-
1
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
-
Xie, X.; Lu, J.; Kulbokas, E. J.; Golub, T. R.; Mootha, V.; Lindblad-Toh, K.; Lander, E. S.; Kellis, M. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 2005, 434, 338-345.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
2
-
-
34249907843
-
-
Wells, R. D. Non-B DNA conformations, mutagenesis and disease. Trends Biochem. Sci. 2007, 32, 271-278.
-
Wells, R. D. Non-B DNA conformations, mutagenesis and disease. Trends Biochem. Sci. 2007, 32, 271-278.
-
-
-
-
3
-
-
8444231721
-
Non-B DNA conformations, genomic rearrangements, and human disease
-
Bacolla, A.; Wells, R. D. Non-B DNA conformations, genomic rearrangements, and human disease. J. Biol. Chem. 2004, 279, 47411-47414.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 47411-47414
-
-
Bacolla, A.1
Wells, R.D.2
-
4
-
-
0034674176
-
A DNA structural atlas for Escherichia coli
-
Pedersen, A. G.; Jensen, L. J.; Brunak, S.; Staerfeldt, H. H.; Ussery, D. W. A DNA structural atlas for Escherichia coli. J. Mol. Biol. 2000, 299, 907-930.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 907-930
-
-
Pedersen, A.G.1
Jensen, L.J.2
Brunak, S.3
Staerfeldt, H.H.4
Ussery, D.W.5
-
5
-
-
0030798605
-
Clues and consequences of DNA bending in transcription
-
Perez-Martin, J.; de Lorenzo, V. Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 1997, 51, 593-628.
-
(1997)
Annu. Rev. Microbiol
, vol.51
, pp. 593-628
-
-
Perez-Martin, J.1
de Lorenzo, V.2
-
7
-
-
0036953237
-
DNA topology-mediated control of global gene expression in Escherichia coli
-
Hatfield, G. W.; Benham, C. J. DNA topology-mediated control of global gene expression in Escherichia coli. Annu. Rev. Genet. 2002, 36, 175-203.
-
(2002)
Annu. Rev. Genet
, vol.36
, pp. 175-203
-
-
Hatfield, G.W.1
Benham, C.J.2
-
8
-
-
0037803571
-
-
Rich, A.; Zhang, S. Timeline: Z-DNA: the long road to biological function. Nat. Rev. Genet. 2003, 4, 566-572.
-
Rich, A.; Zhang, S. Timeline: Z-DNA: the long road to biological function. Nat. Rev. Genet. 2003, 4, 566-572.
-
-
-
-
9
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer, M. A.; Tavazoie, S. Predicting gene expression from sequence. Cell 2004, 117, 185-198.
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
10
-
-
0033775978
-
Human-mouse genome comparisons to locate regulatory sites
-
Wasserman, W. W.; Palumbo, M.; Thompson, W.; Fickett, J. W.; Lawrence, C. E. Human-mouse genome comparisons to locate regulatory sites. Nat. Genet. 2000, 26, 225-228.
-
(2000)
Nat. Genet
, vol.26
, pp. 225-228
-
-
Wasserman, W.W.1
Palumbo, M.2
Thompson, W.3
Fickett, J.W.4
Lawrence, C.E.5
-
11
-
-
22844445585
-
Large-scale structural analysis of the core promoter in mammalian and plant genomes
-
Florquin, K.; Saeys, Y.; Degroeve, S.; Rouze, P.; Van de, P. Y. Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res. 2005, 33, 4255-4264.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4255-4264
-
-
Florquin, K.1
Saeys, Y.2
Degroeve, S.3
Rouze, P.4
Van de, P.Y.5
-
12
-
-
0023788886
-
Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis
-
Sen, D.; Gilbert, W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 1988, 334, 364-366.
-
(1988)
Nature
, vol.334
, pp. 364-366
-
-
Sen, D.1
Gilbert, W.2
-
13
-
-
0027990373
-
Structure and stability of human telomeric sequence
-
Balagurumoorthy, P.; Brahmachari, S. K. Structure and stability of human telomeric sequence. J. Biol. Chem. 1994, 269, 21858-21869.
