-
1
-
-
0012253746
-
Computational analysis of core promoters in the Drosophila genome
-
RE-SEARCH0087
-
Ohler U, Liao GC, Niemann H, Rubin GM (2002) Computational analysis of core promoters in the Drosophila genome. Genome biology 3: RE-SEARCH0087.
-
(2002)
Genome Biology
, vol.3
-
-
Ohler, U.1
Liao, G.C.2
Niemann, H.3
Rubin, G.M.4
-
2
-
-
30044451918
-
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
-
Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM (2006) Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome research 16: 1-10.
-
(2006)
Genome Research
, vol.16
, pp. 1-10
-
-
Cooper, S.J.1
Trinklein, N.D.2
Anton, E.D.3
Nguyen, L.4
Myers, R.M.5
-
3
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
-
5
-
-
0034161329
-
Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation
-
Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends in biochemical sciences 25: 99-104.
-
(2000)
Trends in Biochemical Sciences
, vol.25
, pp. 99-104
-
-
Orlando, V.1
-
7
-
-
0033152516
-
Activation of RNA polymerase II transcription
-
Berk AJ (1999) Activation of RNA polymerase II transcription. Current opinion in cell biology 11: 330-335.
-
(1999)
Current Opinion in Cell Biology
, vol.11
, pp. 330-335
-
-
Berk, A.J.1
-
8
-
-
0036468869
-
Regulatory context is a crucial part of gene function
-
Fessele S, Maier H, Zischek C, Nelson PJ, Werner T (2002) Regulatory context is a crucial part of gene function. Trends in genetics: TIG 18: 60-63.
-
(2002)
Trends in Genetics: TIG
, vol.18
, pp. 60-63
-
-
Fessele, S.1
Maier, H.2
Zischek, C.3
Nelson, P.J.4
Werner, T.5
-
9
-
-
66049096618
-
The basal initiation machinery: Beyond the general transcription factors
-
Sikorski TW, Buratowski S (2009) The basal initiation machinery: beyond the general transcription factors. Current opinion in cell biology 21: 344-351.
-
(2009)
Current Opinion in Cell Biology
, vol.21
, pp. 344-351
-
-
Sikorski, T.W.1
Buratowski, S.2
-
10
-
-
0030249381
-
The role of general initiation factors in transcription by RNA polymerase II
-
Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends in biochemical sciences 21: 327-335.
-
(1996)
Trends in Biochemical Sciences
, vol.21
, pp. 327-335
-
-
Roeder, R.G.1
-
11
-
-
0028347674
-
An RNA polymerase II holoenzyme responsive to activators
-
Koleske AJ, Young RA (1994) An RNA polymerase II holoenzyme responsive to activators. Nature 368: 466-469.
-
(1994)
Nature
, vol.368
, pp. 466-469
-
-
Koleske, A.J.1
Young, R.A.2
-
12
-
-
0032900980
-
Intermediates in formation and activity of the RNA polymerase II preinitiation complex: Holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB
-
Ranish JA, Yudkovsky N, Hahn S (1999) Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes & development 13: 49-63.
-
(1999)
Genes & Development
, vol.13
, pp. 49-63
-
-
Ranish, J.A.1
Yudkovsky, N.2
Hahn, S.3
-
13
-
-
33846214719
-
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
-
Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389: 52-65.
-
(2007)
Gene
, vol.389
, pp. 52-65
-
-
Yang, C.1
Bolotin, E.2
Jiang, T.3
Sladek, F.M.4
Martinez, E.5
-
14
-
-
25444522648
-
Genome wide analysis of Arabidopsis core promoters
-
Molina C, Grotewold E (2005) Genome wide analysis of Arabidopsis core promoters. BMC genomics 6: 25.
-
(2005)
BMC Genomics
, vol.6
, pp. 25
-
-
Molina, C.1
Grotewold, E.2
-
16
-
-
1542328960
-
Identification and distinct regulation of yeast TATA box-containing genes
-
Basehoar AD, Zanton SJ, Pugh BF (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell 116: 699-709.
-
(2004)
Cell
, vol.116
, pp. 699-709
-
-
Basehoar, A.D.1
Zanton, S.J.2
Pugh, B.F.3
-
17
-
-
33745583768
-
A genetic signature of interspecies variations in gene expression
-
Tirosh I, Weinberger A, Carmi M, Barkai N (2006) A genetic signature of interspecies variations in gene expression. Nature genetics 38: 830-834.
-
(2006)
Nature Genetics
, vol.38
, pp. 830-834
-
-
Tirosh, I.1
Weinberger, A.2
Carmi, M.3
Barkai, N.4
-
18
-
-
34250785284
-
Genetic properties influencing the evolvability of gene expression
-
Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL (2007) Genetic properties influencing the evolvability of gene expression. Science 317: 118-121.
-
(2007)
Science
, vol.317
, pp. 118-121
-
-
Landry, C.R.1
Lemos, B.2
Rifkin, S.A.3
Dickinson, W.J.4
Hartl, D.L.5
-
19
-
-
0031882652
-
New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB
-
Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998) New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes & development 12: 34-44.
-
(1998)
Genes & Development
, vol.12
, pp. 34-44
-
-
Lagrange, T.1
Kapanidis, A.N.2
Tang, H.3
Reinberg, D.4
Ebright, R.H.5
-
20
-
-
26944492656
-
A core promoter element downstream of the TATA box that is recognized by TFIIB
-
Deng W, Roberts SG (2005) A core promoter element downstream of the TATA box that is recognized by TFIIB. Genes & development 19: 2418-2423.
-
(2005)
Genes & Development
, vol.19
, pp. 2418-2423
-
-
Deng, W.1
Roberts, S.G.2
-
21
-
-
0034081817
-
The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters
-
Kutach AK, Kadonaga JT (2000) The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Molecular and cellular biology 20: 4754-4764.
-
(2000)
Molecular and Cellular Biology
, vol.20
, pp. 4754-4764
-
-
Kutach, A.K.1
Kadonaga, J.T.2
-
22
-
-
3042784063
-
The MTE, a new core promoter element for transcription by RNA polymerase II
-
Lim CY, Santoso B, Boulay T, Dong E, Ohler U, et al. (2004) The MTE, a new core promoter element for transcription by RNA polymerase II. Genes & development 18: 1606-1617.
