-
1
-
-
0043269205
-
-
Smale,S.T. and Kadonago.J.T. (2N3) The RNA polymerase II core promoter. Annu. Rev. Biochem., 72, 449-479.
-
Smale,S.T. and Kadonago.J.T. (2N3) The RNA polymerase II core promoter. Annu. Rev. Biochem., 72, 449-479.
-
-
-
-
2
-
-
0037108159
-
The RNA polymerase II core promoter: A key component in the regulation of gene expression
-
Butler,J.E. and Kadonaga,J.T. (2002) The RNA polymerase II core promoter: A key component in the regulation of gene expression. Genes Dev., 16, 2583-2592.
-
(2002)
Genes Dev
, vol.16
, pp. 2583-2592
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
3
-
-
0035021811
-
Identification and characterization of the potential promoter regions of 1031 kinds of human genes
-
Suzuki,Y., Tsunoda,T., Sese,J., Tsira,H. Mizushima-Sugano,J., Hata,H., Ota,T., Isogai,T., Tanaka,T. et al. (2001) Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res., 11, 677-684.
-
(2001)
Genome Res
, vol.11
, pp. 677-684
-
-
Suzuki, Y.1
Tsunoda, T.2
Sese, J.3
Tsira, H.4
Mizushima-Sugano, J.5
Hata, H.6
Ota, T.7
Isogai, T.8
Tanaka, T.9
-
4
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci,P., Sandelin,A., Lenhard,B., Katayama,S., Shimokawa,K., Ponjavic,J., Semple,C.A., Taylor,M.S., Engstrom,P.G. et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet., 38, 626-635.
-
(2006)
Nat. Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.7
Taylor, M.S.8
Engstrom, P.G.9
-
5
-
-
33646489947
-
Heterotachy in mammalian promoter evolution
-
Taylor,M.S., Kai,C., Kawai,J., Carninci,P., Hayashizaki,Y. and Semple,C.A. (2006) Heterotachy in mammalian promoter evolution. PLoS Genet., 2, e30.
-
(2006)
PLoS Genet
, vol.2
-
-
Taylor, M.S.1
Kai, C.2
Kawai, J.3
Carninci, P.4
Hayashizaki, Y.5
Semple, C.A.6
-
6
-
-
30044451918
-
Comprehensive analysis of transcriptional promoter structure and function in 1% of the lauman genome
-
Cooper,S.J., Trinklein,N.D., Anton,E.D., Nguyen,L. and Myers,R.M. (2006) Comprehensive analysis of transcriptional promoter structure and function in 1% of the lauman genome. Genome Res., 16, 1-10.
-
(2006)
Genome Res
, vol.16
, pp. 1-10
-
-
Cooper, S.J.1
Trinklein, N.D.2
Anton, E.D.3
Nguyen, L.4
Myers, R.M.5
-
7
-
-
33745152719
-
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
-
Blanchette,M., Bataille,A.R., Chen,X., Poitras,C., Laganiere,J., Lefebvre,C., Deblois,G., Giguere,V., Ferretti,V. et al. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 16, 656-668.
-
(2006)
Genome Res
, vol.16
, pp. 656-668
-
-
Blanchette, M.1
Bataille, A.R.2
Chen, X.3
Poitras, C.4
Laganiere, J.5
Lefebvre, C.6
Deblois, G.7
Giguere, V.8
Ferretti, V.9
-
8
-
-
0037188510
-
Disruption bf a long-range cis-acting regulator for Shh causes preaxial polydactyly
-
Lettice,L.A., Horikoshi,T., Heaney,S.J., van Baren,M.J., van der Linde,H.C., Breedveld,G.J., Joosse,M., Akarsu,N., Oostra,B.A. et al. (2002) Disruption bf a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc. Natl Acad. Sci. USA, 99, 7548-7553.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 7548-7553
-
-
Lettice, L.A.1
Horikoshi, T.2
Heaney, S.J.3
van Baren, M.J.4
van der Linde, H.C.5
Breedveld, G.J.6
Joosse, M.7
Akarsu, N.8
Oostra, B.A.9
-
9
-
-
0036898580
-
Long-range chromatin regulatory interactions in vivo
-
Carter,D., Chakalova,L., Osborne,C.S., Dai,Y.F. and Fraser,P. (2002) Long-range chromatin regulatory interactions in vivo. Nat. Genet., 32, 623-626.