-
(1994)
J. Biol. Chem
, vol.269
, pp. 21858-21869
-
-
Balagurumoorthy, P.1
Brahmachari, S.K.2
-
14
-
-
0035018021
-
-
Simonsson, T. G-quadruplex DNA structures: variations on a theme 34. Biol. Chem. 2001, 382, 621-628.
-
Simonsson, T. G-quadruplex DNA structures: variations on a theme 34. Biol. Chem. 2001, 382, 621-628.
-
-
-
-
15
-
-
0025202253
-
Tetraplex formation of a guanine-containing nonameric DNA fragment
-
Jin, R. Z.; Breslauer, K. J.; Jones, R. A.; Gaffney, B. L. Tetraplex formation of a guanine-containing nonameric DNA fragment. Science 1990, 250, 543-546.
-
(1990)
Science
, vol.250
, pp. 543-546
-
-
Jin, R.Z.1
Breslauer, K.J.2
Jones, R.A.3
Gaffney, B.L.4
-
16
-
-
0027190015
-
DNA sequences at immunoglobulin switch region recombination sites
-
Dunnick, W.; Hertz, G. Z.; Scappino, L.; Gritzmacher, C. DNA sequences at immunoglobulin switch region recombination sites. Nucleic Acids Res. 1993, 21, 365-372.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 365-372
-
-
Dunnick, W.1
Hertz, G.Z.2
Scappino, L.3
Gritzmacher, C.4
-
17
-
-
0023868393
-
Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA
-
Jeffreys, A. J.; Royle, N. J.; Wilson, V.; Wong, Z. Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature 1988, 332, 278-281.
-
(1988)
Nature
, vol.332
, pp. 278-281
-
-
Jeffreys, A.J.1
Royle, N.J.2
Wilson, V.3
Wong, Z.4
-
18
-
-
0031004279
-
DNA secondary structures and the evolution of hypervariable tandem arrays
-
Weitzmann, M. N.; Woodford, K. J.; Usdin, K. DNA secondary structures and the evolution of hypervariable tandem arrays. J. Biol. Chem. 1997, 272, 9517-9523.
-
(1997)
J. Biol. Chem
, vol.272
, pp. 9517-9523
-
-
Weitzmann, M.N.1
Woodford, K.J.2
Usdin, K.3
-
19
-
-
0033034413
-
High affinity interactions of nucleolin with G-G-paired rDNA
-
Hanakahi, L. A.; Sun, H.; Maizels, N. High affinity interactions of nucleolin with G-G-paired rDNA. J. Biol. Chem. 1999, 274, 15908-15912.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 15908-15912
-
-
Hanakahi, L.A.1
Sun, H.2
Maizels, N.3
-
20
-
-
20144364292
-
Prevalence of quadruplexes in the human genome
-
Huppert, J. L.; Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 2005, 33, 2908-2916.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2908-2916
-
-
Huppert, J.L.1
Balasubramanian, S.2
-
21
-
-
20144369806
-
Highly prevalent putative quadruplex sequence motifs in human DNA
-
Todd, A. K.; Johnston, M.; Neidle, S. Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res. 2005, 33, 2901-2907.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2901-2907
-
-
Todd, A.K.1
Johnston, M.2
Neidle, S.3
-
22
-
-
0029670040
-
The chicken beta-globin gene promoter forms a novel "cinched" tetrahelical structure
-
Howell, R. M.; Woodford, K. J.; Weitzmann, M. N.; Usdin, K. The chicken beta-globin gene promoter forms a novel "cinched" tetrahelical structure. J. Biol. Chem. 1996, 271, 5208-5214.
-
(1996)
J. Biol. Chem
, vol.271
, pp. 5208-5214
-
-
Howell, R.M.1
Woodford, K.J.2
Weitzmann, M.N.3
Usdin, K.4
-
23
-
-
0026541582
-
Retinoblastoma susceptibility genes contain 5′ sequences with a high propensity to form guanine-tetrad structures
-
Murchie, A. I.; Lilley, D. M. Retinoblastoma susceptibility genes contain 5′ sequences with a high propensity to form guanine-tetrad structures. Nucleic Acids Res. 1992, 20, 49-53.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 49-53
-
-
Murchie, A.I.1
Lilley, D.M.2
-
24
-
-
0030573027
-
Structure-function correlations of the insulin-linked polymorphic region
-
Catasti, P.; Chen, X.; Moyzis, R. K.; Bradbury, E. M.; Gupta, G. Structure-function correlations of the insulin-linked polymorphic region. J. Mol. Biol. 1996, 264, 534-545.