-
(2004)
Genes & Development
, vol.18
, pp. 1606-1617
-
-
Lim, C.Y.1
Santoso, B.2
Boulay, T.3
Dong, E.4
Ohler, U.5
-
23
-
-
27144506577
-
Functional characterization of core promoter elements: The downstream core element is recognized by TAF1
-
Lee DH, Gershenzon N, Gupta M, Ioshikhes IP, Reinberg D, et al. (2005) Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Molecular and cellular biology 25: 9674-9686.
-
(2005)
Molecular and Cellular Biology
, vol.25
, pp. 9674-9686
-
-
Lee, D.H.1
Gershenzon, N.2
Gupta, M.3
Ioshikhes, I.P.4
Reinberg, D.5
-
24
-
-
33847213513
-
The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters
-
Tokusumi Y, Ma Y, Song X, Jacobson RH, Takada S (2007) The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters. Molecular and cellular biology 27: 1844-1858.
-
(2007)
Molecular and Cellular Biology
, vol.27
, pp. 1844-1858
-
-
Tokusumi, Y.1
Ma, Y.2
Song, X.3
Jacobson, R.H.4
Takada, S.5
-
25
-
-
0029586499
-
A conserved downstream element defines a new class of RNA polymerase II promoters
-
Ince TA, Scotto KW (1995) A conserved downstream element defines a new class of RNA polymerase II promoters. The Journal of biological chemistry 270: 30249-30252.
-
(1995)
The Journal of Biological Chemistry
, vol.270
, pp. 30249-30252
-
-
Ince, T.A.1
Scotto, K.W.2
-
26
-
-
0026754386
-
Promoter of the gene for the multifunctional protein disulfide isomerase polypeptide. Functional significance of the six CCAAT boxes and other promoter elements
-
Tasanen K, Oikarinen J, Kivirikko KI, Pihlajaniemi T (1992) Promoter of the gene for the multifunctional protein disulfide isomerase polypeptide. Functional significance of the six CCAAT boxes and other promoter elements. The Journal of biological chemistry 267: 11513-11519.
-
(1992)
The Journal of Biological Chemistry
, vol.267
, pp. 11513-11519
-
-
Tasanen, K.1
Oikarinen, J.2
Kivirikko, K.I.3
Pihlajaniemi, T.4
-
27
-
-
0026593681
-
Synergistic effect of upstream sequences, CCAAT box elements, and HSE sequences for enhanced expression of chimaeric heat shock genes in transgenic tobacco
-
Rieping M, Schoffl F (1992) Synergistic effect of upstream sequences, CCAAT box elements, and HSE sequences for enhanced expression of chimaeric heat shock genes in transgenic tobacco. Molecular & general genetics: MGG 231: 226-232.
-
(1992)
Molecular & General Genetics: MGG
, vol.231
, pp. 226-232
-
-
Rieping, M.1
Schoffl, F.2
-
28
-
-
0029391489
-
A far-upstream sequence of the wheat histone H3 promoter functions differently in rice and tobacco cultured cells
-
Ito T, Fujimoto Y, Nakayama T, Iwabuchi M (1995) A far-upstream sequence of the wheat histone H3 promoter functions differently in rice and tobacco cultured cells. Plant & cell physiology 36: 1281-1289.
-
(1995)
Plant & Cell Physiology
, vol.36
, pp. 1281-1289
-
-
Ito, T.1
Fujimoto, Y.2
Nakayama, T.3
Iwabuchi, M.4
-
29
-
-
0028486232
-
Two 10-bp regions are critical for phytochrome regulation of a Lemna gibba Lhcb gene promoter
-
Kehoe DM, Degenhardt J, Winicov I, Tobin EM (1994) Two 10-bp regions are critical for phytochrome regulation of a Lemna gibba Lhcb gene promoter. The Plant cell 6: 1123-1134.
-
(1994)
The Plant Cell
, vol.6
, pp. 1123-1134
-
-
Kehoe, D.M.1
Degenhardt, J.2
Winicov, I.3
Tobin, E.M.4
-
30
-
-
35548954661
-
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis
-
Yamamoto YY, Ichida H, Abe T, Suzuki Y, Sugano S, et al. (2007) Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic acids research 35: 6219-6226.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 6219-6226
-
-
Yamamoto, Y.Y.1
Ichida, H.2
Abe, T.3
Suzuki, Y.4
Sugano, S.5
-
31
-
-
0030669466
-
The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila
-
Burke TW, Kadonaga JT (1997) The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes & development 11: 3020-3031.
-
(1997)
Genes & Development
, vol.11
, pp. 3020-3031
-
-
Burke, T.W.1
Kadonaga, J.T.2
-
32
-
-
0034653778
-
The initiator element of the Drosophila beta2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression
-
Santel A, Kaufmann J, Hyland R, Renkawitz-Pohl R (2000) The initiator element of the Drosophila beta2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression. Nucleic acids research 28: 1439-1446.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 1439-1446
-
-
Santel, A.1
Kaufmann, J.2
Hyland, R.3
Renkawitz-Pohl, R.4
-
33
-
-
0035135025
-
Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter from Drosophila melanogaster
-
Wu CH, Madabusi L, Nishioka H, Emanuel P, Sypes M, et al. (2001) Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter from Drosophila melanogaster. Molecular and cellular biology 21: 1593-1602.
-
(2001)
Molecular and Cellular Biology
, vol.21
, pp. 1593-1602
-
-
Wu, C.H.1
Madabusi, L.2
Nishioka, H.3
Emanuel, P.4
Sypes, M.5
-
34
-
-
13744259855
-
Core promoter sequences contribute to ovo-B regulation in the Drosophila melanogaster germline
-
Bielinska B, Lu J, Sturgill D, Oliver B (2005) Core promoter sequences contribute to ovo-B regulation in the Drosophila melanogaster germline. Genetics 169: 161-172.
-
(2005)
Genetics
, vol.169
, pp. 161-172
-
-
Bielinska, B.1
Lu, J.2
Sturgill, D.3
Oliver, B.4
-
35
-
-
33845622415
-
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
-
Ohler U (2006) Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic acids research 34: 5943-5950.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 5943-5950
-
-
Ohler, U.1
-
36
-
-
45549093494
-
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
-
Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS (2008) Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America 105: 7762-7767.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 7762-7767
-
-
Hendrix, D.A.1
Hong, J.W.2
Zeitlinger, J.3
Rokhsar, D.S.4
Levine, M.S.5
-
37
-
-
74549132843
-
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
-
Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, et al. (2010) Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327: 335-338.