-
(2002)
Nat. Genet
, vol.32
, pp. 623-626
-
-
Carter, D.1
Chakalova, L.2
Osborne, C.S.3
Dai, Y.F.4
Fraser, P.5
-
10
-
-
0027912333
-
Detecting subtle sequence signals: A Gibbs sampling strategy for multiple allgmnent
-
Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple allgmnent. Science, 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
11
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
Roth,F.P., Hughes,J.D., Estep,P.W. and Church,G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
-
(1998)
Nat. Biotechnol
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
13
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden,J., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281, 827-842.
-
(1998)
J. Mol. Biol
, vol.281
, pp. 827-842
-
-
van Helden, J.1
Andre, B.2
Collado-Vides, J.3
-
14
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
15
-
-
2342647392
-
Statistical analysis of over-represented words in human promoter sequences
-
Marino-Ramirez,L., Spouge,J.L., Kanga,G.C. and Landsman,D. (2004) Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res., 32, 949-958.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 949-958
-
-
Marino-Ramirez, L.1
Spouge, J.L.2
Kanga, G.C.3
Landsman, D.4
-
16
-
-
0034669669
-
Predicting regulons and their cis-regulatory motifs by comparative genomics
-
Manson McGuire,A. and Church,G.M. (2000) Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res., 28, 4523-4530.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 4523-4530
-
-
Manson McGuire, A.1
Church, G.M.2
-
17
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis,M., Patterson,N., Endrizzi,M., Birren,B. and Lander,E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
18
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison,C.T., Gordon,D.B., Lee,T.I., Rinaldi,N.J., Macisaac,K.D., Danford,T.W., Hannett,N.M., Tagne,J.B., Reynolds,D.B. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
-
19
-
-
27144476523
-
Discovery of regulatory elements in vertebrates through comparative genomics
-
Prakash,A. and Tompa,M. (2005) Discovery of regulatory elements in vertebrates through comparative genomics. Nat. Biotechnol., 23 1249-1256.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 1249-1256
-
-
Prakash, A.1
Tompa, M.2
-
20
-
-
0038444122
-
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
-
Elkon,R., Linhart,C., Sharan,R., Shamir,R. and Shiloh,Y. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
-
(2003)
Genome Res
, vol.13
, pp. 773-780
-
-
Elkon, R.1
Linhart, C.2
Sharan, R.3
Shamir, R.4
Shiloh, Y.5
-
21
-
-
4444362206
-
Clustering of DNA sequences in human promoters
-
FitzGerald,P.C., Shlyakhtenko,A., Mir,A.A. and Vinson,C. (2004) Clustering of DNA sequences in human promoters. Genome Res., 14 1562-1574.
-
(2004)
Genome Res
, vol.14
, pp. 1562-1574
-
-
FitzGerald, P.C.1
Shlyakhtenko, A.2
Mir, A.A.3
Vinson, C.4
-
22
-
-
33947362037
-
Frequency distribution of TATA Box and extension sequences on human promoters
-
Shi,W. and Zhou,W. (2006) Frequency distribution of TATA Box and extension sequences on human promoters. BMC Bioinformatics, 7(Suppl. 4), S2.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 4
-
-
Shi, W.1
Zhou, W.2
-
23
-
-
29144442902
-
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
-
Tharakaraman,K., Marino-Ramirez,L., Sheetlin,S., Landsman,D. and Spouge,J.L. (2005) Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics, 21(Suppl. 1), 440-448.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
, pp. 440-448
-
-
Tharakaraman, K.1
Marino-Ramirez, L.2
Sheetlin, S.3
Landsman, D.4
Spouge, J.L.5
-
24
-
-
8344288229
-
Promoter prediction analysis on the whole human genome
-
Bajic,V.B., Tan,S.L., Suzuki,Y. and Sugano,S. (2004) Promoter prediction analysis on the whole human genome. Nat. Biotechnol., 22, 1467-1473.