-
(1996)
J. Mol. Biol
, vol.264
, pp. 534-545
-
-
Catasti, P.1
Chen, X.2
Moyzis, R.K.3
Bradbury, E.M.4
Gupta, G.5
-
25
-
-
0023002908
-
Unusual DNA structures in the adenovirus genome
-
Kilpatrick, M. W.; Torri, A.; Kang, D. S.; Engler, J. A.; Wells, R. D. Unusual DNA structures in the adenovirus genome. J. Biol. Chem. 1986, 261, 11350-11354.
-
(1986)
J. Biol. Chem
, vol.261
, pp. 11350-11354
-
-
Kilpatrick, M.W.1
Torri, A.2
Kang, D.S.3
Engler, J.A.4
Wells, R.D.5
-
26
-
-
0037059740
-
NM23-H1 and NM23-H2 repress transcriptional activities of nuclease-hypersensitive elements in the platelet-derived growth factor-A promoter
-
Ma, D.; Xing, Z.; Liu, B.; Pedigo, N. G.; Zimmer, S. G.; Bai, Z.; Postel, E. H.; Kaetzel, D. M. NM23-H1 and NM23-H2 repress transcriptional activities of nuclease-hypersensitive elements in the platelet-derived growth factor-A promoter. J. Biol. Chem. 2002, 277, 1560-1567.
-
(2002)
J. Biol. Chem
, vol.277
, pp. 1560-1567
-
-
Ma, D.1
Xing, Z.2
Liu, B.3
Pedigo, N.G.4
Zimmer, S.G.5
Bai, Z.6
Postel, E.H.7
Kaetzel, D.M.8
-
27
-
-
23044485047
-
Putative DNA quadruplex formation within the human c-kit oncogene
-
Rankin, S.; Reszka, A. P.; Huppert, J.:, Zloh, M.; Parkinson, G. N.; Todd, A. K.; Ladame, S.; Balasubramanian, S.; Neidle, S. Putative DNA quadruplex formation within the human c-kit oncogene. J. Am. Chem. Soc. 2005, 127, 10584-10589.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 10584-10589
-
-
Rankin, S.1
Reszka, A.P.2
Huppert, J.3
Zloh, M.4
Parkinson, G.N.5
Todd, A.K.6
Ladame, S.7
Balasubramanian, S.8
Neidle, S.9
-
28
-
-
28944442742
-
Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1 alpha promoter
-
De, A. R.; Wood, S.; Sun, D.; Hurley, L. H.; Ebbinghaus, S. W. Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1 alpha promoter. Biochemistry 2005, 44, 16341-16350.
-
(2005)
Biochemistry
, vol.44
, pp. 16341-16350
-
-
De, A.R.1
Wood, S.2
Sun, D.3
Hurley, L.H.4
Ebbinghaus, S.W.5
-
29
-
-
33646462913
-
Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter
-
Dexheimer, T. S.; Sun, D.; Hurley, L. H. Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter. J. Am. Chem. Soc. 2006, 128, 5404-5415.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 5404-5415
-
-
Dexheimer, T.S.1
Sun, D.2
Hurley, L.H.3
-
30
-
-
0037015078
-
Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription
-
Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11593-11598.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A
, vol.99
, pp. 11593-11598
-
-
Siddiqui-Jain, A.1
Grand, C.L.2
Bearss, D.J.3
Hurley, L.H.4
-
31
-
-
0032030327
-
DNA tetraplex formation in the control region of c-myc
-
Simonsson, T.; Pecinka, P.; Kubista, M. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 1998, 26, 1167-1172.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1167-1172
-
-
Simonsson, T.1
Pecinka, P.2
Kubista, M.3
-
32
-
-
27144451010
-
Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo
-
Paeschke, K.; Simonsson, T.; Postberg, J.; Rhodes, D.; Lipps, H. J. Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat. Struct. Mol. Biol. 2005, 12, 847-854.