-
(2010)
Science
, vol.327
, pp. 335-338
-
-
Nechaev, S.1
Fargo, D.C.2
Dos Santos, G.3
Liu, L.4
Gao, Y.5
-
38
-
-
79551610291
-
Genome-wide analysis of promoter architecture in Drosophila melanogaster
-
Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, et al. (2011) Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome research 21: 182-192.
-
(2011)
Genome Research
, vol.21
, pp. 182-192
-
-
Hoskins, R.A.1
Landolin, J.M.2
Brown, J.B.3
Sandler, J.E.4
Takahashi, H.5
-
39
-
-
64249139132
-
RNA Pol II accumulates at promoters of growth genes during developmental arrest
-
Baugh LR, Demodena J, Sternberg PW (2009) RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324: 92-94.
-
(2009)
Science
, vol.324
, pp. 92-94
-
-
Baugh, L.R.1
Demodena, J.2
Sternberg, P.W.3
-
40
-
-
77949434450
-
[Act-1 core promoter region introduces high-performance transcription of EGFP gene expressed in Caenorhabditis elegans]
-
Zhou Q, Jiang X, Zhang H, Du A (2009) [Act-1 core promoter region introduces high-performance transcription of EGFP gene expressed in Caenorhabditis elegans]. Sheng wu gong cheng xue bao = Chinese journal of biotechnology 25: 336-340.
-
(2009)
Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology
, vol.25
, pp. 336-340
-
-
Zhou, Q.1
Jiang, X.2
Zhang, H.3
Du, A.4
-
41
-
-
79955567707
-
Core promoter T-blocks correlate with gene expression levels in C. Elegans
-
Grishkevich V, Hashimshony T, Yanai I (2011) Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome research 21: 707-717.
-
(2011)
Genome Research
, vol.21
, pp. 707-717
-
-
Grishkevich, V.1
Hashimshony, T.2
Yanai, I.3
-
42
-
-
0023653140
-
Regions upstream from the core promoter of the rat ribosomal gene are required for the formation of a stable transcription initiation complex by RNA polymerase i in vitro
-
Cassidy B, Haglund R, Rothblum LI (1987) Regions upstream from the core promoter of the rat ribosomal gene are required for the formation of a stable transcription initiation complex by RNA polymerase I in vitro. Biochimica et biophysica acta 909: 133-144.
-
(1987)
Biochimica et Biophysica Acta
, vol.909
, pp. 133-144
-
-
Cassidy, B.1
Haglund, R.2
Rothblum, L.I.3
-
43
-
-
0024543418
-
A 37-base pair element in the far upstream spacer region can enhance transcription of rat rDNA in vitro and can bind to the core promoter-binding factor(s)
-
Garg LC, Dixit A, Jacob ST (1989) A 37-base pair element in the far upstream spacer region can enhance transcription of rat rDNA in vitro and can bind to the core promoter-binding factor(s). The Journal of biological chemistry 264: 220-224.
-
(1989)
The Journal of Biological Chemistry
, vol.264
, pp. 220-224
-
-
Garg, L.C.1
Dixit, A.2
Jacob, S.T.3
-
44
-
-
0024990257
-
Purification and characterization of a novel factor which stimulates rat ribosomal gene transcription in vitro by interacting with enhancer and core promoter elements
-
Zhang J, Jacob ST (1990) Purification and characterization of a novel factor which stimulates rat ribosomal gene transcription in vitro by interacting with enhancer and core promoter elements. Molecular and cellular biology 10: 5177-5186.
-
(1990)
Molecular and Cellular Biology
, vol.10
, pp. 5177-5186
-
-
Zhang, J.1
Jacob, S.T.2
-
45
-
-
0028095108
-
An enhancer core element mediates stimulation of the rat beta-myosin heavy chain promoter by an alpha 1-adrenergic agonist and activated beta-protein kinase C in hypertrophy of cardiac myocytes
-
Kariya K, Karns LR, Simpson PC (1994) An enhancer core element mediates stimulation of the rat beta-myosin heavy chain promoter by an alpha 1-adrenergic agonist and activated beta-protein kinase C in hypertrophy of cardiac myocytes. The Journal of biological chemistry 269: 3775-3782.
-
(1994)
The Journal of Biological Chemistry
, vol.269
, pp. 3775-3782
-
-
Kariya, K.1
Karns, L.R.2
Simpson, P.C.3
-
46
-
-
0029202504
-
E1BF/Ku interacts physically and functionally with the core promoter binding factor CPBF and promotes the basal transcription of rat and human ribosomal RNA genes
-
Niu H, Zhang J, Jacob ST (1995) E1BF/Ku interacts physically and functionally with the core promoter binding factor CPBF and promotes the basal transcription of rat and human ribosomal RNA genes. Gene expression 4: 111-124.
-
(1995)
Gene Expression
, vol.4
, pp. 111-124
-
-
Niu, H.1
Zhang, J.2
Jacob, S.T.3
-
47
-
-
0031205937
-
Identification of a leader exon and a core promoter for the rat tuberous sclerosis 2 (Tsc2) gene and structural comparison with the human homolog
-
Kobayashi T, Urakami S, Cheadle JP, Aspinwall R, Harris P, et al. (1997) Identification of a leader exon and a core promoter for the rat tuberous sclerosis 2 (Tsc2) gene and structural comparison with the human homolog. Mammalian genome: official journal of the International Mammalian Genome Society 8: 554-558.
-
(1997)
Mammalian Genome: Official Journal of the International Mammalian Genome Society
, vol.8
, pp. 554-558
-
-
Kobayashi, T.1
Urakami, S.2
Cheadle, J.P.3
Aspinwall, R.4
Harris, P.5
-
48
-
-
0035168068
-
Core promoter involvement in the induction of rat ornithine decarboxylase by phorbol esters
-
Zhao B, Butler AP (2001) Core promoter involvement in the induction of rat ornithine decarboxylase by phorbol esters. Molecular carcinogenesis 32: 92-99.
-
(2001)
Molecular Carcinogenesis
, vol.32
, pp. 92-99
-
-
Zhao, B.1
Butler, A.P.2
-
49
-
-
0023046296
-
The core promoter of mouse rDNA consists of two functionally distinct domains
-
Clos J, Normann A, Ohrlein A, Grummt I (1986) The core promoter of mouse rDNA consists of two functionally distinct domains. Nucleic acids research 14: 7581-7595.
