-
Blaiseau, P.L.1
Thomas, D.2
-
6
-
-
0030979616
-
Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism
-
Blaiseau PL, Isnard AD, Surdin-Kerjan Y, Thomas D (1997). Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism. Mol Cell Biol 17, 3640-3648.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 3640-3648
-
-
Blaiseau, P.L.1
Isnard, A.D.2
Surdin-Kerjan, Y.3
Thomas, D.4
-
7
-
-
0037474301
-
The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur
-
Boer VM, De Winde JH, Pronk JT, Piper MDW (2003). The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278, 3265-3274.
-
(2003)
J Biol Chem
, vol.278
, pp. 3265-3274
-
-
Boer, V.M.1
De Winde, J.H.2
Pronk, J.T.3
Piper, M.D.W.4
-
8
-
-
12344269924
-
GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G (2004). GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20, 3710-3715.
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
9
-
-
0023064359
-
Isolation of a Saccharomyces cerevisiae centromere DNA-binding protein, its human homolog, and its possible role as a transcription factor
-
Bram R, Kornberg R (1987). Isolation of a Saccharomyces cerevisiae centromere DNA-binding protein, its human homolog, and its possible role as a transcription factor. Mol Cell Biol 7, 403-409.
-
(1987)
Mol Cell Biol
, vol.7
, pp. 403-409
-
-
Bram, R.1
Kornberg, R.2
-
10
-
-
0025283868
-
Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy
-
Cai M, Davis RW (1990). Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy. Cell 61, 437-446.
-
(1990)
Cell
, vol.61
, pp. 437-446
-
-
Cai, M.1
Davis, R.W.2
-
11
-
-
84984933073
-
Structure and function of a transcriptional network activated by the MAPK Hog1
-
Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, O'Shea EK (2008). Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 40, 1300-1306.
-
(2008)
Nat Genet
, vol.40
, pp. 1300-1306
-
-
Capaldi, A.P.1
Kaplan, T.2
Liu, Y.3
Habib, N.4
Regev, A.5
Friedman, N.6
O'Shea, E.K.7
-
12
-
-
3142667831
-
Transcription of the yeast iron regulon does not respond directly to iron but rather to iron-sulfur cluster biosynthesis
-
Chen OS, Crisp RJ, Valachovic M, Bard M, Winge DR, Kaplan J (2004). Transcription of the yeast iron regulon does not respond directly to iron but rather to iron-sulfur cluster biosynthesis. J Biol Chem 279, 29513-29518.
-
(2004)
J Biol Chem
, vol.279
, pp. 29513-29518
-
-
Chen, O.S.1
Crisp, R.J.2
Valachovic, M.3
Bard, M.4
Winge, D.R.5
Kaplan, J.6
-
13
-
-
77956098139
-
Transcriptional plasticity through differential assembly of a multiprotein activation complex
-
Cormier L, Barbey R, Kuras L (2010). Transcriptional plasticity through differential assembly of a multiprotein activation complex. Nucleic Acids Res 38, 4998-5014.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 4998-5014
-
-
Cormier, L.1
Barbey, R.2
Kuras, L.3
-
14
-
-
80655144718
-
Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast
-
Hickman MJ, Petti AA, Ho-Shing O, Silverman SJ, McIsaac RS, Lee TA, Botstein D (2011). Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast. Mol Biol Cell 22, 4192-4204.
-
(2011)
Mol Biol Cell
, vol.22
, pp. 4192-4204
-
-
Hickman, M.J.1
Petti, A.A.2
Ho-Shing, O.3
Silverman, S.J.4
McIsaac, R.S.5
Lee, T.A.6
Botstein, D.7
-
15
-
-
34248354813
-
The yeast ubiquitin ligase SCFMet30: Connecting environmental and intracellular conditions to cell division
-
Kaiser P, Su N-Y, Yen JL, Ouni I, Flick K (2006). The yeast ubiquitin ligase SCFMet30: connecting environmental and intracellular conditions to cell division. Cell Div 1, 16.
-
(2006)
Cell Div
, vol.1
, pp. 16
-
-
Kaiser, P.1
Su, N.-Y.2
Yen, J.L.3
Ouni, I.4
Flick, K.5
-
16
-
-
0028936193
-
Functional analysis of Met4, a yeast transcriptional activator responsive to S-adenosylmethionine
-
Kuras L, Thomas D (1995a). Functional analysis of Met4, a yeast transcriptional activator responsive to S-adenosylmethionine. Mol Cell Biol 15, 208-216.