-
(2005)
Nat. Struct. Mol. Biol
, vol.12
, pp. 847-854
-
-
Paeschke, K.1
Simonsson, T.2
Postberg, J.3
Rhodes, D.4
Lipps, H.J.5
-
33
-
-
33947310727
-
An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation
-
Kumari, S.; Bugaut, A.; Huppert, J. L.; Balasubramanian, S. An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol. 2007, 3, 218.
-
(2007)
Nat. Chem. Biol
, vol.3
, pp. 218
-
-
Kumari, S.1
Bugaut, A.2
Huppert, J.L.3
Balasubramanian, S.4
-
34
-
-
34447541999
-
RNA quadruplex-based modulation of gene expression
-
Wieland, M.; Hartig, J. S. RNA quadruplex-based modulation of gene expression. Chem. Biol. 2007, 14, 757-763.
-
(2007)
Chem. Biol
, vol.14
, pp. 757-763
-
-
Wieland, M.1
Hartig, J.S.2
-
35
-
-
0037022658
-
Cell senescence and telomere shortening induced by a new series of specific G-quadruplex DNA ligands
-
Riou, J. F.; Guittat, L.; Mailliet, P.; Laoui, A.; Renou, E.; Petitgenet, O.; Megnin-Chanet, F.; Helene, C.; Mergny, J. L. Cell senescence and telomere shortening induced by a new series of specific G-quadruplex DNA ligands. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2672-2677.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A
, vol.99
, pp. 2672-2677
-
-
Riou, J.F.1
Guittat, L.2
Mailliet, P.3
Laoui, A.4
Renou, E.5
Petitgenet, O.6
Megnin-Chanet, F.7
Helene, C.8
Mergny, J.L.9
-
36
-
-
31544441946
-
Senescence and telomere shortening induced by novel potent G-quadruplex interactive agents, quindoline derivatives, in human cancer cell lines
-
Zhou, J. M.; Zhu, X. F.; Lu, Y. J.; Deng, R.; Huang, Z. S.; Mei, Y. P.; Wang, Y.; Huang, W. L.; Liu, Z. C.; Gu, L. Q.; Zeng, Y. X. Senescence and telomere shortening induced by novel potent G-quadruplex interactive agents, quindoline derivatives, in human cancer cell lines. Oncogene 2006, 25, 503-511.
-
(2006)
Oncogene
, vol.25
, pp. 503-511
-
-
Zhou, J.M.1
Zhu, X.F.2
Lu, Y.J.3
Deng, R.4
Huang, Z.S.5
Mei, Y.P.6
Wang, Y.7
Huang, W.L.8
Liu, Z.C.9
Gu, L.Q.10
Zeng, Y.X.11
-
37
-
-
0036597090
-
The Cationic Porphyrin TMPyP4 Down-Regulates c-MYC and Human Telomerase Reverse Transcriptase Expression and Inhibits Tumor Growth in Vivo
-
Grand, C. L.; Han, H.; Munoz, R. M.; Weitman, S.; Von Hoff, D. D.; Hurley, L. H.; Bearss, D. J. The Cationic Porphyrin TMPyP4 Down-Regulates c-MYC and Human Telomerase Reverse Transcriptase Expression and Inhibits Tumor Growth in Vivo. Mol. Cancer Ther. 2002, 1, 565-573.
-
(2002)
Mol. Cancer Ther
, vol.1
, pp. 565-573
-
-
Grand, C.L.1
Han, H.2
Munoz, R.M.3
Weitman, S.4
Von Hoff, D.D.5
Hurley, L.H.6
Bearss, D.J.7
-
38
-
-
33846928449
-
G-quadruplexes in promoters throughout the human genome
-
Huppert, J. L.; Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 2007, 35, 406-413.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 406-413
-
-
Huppert, J.L.1
Balasubramanian, S.2
-
39
-
-
34247645020
-
Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals
-
Zhao, Y.; Du, Z.; Li, N. Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals. FEBS Lett. 2007, 581, 1951-1956.
