-
1
-
-
9344230857
-
Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription
-
47
-
O. Alter G.H. Golub 2004 Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription Proc. Natl. Acad. Sci. U.S.A. 101 47 16577 16582
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 16577-16582
-
-
Alter, O.1
Golub, G.H.2
-
3
-
-
23744491001
-
Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach
-
A.L. Boulesteix K. Strimmer 2005 Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach Theor. Biol. Med. Model. 2 23
-
(2005)
Theor. Biol. Med. Model.
, vol.2
, pp. 23
-
-
Boulesteix, A.L.1
Strimmer, K.2
-
5
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
2
-
H.J. Bussemaker H. Li 2001 Regulatory element detection using correlation with expression Nat. Genet. 27 2 167 171
-
(2001)
Nat. Genet.
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
-
6
-
-
0028111825
-
The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli
-
3
-
J.M. Calvo R.G. Matthews 1994 The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli Microbiol. Rev. 58 3 466 490
-
(1994)
Microbiol. Rev.
, vol.58
, pp. 466-490
-
-
Calvo, J.M.1
Matthews, R.G.2
-
7
-
-
0242584878
-
RegR, a global LacI/GalR family regulator, modulates virulence and competence in Streptococcus pneumoniae
-
5
-
S. Chapuy-Regaud A.D. Ogunniyi 2003 RegR, a global LacI/GalR family regulator, modulates virulence and competence in Streptococcus pneumoniae Infect. Immun. 71 5 2615 2625
-
(2003)
Infect. Immun.
, vol.71
, pp. 2615-2625
-
-
Chapuy-Regaud, S.1
Ogunniyi, A.D.2
-
8
-
-
17644392863
-
LeuO protein delimits the transcriptionally active and repressive domains on the bacterial chromosome
-
15
-
C.C. Chen H.Y. Wu 2005 LeuO protein delimits the transcriptionally active and repressive domains on the bacterial chromosome J. Biol. Chem. 280 15 15111 15121
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 15111-15121
-
-
Chen, C.C.1
Wu, H.Y.2
-
9
-
-
20844452570
-
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
-
12
-
K.C. Chen T.Y. Wang 2005 A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae Bioinformatics 21 12 2883 2890
-
(2005)
Bioinformatics
, vol.21
, pp. 2883-2890
-
-
Chen, K.C.1
Wang, T.Y.2
-
10
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
6987
-
M.W. Covert E.M. Knight 2004 Integrating high-throughput and computational data elucidates bacterial networks Nature 429 6987 92 96
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
-
11
-
-
0026713687
-
Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A
-
12
-
C.C. DiRusso T.L. Heimert 1992 Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A J. Biol. Chem. 267 12 8685 8691
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 8685-8691
-
-
Dirusso, C.C.1
Heimert, T.L.2
-
12
-
-
0030001055
-
Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p)
-
6
-
C.M. Drazinic J.B. Smerage 1996 Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p) Mol. Cell. Biol. 16 6 3187 3196
-
(1996)
Mol. Cell. Biol.
, vol.16
, pp. 3187-3196
-
-
Drazinic, C.M.1
Smerage, J.B.2
-
13
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
F. Gao B.C. Foat 2004 Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data BMC Bioinformatics 5 31
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
-
14
-
-
0026740416
-
The rcsB gene, a positive regulator of colanic acid biosynthesis in Escherichia coli, is also an activator of ftsZ expression
-
12
-
F.G. Gervais P. Phoenix 1992 The rcsB gene, a positive regulator of colanic acid biosynthesis in Escherichia coli, is also an activator of ftsZ expression J. Bacteriol. 174 12 3964 3971
-
(1992)
J. Bacteriol.
, vol.174
, pp. 3964-3971
-
-
Gervais, F.G.1
Phoenix, P.2
-
15
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
7004
-
C.T. Harbison D.B. Gordon 2004 Transcriptional regulatory code of a eukaryotic genome Nature 431 7004 99 104
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
-
16
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
6819
-
V.R. Iyer C.E. Horak 2001 Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 409 6819 533 538
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
-
17
-
-
0028834991
-
An Escherichia coli curved DNA-binding protein whose expression is affected by the stationary phase-specific sigma factor sigma S
-
5
-
M. Kakeda C. Ueguchi 1995 An Escherichia coli curved DNA-binding protein whose expression is affected by the stationary phase-specific sigma factor sigma S Mol. Gen. Genet. 248 5 629 634
-
(1995)
Mol. Gen. Genet.