-
(1995)
Mol Cell Biol
, vol.15
, pp. 208-216
-
-
Kuras, L.1
Thomas, D.2
-
17
-
-
0029018651
-
Identification of the yeast methionine biosynthetic genes that require the centromere binding factor 1 for their transcriptional activation
-
Kuras L, Thomas D (1995b). Identification of the yeast methionine biosynthetic genes that require the centromere binding factor 1 for their transcriptional activation. FEBS Lett 367, 15-18.
-
(1995)
FEBS Lett
, vol.367
, pp. 15-18
-
-
Kuras, L.1
Thomas, D.2
-
18
-
-
77950553742
-
Evolutionary tinkering with conserved components of a transcriptional regulatory network
-
Lavoie H, Hogues H, Mallick J, Sellam A, Nantel A, Whiteway M (2010). Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol 8, e1000329.
-
(2010)
PLoS Biol
, vol.8
-
-
Lavoie, H.1
Hogues, H.2
Mallick, J.3
Sellam, A.4
Nantel, A.5
Whiteway, M.6
-
19
-
-
77957273682
-
Identifying the genetic determinants of transcription factor activity
-
Lee E, Bussemaker HJ (2010). Identifying the genetic determinants of transcription factor activity. Mol Syst Biol 6, 412.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 412
-
-
Lee, E.1
Bussemaker, H.J.2
-
20
-
-
76049086964
-
Dissection of combinatorial control by the Met4 transcriptional complex
-
Lee TA, Jorgensen P, Bognar AL, Peyraud C, Thomas D, Tyers M (2010). Dissection of combinatorial control by the Met4 transcriptional complex. Mol Biol Cell 21, 456-469.
-
(2010)
Mol Biol Cell
, vol.21
, pp. 456-469
-
-
Lee, T.A.1
Jorgensen, P.2
Bognar, A.L.3
Peyraud, C.4
Thomas, D.5
Tyers, M.6
-
21
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee TI et al. (2002). Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
22
-
-
33645769260
-
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
-
MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, 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
-
23
-
-
84864751449
-
Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway
-
McIsaac RS, Petti AA, Bussemaker HJ, Botstein D (2012). Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell 23, 2993-3007.
-
(2012)
Mol Biol Cell
, vol.23
, pp. 2993-3007
-
-
McIsaac, R.S.1
Petti, A.A.2
Bussemaker, H.J.3
Botstein, D.4
-
24
-
-
80655143315
-
Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae
-
McIsaac RS, Silverman SJ, Mcclean MN, Gibney PA, Macinskas J, Hickman MJ, Petti AA, Botstein D (2011). Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Mol Biol Cell 22, 4447-4459.
-
(2011)
Mol Biol Cell
, vol.22
, pp. 4447-4459
-
-
McIsaac, R.S.1
Silverman, S.J.2
Mcclean, M.N.3
Gibney, P.A.4
Macinskas, J.5
Hickman, M.J.6
Petti, A.A.7
Botstein, D.8
-
25
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002). Network motifs: simple building blocks of complex networks. Science 298, 824-827.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
27
-
-
34548749776
-
Context-sensitive data integration and prediction of biological networks
-
Myers CL, Troyanskaya OG (2007). Context-sensitive data integration and prediction of biological networks. Bioinformatics 23, 2322-2330.
-
(2007)
Bioinformatics
, vol.23
, pp. 2322-2330
-
-
Myers, C.L.1
Troyanskaya, O.G.2
-
28
-
-
0034599725
-
SCF(Met30)-mediated control of the transcriptional activator Met4 is required for the G(1)-S transition
-
Patton EE, Peyraud C, Rouillon A, Surdin-Kerjan Y, Tyers M, Thomas D (2000). SCF(Met30)-mediated control of the transcriptional activator Met4 is required for the G(1)-S transition. EMBO J 19, 1613-1624.
-
(2000)
EMBO J
, vol.19
, pp. 1613-1624
-
-
Patton, E.E.1
Peyraud, C.2
Rouillon, A.3
Surdin-Kerjan, Y.4
Tyers, M.5
Thomas, D.6
-
29
-
-
80655136471
-
Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function
-
Petti AA, Crutchfield CA, Rabinowitz JD, Botstein D (2011). Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc Natl Acad Sci USA 108, E1089-E1098.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
-
-
Petti, A.A.1
Crutchfield, C.A.2
Rabinowitz, J.D.3
Botstein, D.4
-
30
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel Y, Sudarsanam P, Church GM (2001). Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29, 153-159.
-
(2001)
Nat Genet
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
Sudarsanam, P.2
Church, G.M.3
-
31
-
-
0034677224
-
Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCFMet30 complex
-
Rouillon A, Barbey R, Patton EE, Tyers M, Thomas D (2000). Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCFMet30 complex. EMBO J 19, 282-294.