-
(1986)
Nucleic Acids Research
, vol.14
, pp. 7581-7595
-
-
Clos, J.1
Normann, A.2
Ohrlein, A.3
Grummt, I.4
-
50
-
-
0024996276
-
Core promoter of the mouse myelin basic protein gene governs brain-specific transcription in vitro
-
Tamura T, Sumita K, Hirose S, Mikoshiba K (1990) Core promoter of the mouse myelin basic protein gene governs brain-specific transcription in vitro. The EMBO journal 9: 3101-3108.
-
(1990)
The EMBO Journal
, vol.9
, pp. 3101-3108
-
-
Tamura, T.1
Sumita, K.2
Hirose, S.3
Mikoshiba, K.4
-
51
-
-
0026083295
-
Structure of the core promoter of human and mouse ribosomal RNA gene. Asymmetry of species-specific transcription
-
Ishikawa Y, Safrany G, Hisatake K, Tanaka N, Maeda Y, et al. (1991) Structure of the core promoter of human and mouse ribosomal RNA gene. Asymmetry of species-specific transcription. Journal of molecular biology 218: 55-67.
-
(1991)
Journal of Molecular Biology
, vol.218
, pp. 55-67
-
-
Ishikawa, Y.1
Safrany, G.2
Hisatake, K.3
Tanaka, N.4
Maeda, Y.5
-
52
-
-
0025937647
-
Sequences involved in brain-specific in vitro transcription from the core promoter of the mouse myelin basic protein gene
-
Tamura T, Sumita K, Mikoshiba K (1991) Sequences involved in brain-specific in vitro transcription from the core promoter of the mouse myelin basic protein gene. Biochimica et biophysica acta 1129: 83-86.
-
(1991)
Biochimica et Biophysica Acta
, vol.1129
, pp. 83-86
-
-
Tamura, T.1
Sumita, K.2
Mikoshiba, K.3
-
53
-
-
0026515546
-
Negative and positive cis-acting elements in the promoter of the mouse gene that encodes the serine/glycine-rich peptide core of secretory granule proteoglycans
-
Avraham S, Avraham H, Austen KF, Stevens RL (1992) Negative and positive cis-acting elements in the promoter of the mouse gene that encodes the serine/glycine-rich peptide core of secretory granule proteoglycans. The Journal of biological chemistry 267: 610-617.
-
(1992)
The Journal of Biological Chemistry
, vol.267
, pp. 610-617
-
-
Avraham, S.1
Avraham, H.2
Austen, K.F.3
Stevens, R.L.4
-
54
-
-
0030063033
-
Structure and expression of the mouse necdin gene. Identification of a postmitotic neuron-restrictive core promoter
-
Uetsuki T, Takagi K, Sugiura H, Yoshikawa K (1996) Structure and expression of the mouse necdin gene. Identification of a postmitotic neuron-restrictive core promoter. The Journal of biological chemistry 271: 918-924.
-
(1996)
The Journal of Biological Chemistry
, vol.271
, pp. 918-924
-
-
Uetsuki, T.1
Takagi, K.2
Sugiura, H.3
Yoshikawa, K.4
-
55
-
-
0242266908
-
Identification of a core promoter and a novel isoform of the human TSC1 gene transcript and structural comparison with mouse homolog
-
Ali M, Girimaji SC, Kumar A (2003) Identification of a core promoter and a novel isoform of the human TSC1 gene transcript and structural comparison with mouse homolog. Gene 320: 145-154.
-
(2003)
Gene
, vol.320
, pp. 145-154
-
-
Ali, M.1
Girimaji, S.C.2
Kumar, A.3
-
56
-
-
1242326890
-
CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments
-
Sharan R, Ovcharenko I, Ben-Hur A, Karp RM (2003) CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 19 Suppl 1: i283-291.
-
(2003)
Bioinformatics
, vol.19
, pp. i283-291
-
-
Sharan, R.1
Ovcharenko, I.2
Ben-Hur, A.3
Karp, R.M.4
-
57
-
-
3042833433
-
Identification of a functional CBF-binding CCAAT-like motif in the core promoter of the mouse pro-alpha 1(V) collagen gene (Col5a1)
-
Sakata-Takatani K, Matsuo N, Sumiyoshi H, Tsuda T, Yoshioka H (2004) Identification of a functional CBF-binding CCAAT-like motif in the core promoter of the mouse pro-alpha 1(V) collagen gene (Col5a1). Matrix biology: journal of the International Society for Matrix Biology 23: 87-99.
-
(2004)
Matrix Biology: Journal of the International Society for Matrix Biology
, vol.23
, pp. 87-99
-
-
Sakata-Takatani, K.1
Matsuo, N.2
Sumiyoshi, H.3
Tsuda, T.4
Yoshioka, H.5
-
58
-
-
20444457552
-
CAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis
-
Somboonthum P, Ohta H, Yamada S, Onishi M, Ike A, et al. (2005) cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis. Nucleic acids research 33: 3401-3411.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 3401-3411
-
-
Somboonthum, P.1
Ohta, H.2
Yamada, S.3
Onishi, M.4
Ike, A.5
-
59
-
-
33847173310
-
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs
-
Jin VX, Singer GA, Agosto-Perez FJ, Liyanarachchi S, Davuluri RV (2006) Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC bioinformatics 7: 114.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 114
-
-
Jin, V.X.1
Singer, G.A.2
Agosto-Perez, F.J.3
Liyanarachchi, S.4
Davuluri, R.V.5
-
61
-
-
78651308679
-
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq
-
Sun H, Wu J, Wickramasinghe P, Pal S, Gupta R, et al. (2011) Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic acids research 39: 190-201.
-
(2011)
Nucleic Acids Research
, vol.39
, pp. 190-201
-
-
Sun, H.1
Wu, J.2
Wickramasinghe, P.3
Pal, S.4
Gupta, R.5
-
62
-
-
0028021762
-
Novel cis-acting elements in the human platelet-derived growth factor B-chain core promoter that mediate gene expression in cultured vascular endothelial cells
-
Khachigian LM, Fries JW, Benz MW, Bonthron DT, Collins T (1994) Novel cis-acting elements in the human platelet-derived growth factor B-chain core promoter that mediate gene expression in cultured vascular endothelial cells. The Journal of biological chemistry 269: 22647-22656.