-
(2007)
FEBS Lett
, vol.581
, pp. 1951-1956
-
-
Zhao, Y.1
Du, Z.2
Li, N.3
-
40
-
-
39049170386
-
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
-
Du, Z.; Zhao, Y.; Li, N. Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription. Genome Res. 2008, 18, 233-241.
-
(2008)
Genome Res
, vol.18
, pp. 233-241
-
-
Du, Z.1
Zhao, Y.2
Li, N.3
-
41
-
-
43349085046
-
The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements
-
Todd, A. K.; Neidle, S. The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements. Nucleic Acids Res. 2008, 36, 2700-2704.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2700-2704
-
-
Todd, A.K.1
Neidle, S.2
-
42
-
-
33846786859
-
Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome
-
Du, Z.; Kong, P.; Gao, Y.; Li, N. Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome. Biochem. Biophys. Res. Commun. 2007, 354, 1067-1070.
-
(2007)
Biochem. Biophys. Res. Commun
, vol.354
, pp. 1067-1070
-
-
Du, Z.1
Kong, P.2
Gao, Y.3
Li, N.4
-
43
-
-
33745121203
-
Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation
-
Rawal, P.; Kummarasetti, V. B.; Ravindran, J.; Kumar, N.; Halder, K.; Sharma, R.; Mukerji, M.; Das, S. K.; Chowdhury, S. Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res. 2006, 16, 644-655.
-
(2006)
Genome Res
, vol.16
, pp. 644-655
-
-
Rawal, P.1
Kummarasetti, V.B.2
Ravindran, J.3
Kumar, N.4
Halder, K.5
Sharma, R.6
Mukerji, M.7
Das, S.K.8
Chowdhury, S.9
-
44
-
-
38549092075
-
QuadBase: Genome-wide database of G4 DNA: occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
-
Yadav, V. K.; Abraham, J. K.; Mani, P.; Kulshrestha, R.; Chowdhury, S. QuadBase: genome-wide database of G4 DNA: occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes. Nucleic Acids Res. 2008, D381.
-
(2008)
Nucleic Acids Res
-
-
Yadav, V.K.1
Abraham, J.K.2
Mani, P.3
Kulshrestha, R.4
Chowdhury, S.5
-
45
-
-
0033982936
-
-
Kanehisa, M.; Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000, 28, 27-30.
-
Kanehisa, M.; Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000, 28, 27-30.
-
-
-
-
46
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su, A. I.; Wiltshire, T.; Batalov, S.; Lapp, H.; Ching, K. A.; Block, D.; Zhang, J.; Soden, R.; Hayakawa, M.; Kreiman, G.; Cooke, M. P.; Walker, J. R.; Hogenesch, J. B. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A. 2004, 107, 6062-6067.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.107
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
Cooke, M.P.11
Walker, J.R.12
Hogenesch, J.B.13
-
47
-
-
0036261715
-
Computational analysis of composite regulatory elements
-
Qiu, P.; Ding, W.; Jiang, Y.; Greene, J. R.; Wang, L. Computational analysis of composite regulatory elements. Mamm. Genome 2002, 13, 327-332.
-
(2002)
Mamm. Genome
, vol.13
, pp. 327-332
-
-
Qiu, P.1
Ding, W.2
Jiang, Y.3
Greene, J.R.4
Wang, L.5
-
48
-
-
20444365683
-
GOToolBox: Functional analysis of gene datasets based on gene ontology
-
Martin, D.; Brun, C.; Remy, E.; Mouren, P.; Thieffry, D.; Jacq, B. GOToolBox: functional analysis of gene datasets based on gene ontology. Genome Biol. 2004, 5, R101.
-
(2004)
Genome Biol
, vol.5
-
-
Martin, D.1
Brun, C.2
Remy, E.3
Mouren, P.4
Thieffry, D.5
Jacq, B.6
-
49
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
50
-
-
0037108159
-
The RNA polymerase II core promoter: A key component in the regulation of gene expression
-
Butler, J. E.; Kadonaga, J. T. The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 2002, 16, 2583-2592.