-
(2000)
EMBO J
, vol.19
, pp. 282-294
-
-
Rouillon, A.1
Barbey, R.2
Patton, E.E.3
Tyers, M.4
Thomas, D.5
-
32
-
-
0033105258
-
MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene
-
Rupp S, Summers E, Lo H-J, Madhani H, Fink G (1999). MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. EMBO J 18, 1257-1269.
-
(1999)
EMBO J
, vol.18
, pp. 1257-1269
-
-
Rupp, S.1
Summers, E.2
Lo, H.-J.3
Madhani, H.4
Fink, G.5
-
33
-
-
33747894577
-
TM4 microarray software suite
-
Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J (2006). TM4 microarray software suite. Methods Enzymol 411, 134-193.
-
(2006)
Methods Enzymol
, vol.411
, pp. 134-193
-
-
Saeed, A.I.1
Bhagabati, N.K.2
Braisted, J.C.3
Liang, W.4
Sharov, V.5
Howe, E.A.6
Li, J.7
Thiagarajan, M.8
White, J.A.9
Quackenbush, J.10
-
34
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U (2002). Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31, 64-68.
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
35
-
-
83455164709
-
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
-
Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML (2011). Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol Syst Biol 7, 1-14.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 1-14
-
-
Siggers, T.1
Duyzend, M.H.2
Reddy, J.3
Khan, S.4
Bulyk, M.L.5
-
36
-
-
34249931654
-
Transcriptional responses to fatty acid are coordinated by combinatorial control
-
Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD (2007). Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol Syst Biol 3, 115.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 115
-
-
Smith, J.J.1
Ramsey, S.A.2
Marelli, M.3
Marzolf, B.4
Hwang, D.5
Saleem, R.A.6
Rachubinski, R.A.7
Aitchison, J.D.8
-
37
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-3297.
-
(1998)
Mol Biol Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
38
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100, 9440-9445.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
39
-
-
45549093005
-
A dominant suppressor mutation of the met30 cell cycle defect suggests regulation of the Saccharomyces cerevisiae Met4-Cbf1 transcription complex by Met32
-
Su N-Y, Ouni I, Papagiannis CV, Kaiser P (2008). A dominant suppressor mutation of the met30 cell cycle defect suggests regulation of the Saccharomyces cerevisiae Met4-Cbf1 transcription complex by Met32. J Biol Chem 283, 11615-11624.
-
(2008)
J Biol Chem
, vol.283
, pp. 11615-11624
-
-
Su, N.-Y.1
Ouni, I.2
Papagiannis, C.V.3
Kaiser, P.4
-
40
-
-
0031457095
-
Metabolism of sulfur amino acids in Saccharomyces cerevisiae
-
Thomas D, Surdin-Kerjan Y (1997). Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61, 503-532.
-
(1997)
Microbiol Mol Biol Rev
, vol.61
, pp. 503-532
-
-
Thomas, D.1
Surdin-Kerjan, Y.2
-
41
-
-
79959954386
-
RSAT 2011: Regulatory sequence analysis tools
-
Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J (2011). RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res 39, W86-W91.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Thomas-Chollier, M.1
Defrance, M.2
Medina-Rivera, A.3
Sand, O.4
Herrmann, C.5
Thieffry, D.6
Van Helden, J.7
-
42
-
-
27944487902
-
Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
-
Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005). Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310, 1152-1158.
-
(2005)
Science
, vol.310
, pp. 1152-1158
-
-
Tu, B.P.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.L.4
-
43
-
-
0017068871
-
Control of cell division in Saccharomyces cerevisiae by methionyl-tRNA
-
Unger MW, Hartwell LH (1976). Control of cell division in Saccharomyces cerevisiae by methionyl-tRNA. Proc Natl Acad Sci USA 73, 1664-1668.
-
(1976)
Proc Natl Acad Sci USA
, vol.73
, pp. 1664-1668
-
-
Unger, M.W.1
Hartwell, L.H.2
-
45
-
-
0028961739
-
AFT1: A mediator of iron regulated transcriptional control in Saccharomyces cerevisiae
-
Yamaguchi-Iwai Y, Dancis A, Klausner RD (1995). AFT1: a mediator of iron regulated transcriptional control in Saccharomyces cerevisiae. EMBO J 14, 1231-1239.
-
(1995)
EMBO J
, vol.14
, pp. 1231-1239
-
-
Yamaguchi-Iwai, Y.1
Dancis, A.2
Klausner, R.D.3
-
46
-
-
63849315606
-
High-resolution DNA binding specificity analysis of yeast transcription factors
-
Zhu C 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
|