-
(1994)
The Journal of Biological Chemistry
, vol.269
, pp. 22647-22656
-
-
Khachigian, L.M.1
Fries, J.W.2
Benz, M.W.3
Bonthron, D.T.4
Collins, T.5
-
63
-
-
0028971175
-
A SP1 binding site in the GC-rich region is essential for a core promoter activity of the human endothelial nitric oxide synthase gene
-
Wariishi S, Miyahara K, Toda K, Ogoshi S, Doi Y, et al. (1995) A SP1 binding site in the GC-rich region is essential for a core promoter activity of the human endothelial nitric oxide synthase gene. Biochemical and biophysical research communications 216: 729-735.
-
(1995)
Biochemical and Biophysical Research Communications
, vol.216
, pp. 729-735
-
-
Wariishi, S.1
Miyahara, K.2
Toda, K.3
Ogoshi, S.4
Doi, Y.5
-
64
-
-
0030842463
-
A conserved tissue-specific structure at a human T-cell receptor beta-chain core promoter
-
Halle JP, Haus-Seuffert P, Woltering C, Stelzer G, Meisterernst M (1997) A conserved tissue-specific structure at a human T-cell receptor beta-chain core promoter. Molecular and cellular biology 17: 4220-4229.
-
(1997)
Molecular and Cellular Biology
, vol.17
, pp. 4220-4229
-
-
Halle, J.P.1
Haus-Seuffert, P.2
Woltering, C.3
Stelzer, G.4
Meisterernst, M.5
-
65
-
-
0030960781
-
A novel human zinc finger protein that interacts with the core promoter element of a TATA box-less gene
-
Koritschoner NP, Bocco JL, Panzetta-Dutari GM, Dumur CI, Flury A, et al. (1997) A novel human zinc finger protein that interacts with the core promoter element of a TATA box-less gene. The Journal of biological chemistry 272: 9573-9580.
-
(1997)
The Journal of Biological Chemistry
, vol.272
, pp. 9573-9580
-
-
Koritschoner, N.P.1
Bocco, J.L.2
Panzetta-Dutari, G.M.3
Dumur, C.I.4
Flury, A.5
-
66
-
-
0031795920
-
Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex
-
Martinez E, Ge H, Tao Y, Yuan CX, Palhan V, et al. (1998) Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex. Molecular and cellular biology 18: 6571-6583.
-
(1998)
Molecular and Cellular Biology
, vol.18
, pp. 6571-6583
-
-
Martinez, E.1
Ge, H.2
Tao, Y.3
Yuan, C.X.4
Palhan, V.5
-
67
-
-
0033027728
-
The general transcription factors IIA, IIB, IIF, and IIE are required for RNA polymerase II transcription from the human U1 small nuclear RNA promoter
-
Kuhlman TC, Cho H, Reinberg D, Hernandez N (1999) The general transcription factors IIA, IIB, IIF, and IIE are required for RNA polymerase II transcription from the human U1 small nuclear RNA promoter. Molecular and cellular biology 19: 2130-2141.
-
(1999)
Molecular and Cellular Biology
, vol.19
, pp. 2130-2141
-
-
Kuhlman, T.C.1
Cho, H.2
Reinberg, D.3
Hernandez, N.4
-
68
-
-
0033555543
-
Identification and characterization of the cis-acting elements of the human CD155 gene core promoter
-
Solecki D, Wimmer E, Lipp M, Bernhardt G (1999) Identification and characterization of the cis-acting elements of the human CD155 gene core promoter. The Journal of biological chemistry 274: 1791-1800.
-
(1999)
The Journal of Biological Chemistry
, vol.274
, pp. 1791-1800
-
-
Solecki, D.1
Wimmer, E.2
Lipp, M.3
Bernhardt, G.4
-
69
-
-
0034602843
-
Structural basis of preinitiation complex assembly on human pol II promoters
-
Tsai FT, Sigler PB (2000) Structural basis of preinitiation complex assembly on human pol II promoters. The EMBO journal 19: 25-36.
-
(2000)
The EMBO Journal
, vol.19
, pp. 25-36
-
-
Tsai, F.T.1
Sigler, P.B.2
-
70
-
-
0036798114
-
Sp1 and AP2 regulate but do not constitute TATA-less human TAF(II)55 core promoter activity
-
Zhou T, Chiang CM (2002) Sp1 and AP2 regulate but do not constitute TATA-less human TAF(II)55 core promoter activity. Nucleic acids research 30: 4145-4157.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 4145-4157
-
-
Zhou, T.1
Chiang, C.M.2
-
71
-
-
0347694724
-
SP3 acts as a positive regulator on the core promoter of human ZPK gene
-
Itoh A, Wang Z, Ito Y, Reddy UR, Itoh T (2004) SP3 acts as a positive regulator on the core promoter of human ZPK gene. Biochemical and biophysical research communications 313: 612-618.
-
(2004)
Biochemical and Biophysical Research Communications
, vol.313
, pp. 612-618
-
-
Itoh, A.1
Wang, Z.2
Ito, Y.3
Reddy, U.R.4
Itoh, T.5
-
72
-
-
44449113335
-
Diversity of core promoter elements comprising human bidirectional promoters
-
Yang MQ, Elnitski LL (2008) Diversity of core promoter elements comprising human bidirectional promoters. BMC genomics 9 Suppl 2: S3.
-
(2008)
BMC Genomics
, vol.9
, pp. S3
-
-
Yang, M.Q.1
Elnitski, L.L.2
-
73
-
-
79952699998
-
Exceptional human core promoter nucleotide compositions
-
Darvish H, Nabi MO, Firouzabadi SG, Karimlou M, Heidari A, et al. (2011) Exceptional human core promoter nucleotide compositions. Gene 475: 79-86.
-
(2011)
Gene
, vol.475
, pp. 79-86
-
-
Darvish, H.1
Nabi, M.O.2
Firouzabadi, S.G.3
Karimlou, M.4
Heidari, A.5
-
74
-
-
79955550076
-
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
-
Yamashita R, Sathira NP, Kanai A, Tanimoto K, Arauchi T, et al. (2011) Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome research 21: 775-789.
-
(2011)
Genome Research
, vol.21
, pp. 775-789
-
-
Yamashita, R.1
Sathira, N.P.2
Kanai, A.3
Tanimoto, K.4
Arauchi, T.5
-
75
-
-
29244442328
-
Computational analysis of plant RNA Pol-II promoters
-
Pandey SP, Krishnamachari A (2006) Computational analysis of plant RNA Pol-II promoters. Bio Systems 83: 38-50.