-
(2004)
Nat. Biotechnol
, vol.22
, pp. 1467-1473
-
-
Bajic, V.B.1
Tan, S.L.2
Suzuki, Y.3
Sugano, S.4
-
25
-
-
33847110142
-
The features of Drosophila core promoters revealed by statistical analysis
-
Gershenzon,N.I., Trifonov,E.N. and loshikhes,I.P. (2006) The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics, 7, 161.
-
(2006)
BMC Genomics
, vol.7
, pp. 161
-
-
Gershenzon, N.I.1
Trifonov, E.N.2
loshikhes, I.P.3
-
26
-
-
33947667480
-
Identification of plant promoter constituents by analysis of local distribution of short sequences
-
Yamamoto,Y.Y., Ichida,H., Matsui,M., Obokata,J., Sakurai,T., Satou,M., Seki,M., Shinozaki,K. and Abe,T. (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
Satou, M.6
Seki, M.7
Shinozaki, K.8
Abe, T.9
-
27
-
-
20244377471
-
Functional annotation of a full-length Arabidopsis cDNA collection
-
Seki,M., Narusaka,M., Kamiya,A., Ishida,J., Satou,M., Sakurai,T., Nakajima,M., Enju,A., Akiyama,K. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141-145.
-
(2002)
Science
, vol.296
, pp. 141-145
-
-
Seki, M.1
Narusaka, M.2
Kamiya, A.3
Ishida, J.4
Satou, M.5
Sakurai, T.6
Nakajima, M.7
Enju, A.8
Akiyama, K.9
-
28
-
-
33644874185
-
DBTSS: Database of human transcription start sites, progress
-
Yamashita,R., Suzuki,Y., Wakaguri,H., Tsuritani,K., Nakai,K. and Sugano,S. (2006) DBTSS: Database of human transcription start sites, progress report 2006. Nucleic Acids Res., 34, D86-D89.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Yamashita, R.1
Suzuki, Y.2
Wakaguri, H.3
Tsuritani, K.4
Nakai, K.5
Sugano, S.6
-
29
-
-
0032851812
-
The molecular biology of the CCAAT-binding factor NF-Y
-
Mantovani,R. (1999) The molecular biology of the CCAAT-binding factor NF-Y. Gene, 239, 15-27.
-
(1999)
Gene
, vol.239
, pp. 15-27
-
-
Mantovani, R.1
-
30
-
-
0035515347
-
The ETS-domain transcription factor family
-
Sharrocks,A.D. (2001) The ETS-domain transcription factor family. Nat. Rev. Mol. Cell. Biol., 2, 827-837.
-
(2001)
Nat. Rev. Mol. Cell. Biol
, vol.2
, pp. 827-837
-
-
Sharrocks, A.D.1
-
31
-
-
0037029049
-
Transcriptional activators and coactivators in the nuclear control of mitochondrial function in mammalian cells
-
Scarpulla,R.C. (2002) Transcriptional activators and coactivators in the nuclear control of mitochondrial function in mammalian cells. Gene 286, 81-89.
-
(2002)
Gene
, vol.286
, pp. 81-89
-
-
Scarpulla, R.C.1
-
32
-
-
33748760603
-
The TATA-box sequence in the basal promoter contributes to-determining fight-dependent gene expression in plants
-
Kiran,K., Ansari,S.A., Srivastava,R., Lodhi,N., Chaturvedi,C.P., Sawant,S.V. and Tuli,R. (2006) The TATA-box sequence in the basal promoter contributes to-determining fight-dependent gene expression in plants. Plant Physiol., 142, 364-376.