, vol.248
, pp. 629-634
-
-
Kakeda, M.1
Ueguchi, C.2
-
18
-
-
0345743695
-
Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
-
2
-
K.C. Kao Y.L. Yang 2004 Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis Proc. Natl. Acad. Sci. U.S.A. 101 2 641 646
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 641-646
-
-
Kao, K.C.1
Yang, Y.L.2
-
19
-
-
27744573112
-
A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis
-
43
-
K.C. Kao L.M. Tran 2005 A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis J. Biol. Chem. 280 43 36079 36087
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 36079-36087
-
-
Kao, K.C.1
Tran, L.M.2
-
20
-
-
13544254744
-
Identifying combinatorial regulation of transcription factors and binding motifs
-
8
-
M. Kato N. Hata 2004 Identifying combinatorial regulation of transcription factors and binding motifs Genome Biol. 5 8 R56
-
(2004)
Genome Biol.
, vol.5
, pp. 56
-
-
Kato, M.1
Hata, N.2
-
21
-
-
0028063267
-
Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB
-
21
-
P. Landini L.I. Hajec 1994 Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB J. Bacteriol. 176 21 6583 6589
-
(1994)
J. Bacteriol.
, vol.176
, pp. 6583-6589
-
-
Landini, P.1
Hajec, L.I.2
-
22
-
-
0027987492
-
Regulation of aroL expression by TyrR protein and Trp repressor in Escherichia coli K-12
-
22
-
B. Lawley A.J. Pittard 1994 Regulation of aroL expression by TyrR protein and Trp repressor in Escherichia coli K-12 J. Bacteriol. 176 22 6921 6930
-
(1994)
J. Bacteriol.
, vol.176
, pp. 6921-6930
-
-
Lawley, B.1
Pittard, A.J.2
-
23
-
-
0028893760
-
The TyrR protein of Escherichia coli is a class i transcription activator
-
1
-
B. Lawley N. Fujita 1995 The TyrR protein of Escherichia coli is a class I transcription activator J. Bacteriol. 177 1 238 241
-
(1995)
J. Bacteriol.
, vol.177
, pp. 238-241
-
-
Lawley, B.1
Fujita, N.2
-
24
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
5594
-
T.I. Lee N.J. Rinaldi 2002 Transcriptional regulatory networks in Saccharomyces cerevisiae Science 298 5594 799 804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
-
25
-
-
33645549982
-
Multiple promoters control expression of the Yersinia enterocolitica phage-shock-protein A (pspA) operon
-
Pt 4
-
M.E. Maxson A.J. Darwin 2006 Multiple promoters control expression of the Yersinia enterocolitica phage-shock-protein A (pspA) operon Microbiology 152 Pt 4 1001 1010
-
(2006)
Microbiology
, vol.152
, pp. 1001-1010
-
-
Maxson, M.E.1
Darwin, A.J.2
-
26
-
-
33644875750
-
PSTIING: A 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
-
Database issue
-
A. Ng B. Bursteinas 2006 pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer Nucleic Acids Res. 34 Database issue D527 D534
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Ng, A.1
Bursteinas, B.2
-
27
-
-
0037066717
-
Global expression profiling of acetate-grown Escherichia coli
-
15
-
M.K. Oh L. Rohlin 2002 Global expression profiling of acetate-grown Escherichia coli J. Biol. Chem. 277 15 13175 13183
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 13175-13183
-
-
Oh, M.K.1
Rohlin, L.2
-
28
-
-
33947409985
-
Factor analysis for gene regulatory networks and transcription factor activity profiles
-
I. Pournara L. Wernisch 2007 Factor analysis for gene regulatory networks and transcription factor activity profiles BMC Bioinformatics 8 61
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 61
-
-
Pournara, I.1
Wernisch, L.2
-
29
-
-
0024263352
-
Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator
-
36
-