-
(2006)
Bio Systems
, vol.83
, pp. 38-50
-
-
Pandey, S.P.1
Krishnamachari, A.2
-
77
-
-
33947667480
-
Identification of plant promoter constituents by analysis of local distribution of short sequences
-
Yamamoto YY, Ichida H, Matsui M, Obokata J, Sakurai T, et al. (2007) Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC genomics 8: 67.
-
(2007)
BMC Genomics
, vol.8
, pp. 67
-
-
Yamamoto, Y.Y.1
Ichida, H.2
Matsui, M.3
Obokata, J.4
Sakurai, T.5
-
78
-
-
79959928088
-
DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes
-
Morey C, Mookherjee S, Rajasekaran G, Bansal M (2011) DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes. Plant physiology 156: 1300-1315.
-
(2011)
Plant Physiology
, vol.156
, pp. 1300-1315
-
-
Morey, C.1
Mookherjee, S.2
Rajasekaran, G.3
Bansal, M.4
-
79
-
-
0033538531
-
Fundamentally different logic of gene regulation in eukaryotes and prokaryotes
-
Struhl K (1999) Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98: 1-4.
-
(1999)
Cell
, vol.98
, pp. 1-4
-
-
Struhl, K.1
-
80
-
-
0036133034
-
Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach
-
Klingenhoff A, Frech K, Werner T (2002) Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach. In silico biology 2: S17-26.
-
(2002)
Silico Biology
, vol.2
, pp. S17-26
-
-
Klingenhoff, A.1
Frech, K.2
Werner, T.3
-
81
-
-
22844445585
-
Large-scale structural analysis of the core promoter in mammalian and plant genomes
-
Florquin K, Saeys Y, Degroeve S, Rouze P, Van de Peer Y (2005) Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic acids research 33: 4255-4264.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 4255-4264
-
-
Florquin, K.1
Saeys, Y.2
Degroeve, S.3
Rouze, P.4
Van De Peer, Y.5
-
82
-
-
77951167496
-
TC-motifs at the TATA-box expected position in plant genes: A novel class of motifs involved in the transcription regulation
-
Bernard V, Brunaud V, Lecharny A (2010) TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. BMC genomics 11: 166.
-
(2010)
BMC Genomics
, vol.11
, pp. 166
-
-
Bernard, V.1
Brunaud, V.2
Lecharny, A.3
-
83
-
-
0038376923
-
Computational approaches to identify promoters and cis-regulatory elements in plant genomes
-
Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, et al. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant physiology 132: 1162-1176.
-
(2003)
Plant Physiology
, vol.132
, pp. 1162-1176
-
-
Rombauts, S.1
Florquin, K.2
Lescot, M.3
Marchal, K.4
Rouze, P.5
-
84
-
-
35348955882
-
A universal framework for regulatory element discovery across all genomes and data types
-
Elemento O, Slonim N, Tavazoie S (2007) A universal framework for regulatory element discovery across all genomes and data types. Molecular cell 28: 337-350.
-
(2007)
Molecular Cell
, vol.28
, pp. 337-350
-
-
Elemento, O.1
Slonim, N.2
Tavazoie, S.3
-
85
-
-
44349109637
-
Eukaryotic transcription factor binding sites-modeling and integrative search methods
-
Hannenhalli S (2008) Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics 24: 1325-1331.
-
(2008)
Bioinformatics
, vol.24
, pp. 1325-1331
-
-
Hannenhalli, S.1
-
86
-
-
47249118465
-
Extracting sequence features to predict protein-DNA interactions: A comparative study
-
Zhou Q, Liu JS (2008) Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic acids research 36: 4137-4148.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 4137-4148
-
-
Zhou, Q.1
Liu, J.S.2
-
89
-
-
0742306815
-
Computational prediction of transcription-factor binding site locations
-
Bulyk ML (2003) Computational prediction of transcription-factor binding site locations. Genome biology 5: 201.
-
(2003)
Genome Biology
, vol.5
, pp. 201
-
-
Bulyk, M.L.1
-
90
-
-
33748132234
-
MicroRNA promoter element discovery in Arabidopsis
-
Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, et al. (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12: 1612-1619.
-
(2006)
RNA
, vol.12
, pp. 1612-1619
-
-
Megraw, M.1
Baev, V.2
Rusinov, V.3
Jensen, S.T.4
Kalantidis, K.5
-
91
-
-
84867053770
-
Advances in the study of protein-DNA interaction
-
Cai YH, Huang H (2012) Advances in the study of protein-DNA interaction. Amino acids 43: 1141-1146.
-
(2012)
Amino Acids
, vol.43
, pp. 1141-1146
-
-
Cai, Y.H.1
Huang, H.2
-
92
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic acids research 36: 5221-5231.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
93
-
-
36248989105
-
ChIP-Seq data reveal nucleosome architecture of human promoters
-
author reply 832-833
-
Schmid CD, Bucher P (2007) ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131:831-832; author reply 832-833.
-
(2007)
Cell
, vol.131
, pp. 831-832
-
-
Schmid, C.D.1
Bucher, P.2
-
94
-
-
33747044757
-
Analysis of computational approaches for motif discovery
-
Li N, Tompa M (2006) Analysis of computational approaches for motif discovery. Algorithms for molecular biology: AMB 1: 8.
-
(2006)
Algorithms for Molecular Biology: AMB
, vol.1
, pp. 8
-
-
Li, N.1
Tompa, M.2
-
95
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. Journal of molecular biology 296: 1205-1214.
-
(2000)
Journal of Molecular Biology
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
96
-
-
41449103756
-
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
-
Casimiro AC, Vinga S, Freitas AT, Oliveira AL (2008) An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. BMC bioinformatics 9: 89.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 89
-
-
Casimiro, A.C.1
Vinga, S.2
Freitas, A.T.3
Oliveira, A.L.4
-
98
-
-
0035477896
-
Core promoters: Active contributors to combinatorial gene regulation
-
Smale ST (2001) Core promoters: active contributors to combinatorial gene regulation. Genes & development 15: 2503-2508.