-
(2002)
Genes Dev
, vol.16
, pp. 2583-2592
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
51
-
-
0034081817
-
The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters
-
Kutach, A. K.; Kadonaga, J. T. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 2000, 20, 4754-4764.
-
(2000)
Mol. Cell. Biol
, vol.20
, pp. 4754-4764
-
-
Kutach, A.K.1
Kadonaga, J.T.2
-
52
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
Kim, T. H.; Barrera, L. O.; Zheng, M.; Qu, C.; Singer, M. A.; Richmond, T. A.; Wu, Y.; Green, R. D.; Ren, B. A high-resolution map of active promoters in the human genome. Nature 2005, 436, 876-880.
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
Barrera, L.O.2
Zheng, M.3
Qu, C.4
Singer, M.A.5
Richmond, T.A.6
Wu, Y.7
Green, R.D.8
Ren, B.9
-
53
-
-
0033083378
-
Effects of cationic porphyrins as G-quadruplex interactive agents in human tumor cells
-
Izbicka, E.; Wheelhouse, R. T.; Raymond, E.; Davidson, K. K.; Lawrence, R. A.; Sun, D.; Windle, B. E.; Hurley, L. H.; Von Hoff, D. D. Effects of cationic porphyrins as G-quadruplex interactive agents in human tumor cells. Cancer Res. 1999, 59, 639-644.
-
(1999)
Cancer Res
, vol.59
, pp. 639-644
-
-
Izbicka, E.1
Wheelhouse, R.T.2
Raymond, E.3
Davidson, K.K.4
Lawrence, R.A.5
Sun, D.6
Windle, B.E.7
Hurley, L.H.8
Von Hoff, D.D.9
-
54
-
-
3242691283
-
The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4
-
Seenisamy, J.; Rezler, E. M.; Powell, T. J.; Tye, D.; Gokhale, V.; Joshi, C. S.; Siddiqui-Jain, A.; Hurley, L. H. The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. J. Am. Chem. Soc. 2004, 126, 8702-8709.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 8702-8709
-
-
Seenisamy, J.1
Rezler, E.M.2
Powell, T.J.3
Tye, D.4
Gokhale, V.5
Joshi, C.S.6
Siddiqui-Jain, A.7
Hurley, L.H.8
-
55
-
-
0242349126
-
The cationic porphyrin TMPyP4 destabilizes the tetraplex form of the fragile X syndrome expanded sequence d(CGG)n
-
Weisman-Shomer, P.; Cohen, E.; Hershco, I.; Khateb, S.; Wolfovitz-Barchad, O.; Hurley, L. H.; Fry, M. The cationic porphyrin TMPyP4 destabilizes the tetraplex form of the fragile X syndrome expanded sequence d(CGG)n. Nucleic Acids Res. 2003, 31, 3963-3970.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3963-3970
-
-
Weisman-Shomer, P.1
Cohen, E.2
Hershco, I.3
Khateb, S.4
Wolfovitz-Barchad, O.5
Hurley, L.H.6
Fry, M.7
-
56
-
-
0037731436
-
The Different Biological Effects of Telomestatin and TMPyP4 Can Be Attributed to Their Selectivity for Interaction with Intramolecular or Intermolecular G-Quadruplex Structures
-
Kim, M. Y.; Gleason-Guzman, M.; Izbicka, E.; Nishioka, D.; Hurley, L. H. The Different Biological Effects of Telomestatin and TMPyP4 Can Be Attributed to Their Selectivity for Interaction with Intramolecular or Intermolecular G-Quadruplex Structures. Cancer Res. 2003, 63, 3247-3256.
-
(2003)
Cancer Res
, vol.63
, pp. 3247-3256
-
-
Kim, M.Y.1
Gleason-Guzman, M.2
Izbicka, E.3
Nishioka, D.4
Hurley, L.H.5
-
57
-
-
52449097879
-
The differential effects of TMPyP4, TMPyP2, Se2SAP and telomestatin on c-MYC gene expression can be explained by their differential interactions with the G-quadruplex in the c-MYC silencer element
-
Seenisamy, J.; Dexheimer, T.; Rezler, E.; Grand, C.; Bashyam, S.; Hurley, L. The differential effects of TMPyP4, TMPyP2, Se2SAP and telomestatin on c-MYC gene expression can be explained by their differential interactions with the G-quadruplex in the c-MYC silencer element. AACR Meet. Abstr. 2004, 2004, 531-53a.