R.J. Rolfes H. Zalkin 1988 Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator J. Biol. Chem. 263 36 19653 19661
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 19653-19661
-
-
Rolfes, R.J.1
Zalkin, H.2
-
30
-
-
0035162782
-
RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12
-
1
-
H. Salgado A. Santos-Zavaleta 2001 RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 Nucleic Acids Res. 29 1 72 74
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 72-74
-
-
Salgado, H.1
Santos-Zavaleta, A.2
-
32
-
-
0032032780
-
Specificity, free energy and information content in protein-DNA interactions
-
3
-
G.D. Stormo D.S. Fields 1998 Specificity, free energy and information content in protein-DNA interactions Trends Biochem. Sci. 23 3 109 113
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 109-113
-
-
Stormo, G.D.1
Fields, D.S.2
-
33
-
-
33744501241
-
Bayesian error analysis model for reconstructing transcriptional regulatory networks
-
21
-
N. Sun R.J. Carroll 2006 Bayesian error analysis model for reconstructing transcriptional regulatory networks Proc. Natl. Acad. Sci. U.S.A. 103 21 7988 7993
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 7988-7993
-
-
Sun, N.1
Carroll, R.J.2
-
34
-
-
10244252785
-
A model-based optimization framework for the inference on gene regulatory networks from DNA array data
-
17
-
R. Thomas S. Mehrotra 2004 A model-based optimization framework for the inference on gene regulatory networks from DNA array data Bioinformatics 20 17 3221 3235
-
(2004)
Bioinformatics
, vol.20
, pp. 3221-3235
-
-
Thomas, R.1
Mehrotra, S.2
-
35
-
-
15244338624
-
GNCA: A framework for determining transcription factor activity based on transcriptome: Identifiability and numerical implementation
-
2
-
L.M. Tran M.P. Brynildsen 2005 gNCA: A framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation Metab. Eng. 7 2 128 141
-
(2005)
Metab. Eng.
, vol.7
, pp. 128-141
-
-
Tran, L.M.1
Brynildsen, M.P.2
-
36
-
-
0037418234
-
Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding
-
5
-
B. van Steensel J. Delrow 2003 Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding Proc. Natl. Acad. Sci. U.S.A. 100 5 2580 2585
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 2580-2585
-
-
Van Steensel, B.1
Delrow, J.2
-
37
-
-
33846807390
-
Alternative routes and mutational robustness in complex regulatory networks
-
1-2
-
A. Wagner J. Wright 2007 Alternative routes and mutational robustness in complex regulatory networks Biosystems 88 1-2 163 172
-
(2007)
Biosystems
, vol.88
, pp. 163-172
-
-
Wagner, A.1
Wright, J.2
-
38
-
-
0025941965
-
A factor that positively regulates cell division by activating transcription of the major cluster of essential cell division genes of Escherichia coli
-
11
-
X.D. Wang P.A. de Boer 1991 A factor that positively regulates cell division by activating transcription of the major cluster of essential cell division genes of Escherichia coli Embo. J. 10 11 3363 3372
-
(1991)
Embo. J.
, vol.10
, pp. 3363-3372
-
-
Wang, X.D.1
De Boer, P.A.2
-
39
-
-
0037168519
-
A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
-
26
-
W. Wang J.M. Cherry 2002 A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae Proc. Natl. Acad. Sci. U.S.A. 99 26 16893 16898
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 16893-16898
-
-
Wang, W.1
Cherry, J.M.2
-
40
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
9
-
M.K. Yeung J. Tegner 2002 Reverse engineering gene networks using singular value decomposition and robust regression Proc. Natl. Acad. Sci. U.S.A. 99 9 6163 6168
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegner, J.2
|