-
(2001)
Genes & Development
, vol.15
, pp. 2503-2508
-
-
Smale, S.T.1
-
99
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals. Nature 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
-
101
-
-
0037246944
-
PlantProm: A database of plant promoter sequences
-
Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV (2003) PlantProm: a database of plant promoter sequences. Nucleic acids research 31: 114-117.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 114-117
-
-
Shahmuradov, I.A.1
Gammerman, A.J.2
Hancock, J.M.3
Bramley, P.M.4
Solovyev, V.V.5
-
102
-
-
38549096565
-
JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update
-
Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, et al. (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic acids research 36: D102-106.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. D102-106
-
-
Bryne, J.C.1
Valen, E.2
Tang, M.H.3
Marstrand, T.4
Winther, O.5
-
103
-
-
72949097205
-
Relative stability of DNA as a generic criterion for promoter prediction: Whole genome annotation of microbial genomes with varying nucleotide base composition
-
Rangannan V, Bansal M (2009) Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. Molecular bioSystems 5: 1758-1769.
-
(2009)
Molecular BioSystems
, vol.5
, pp. 1758-1769
-
-
Rangannan, V.1
Bansal, M.2
-
104
-
-
13844275301
-
Similarity of position frequency matrices for transcription factor binding sites
-
Schones DE, Sumazin P, Zhang MQ (2005) Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 21: 307-313.
-
(2005)
Bioinformatics
, vol.21
, pp. 307-313
-
-
Schones, D.E.1
Sumazin, P.2
Zhang, M.Q.3
-
107
-
-
0029971668
-
Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters
-
Burke TW, Kadonaga JT (1996) Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes & development 10: 711-724.
-
(1996)
Genes & Development
, vol.10
, pp. 711-724
-
-
Burke, T.W.1
Kadonaga, J.T.2
-
108
-
-
0025278259
-
Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
-
Bucher P (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. Journal of molecular biology 212: 563-578.
-
(1990)
Journal of Molecular Biology
, vol.212
, pp. 563-578
-
-
Bucher, P.1
-
109
-
-
33644873945
-
EPD in its twentieth year: Towards complete promoter coverage of selected model organisms
-
Schmid CD, Perier R, Praz V, Bucher P (2006) EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic acids research 34: D82-85.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D82-85
-
-
Schmid, C.D.1
Perier, R.2
Praz, V.3
Bucher, P.4
-
110
-
-
84858444088
-
Perspectives on the RNA polymerase II core promoter
-
Kadonaga JT (2012) Perspectives on the RNA polymerase II core promoter. WIREs Dev Biol 1: 40-51.
-
(2012)
WIREs Dev Biol
, vol.1
, pp. 40-51
-
-
Kadonaga, J.T.1
-
111
-
-
0037201434
-
The DPE, a core promoter element for transcription by RNA polymerase II
-
Kadonaga JT (2002) The DPE, a core promoter element for transcription by RNA polymerase II. Experimental & molecular medicine 34: 259-264.
-
(2002)
Experimental & Molecular Medicine
, vol.34
, pp. 259-264
-
-
Kadonaga, J.T.1
-
112
-
-
0023704145
-
A 29-nucleotide DNA segment containing an evolutionarily conserved motif is required in cis for cell-type-restricted repression of the chicken alpha-smooth muscle actin gene core promoter
-
Carroll SL, Bergsma DJ, Schwartz RJ (1988) A 29-nucleotide DNA segment containing an evolutionarily conserved motif is required in cis for cell-type-restricted repression of the chicken alpha-smooth muscle actin gene core promoter. Molecular and cellular biology 8: 241-250.
-
(1988)
Molecular and Cellular Biology
, vol.8
, pp. 241-250
-
-
Carroll, S.L.1
Bergsma, D.J.2
Schwartz, R.J.3
-
113
-
-
0027970883
-
Role of core promoter structure in assembly of the RNA polymerase II preinitiation complex. A common pathway for formation of preinitiation intermediates at many TATA and TATA-less promoters
-
Aso T, Conaway JW, Conaway RC (1994) Role of core promoter structure in assembly of the RNA polymerase II preinitiation complex. A common pathway for formation of preinitiation intermediates at many TATA and TATA-less promoters. The Journal of biological chemistry 269: 26575-26583.
-
(1994)
The Journal of Biological Chemistry
, vol.269
, pp. 26575-26583
-
-
Aso, T.1
Conaway, J.W.2
Conaway, R.C.3
-
114
-
-
0028107658
-
Cooperativity in vivo between the E2 transactivator and the TATA box binding protein depends on core promoter structure
-
Ham J, Steger G, Yaniv M (1994) Cooperativity in vivo between the E2 transactivator and the TATA box binding protein depends on core promoter structure. The EMBO journal 13: 147-157.
-
(1994)
The EMBO Journal
, vol.13
, pp. 147-157
-
-
Ham, J.1
Steger, G.2
Yaniv, M.3
-
115
-
-
0028179052
-
Drosophila TAFII150: Similarity to yeast gene TSM-1 and specific binding to core promoter DNA
-
Verrijzer CP, Yokomori K, Chen JL, Tjian R (1994) Drosophila TAFII150: similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science 264: 933-941.
-
(1994)
Science
, vol.264
, pp. 933-941
-
-
Verrijzer, C.P.1
Yokomori, K.2
Chen, J.L.3
Tjian, R.4
-
116
-
-
0028820036
-
The bovine DNA polymerase beta promoter: Cloning, characterization and comparison with the human core promoter
-
Chen KH, Wood T, He F, Narayan S, Wilson SH (1995) The bovine DNA polymerase beta promoter: cloning, characterization and comparison with the human core promoter. Gene 164: 323-327.
-
(1995)
Gene
, vol.164
, pp. 323-327
-
-
Chen, K.H.1
Wood, T.2
He, F.3
Narayan, S.4
Wilson, S.H.5
-
118
-
-
0030602180
-
Core promoter elements are essential as selective determinants for function of the yeast transcription factor GAL11
-
Sakurai H, Ohishi T, Fukasawa T (1996) Core promoter elements are essential as selective determinants for function of the yeast transcription factor GAL11. FEBS letters 398: 113-119.
-
(1996)
FEBS Letters
, vol.398
, pp. 113-119
-
-
Sakurai, H.1
Ohishi, T.2
Fukasawa, T.3
-
119
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
120
-
-
33845723596
-
Functional conservation of a root hair cell-specific cis-element in angiosperms with different root hair distribution patterns
-
Kim DW, Lee SH, Choi SB, Won SK, Heo YK, et al. (2006) Functional conservation of a root hair cell-specific cis-element in angiosperms with different root hair distribution patterns. The Plant cell 18: 2958-2970.