-
(2004)
AACR Meet. Abstr
-
-
Seenisamy, J.1
Dexheimer, T.2
Rezler, E.3
Grand, C.4
Bashyam, S.5
Hurley, L.6
-
58
-
-
33744772345
-
A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs
-
Wei, C.; Jia, G.; Yuan, J.; Feng, Z.; Li, C. A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs. Biochemistry 2006, 45, 6681-6691.
-
(2006)
Biochemistry
, vol.45
, pp. 6681-6691
-
-
Wei, C.1
Jia, G.2
Yuan, J.3
Feng, Z.4
Li, C.5
-
59
-
-
0642287888
-
Telomerase inhibition and cell growth arrest by G-quadruplex interactive agent in multiple myeloma
-
Shammas, M. A.; Shmookler Reis, R. J.; Akiyama, M.; Koley, H.; Chauhan, D.; Hideshima, T.; Goyal, R. K.; Hurley, L. H.; Anderson, K. C.; Munshi, N. C. Telomerase inhibition and cell growth arrest by G-quadruplex interactive agent in multiple myeloma. Mol. Cancer Ther. 2003, 2, 825-833.
-
(2003)
Mol. Cancer Ther
, vol.2
, pp. 825-833
-
-
Shammas, M.A.1
Shmookler Reis, R.J.2
Akiyama, M.3
Koley, H.4
Chauhan, D.5
Hideshima, T.6
Goyal, R.K.7
Hurley, L.H.8
Anderson, K.C.9
Munshi, N.C.10
-
60
-
-
33947647457
-
Biophysical Studies of the c-MYC NHE III1 Promoter: Model Quadruplex Interactions with a Cationic Porphyrin
-
Freyer, M. W.; Buscaglia, R.; Kaplan, K.; Cashman, D.; Hurley, L. H.; Lewis, E. A. Biophysical Studies of the c-MYC NHE III1 Promoter: Model Quadruplex Interactions with a Cationic Porphyrin. Biophys. J. 2007, 92, 2007-2015.
-
(2007)
Biophys. J
, vol.92
, pp. 2007-2015
-
-
Freyer, M.W.1
Buscaglia, R.2
Kaplan, K.3
Cashman, D.4
Hurley, L.H.5
Lewis, E.A.6
-
61
-
-
38049017592
-
Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4
-
Qin, Y.; Rezler, E. M.; Gokhale, V.; Sun, D.; Hurley, L. H. Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4. Nucleic Acids Res. 2007, 35, 7698.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7698
-
-
Qin, Y.1
Rezler, E.M.2
Gokhale, V.3
Sun, D.4
Hurley, L.H.5
-
62
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V. G.; Tibshirani, R.; Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
63
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han, J. D.; Bertin, N.; Hao, T.; Goldberg, D. S.; Berriz, G. F.; Zhang, L. V.; Dupuy, D.; Walhout, A. J.; Cusick, M. E.; Roth, F. P.; Vidal, M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430, 88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
64
-
-
40249084264
-
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
-
Eddy, J.; Maizels, N. Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. Nucleic Acids Res. 2008, 36, 1321-1333.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 1321-1333
-
-
Eddy, J.1
Maizels, N.2
-
65
-
-
38849132828
-
The functional response of upstream DNA to dynamic supercoiling in vivo
-
Kouzine, F.; Sanford, S.; Elisha-Feil, Z.; Levens, D. The functional response of upstream DNA to dynamic supercoiling in vivo. Nat. Struct. Mol. Biol. 2008, 15, 146-154.
-
(2008)
Nat. Struct. Mol. Biol
, vol.15
, pp. 146-154
-
-
Kouzine, F.1
Sanford, S.2
Elisha-Feil, Z.3
Levens, D.4
|