-
(2006)
The Plant Cell
, vol.18
, pp. 2958-2970
-
-
Kim, D.W.1
Lee, S.H.2
Choi, S.B.3
Won, S.K.4
Heo, Y.K.5
-
122
-
-
79851485916
-
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
-
Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, et al. (2011) Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS genetics 7: e1001274.
-
(2011)
PLoS Genetics
, vol.7
, pp. e1001274
-
-
Rach, E.A.1
Winter, D.R.2
Benjamin, A.M.3
Corcoran, D.L.4
Ni, T.5
-
123
-
-
39049163024
-
Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site
-
Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, et al. (2007) Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PloS one 2: e807.
-
(2007)
PloS One
, vol.2
, pp. e807
-
-
Tabach, Y.1
Brosh, R.2
Buganim, Y.3
Reiner, A.4
Zuk, O.5
-
124
-
-
22444448187
-
A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance
-
Fukue Y, Sumida N, Tanase J, Ohyama T (2005) A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance. Nucleic acids research 33: 3821-3827.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 3821-3827
-
-
Fukue, Y.1
Sumida, N.2
Tanase, J.3
Ohyama, T.4
-
125
-
-
9144242657
-
Comprehensive analysis of the base composition around the transcription start site in Metazoa
-
Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B (2004) Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC genomics 5: 34.
-
(2004)
BMC Genomics
, vol.5
, pp. 34
-
-
Aerts, S.1
Thijs, G.2
Dabrowski, M.3
Moreau, Y.4
De Moor, B.5
-
127
-
-
39049168212
-
Generic eukaryotic core promoter prediction using structural features of DNA
-
Abeel T, Saeys Y, Bonnet E, Rouze P, Van de Peer Y (2008) Generic eukaryotic core promoter prediction using structural features of DNA. Genome research 18: 310-323.
-
(2008)
Genome Research
, vol.18
, pp. 310-323
-
-
Abeel, T.1
Saeys, Y.2
Bonnet, E.3
Rouze, P.4
Van De Peer, Y.5
-
128
-
-
34248684091
-
Core promoter elements recognized by transcription factor IIB
-
Deng W, Roberts SG (2006) Core promoter elements recognized by transcription factor IIB. Biochemical Society transactions 34: 1051-1053.
-
(2006)
Biochemical Society Transactions
, vol.34
, pp. 1051-1053
-
-
Deng, W.1
Roberts, S.G.2
-
129
-
-
70349847245
-
Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis
-
Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, et al. (2009) Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. The Plant journal: for cell and molecular biology 60: 350-362.
-
(2009)
The Plant Journal: For Cell and Molecular Biology
, vol.60
, pp. 350-362
-
-
Yamamoto, Y.Y.1
Yoshitsugu, T.2
Sakurai, T.3
Seki, M.4
Shinozaki, K.5
-
132
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nature genetics 38: 626-635.
-
(2006)
Nature Genetics
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
-
133
-
-
33747322165
-
Tagging mammalian transcription complexity
-
Carninci P (2006) Tagging mammalian transcription complexity. Trends in genetics: TIG 22: 501-510.
-
(2006)
Trends in Genetics: TIG
, vol.22
, pp. 501-510
-
-
Carninci, P.1
-
134
-
-
0029055811
-
Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II
-
Verrijzer CP, Chen JL, Yokomori K, Tjian R (1995) Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 81: 1115-1125.
-
(1995)
Cell
, vol.81
, pp. 1115-1125
-
-
Verrijzer, C.P.1
Chen, J.L.2
Yokomori, K.3
Tjian, R.4
-
135
-
-
0023664776
-
An inspection of the domain between putative TATA box and translation start site in 79 plant genes
-
Joshi CP (1987) An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucleic acids research 15: 6643-6653.
-
(1987)
Nucleic Acids Research
, vol.15
, pp. 6643-6653
-
-
Joshi, C.P.1
-
136
-
-
0027665194
-
Structure and expression of a nuclear gene for the PSI-D subunit of photosystem i in Nicotiana sylvestris
-
Yamamoto Y, Tsuji H, Obokata J (1993) Structure and expression of a nuclear gene for the PSI-D subunit of photosystem I in Nicotiana sylvestris. Plant molecular biology 22: 985-994.
-
(1993)
Plant Molecular Biology
, vol.22
, pp. 985-994
-
-
Yamamoto, Y.1
Tsuji, H.2
Obokata, J.3
-
137
-
-
0036007607
-
Photosynthesis nuclear genes generally lack TATA-boxes: A tobacco photosystem i gene responds to light through an initiator
-
Nakamura M, Tsunoda T, Obokata J (2002) Photosynthesis nuclear genes generally lack TATA-boxes: a tobacco photosystem I gene responds to light through an initiator. The Plant journal: for cell and molecular biology 29: 1-10.
-
(2002)
The Plant Journal: For Cell and Molecular Biology
, vol.29
, pp. 1-10
-
-
Nakamura, M.1
Tsunoda, T.2
Obokata, J.3
-
138
-
-
0037108159
-
The RNA polymerase II core promoter: A key component in the regulation of gene expression
-
Butler JE, Kadonaga JT (2002) The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes & development 16: 2583-2592.
-
(2002)
Genes & Development
, vol.16
, pp. 2583-2592
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
141
-
-
58149185123
-
Ensembl 2009
-
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, et al. (2009) Ensembl 2009. Nucleic acids research 37: D690-697.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. D690-697
-
-
Hubbard, T.J.1
Aken, B.L.2
Ayling, S.3
Ballester, B.4
Beal, K.5
-
142
-
-
0030875847
-
Thermodynamics and NMR of internal G.T mismatches in DNA
-
Allawi HT, SantaLucia J, Jr. (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36: 10581-10594.
-
(1997)
Biochemistry
, vol.36
, pp. 10581-10594
-
-
Allawi, H.T.1
Santalucia, Jr.J.2
-
144
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic acids research 34: D108-110.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D108-110
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
-
146
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
147
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13: 2498-2504.
-
(2003)
Genome Research
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
-
148
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y HY (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Statist Soc Ser: 12.
-
(1995)
J Roy Statist Soc ser
, vol.12
-
-
Benjamini, Y.H.Y.1
|