-
(2006)
Plant Physiol
, vol.142
, pp. 364-376
-
-
Kiran, K.1
Ansari, S.A.2
Srivastava, R.3
Lodhi, N.4
Chaturvedi, C.P.5
Sawant, S.V.6
Tuli, R.7
-
33
-
-
0030590260
-
How proteins recognize the TATA box
-
Juo,Z.S., Chiu,T.K., Leiberman,P.M., Baikalov,I., Berk,A.J. and Dickerson,R.E. (1996) How proteins recognize the TATA box. J. Mol. Biol., 261, 239-254.
-
(1996)
J. Mol. Biol
, vol.261
, pp. 239-254
-
-
Juo, Z.S.1
Chiu, T.K.2
Leiberman, P.M.3
Baikalov, I.4
Berk, A.J.5
Dickerson, R.E.6
-
34
-
-
0034671865
-
Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes
-
Riechmann,J.L., Heard,J., Martin,G., Reuber,L., Jiang,C., Keddie,J., Adam,L., Pineda,O., Ratcliffe,O.J. et al. (2000) Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110.
-
(2000)
Science
, vol.290
, pp. 2105-2110
-
-
Riechmann, J.L.1
Heard, J.2
Martin, G.3
Reuber, L.4
Jiang, C.5
Keddie, J.6
Adam, L.7
Pineda, O.8
Ratcliffe, O.J.9
-
35
-
-
0026754698
-
Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1
-
Kriwacki,R.W., Schultz,S.C., Steitz,T.A. and Caradonna,J.P. (1992) Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1. Proc. Natl Acad. Sci. USA, 89, 9759-9763.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 9759-9763
-
-
Kriwacki, R.W.1
Schultz, S.C.2
Steitz, T.A.3
Caradonna, J.P.4
-
36
-
-
0033822364
-
Large-scale human promoter mapping using CpG islands
-
Ioshikhes,I.P. and Zhang,M.Q. (2000) Large-scale human promoter mapping using CpG islands. Nat. Genet., 26, 61-63.
-
(2000)
Nat. Genet
, vol.26
, pp. 61-63
-
-
Ioshikhes, I.P.1
Zhang, M.Q.2
-
37
-
-
0033601073
-
Methylation-indubed repression - belts, braces, and chromatin
-
Bird,A.P. and Wolffe,A.P. (1999) Methylation-indubed repression - belts, braces, and chromatin. Cell, 99, 451-454.
-
(1999)
Cell
, vol.99
, pp. 451-454
-
-
Bird, A.P.1
Wolffe, A.P.2
-
38
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird,A. (2002) DNA methylation patterns and epigenetic memory. Genes Dev., 16, 6-21.
-
(2002)
Genes Dev
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
39
-
-
0037135130
-
Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice
-
Millar,C.B., Guy,J., Sansom,O.J., Selfridge,J., MacDougall,E., Hendrich,B., Keightley,P.D., Bishop,S.M., Clarke,A.R. et al. (2002) Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice. Science, 297, 403-405.
-
(2002)
Science
, vol.297
, pp. 403-405
-
-
Millar, C.B.1
Guy, J.2
Sansom, O.J.3
Selfridge, J.4
MacDougall, E.5
Hendrich, B.6
Keightley, P.D.7
Bishop, S.M.8
Clarke, A.R.9
-
40
-
-
25444522648
-
Genome wide analysis of Arabidopsis core promoters
-
Molina,C. and 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
-
41
-
-
4944234699
-
Skew in CG content near the transcription start site in Arabidopsis thaliana
-
Tatarinova,T., Brover,V., Troukhan,M. and Alexandrov,N. (2003) Skew in CG content near the transcription start site in Arabidopsis thaliana. Bioinformatics, 19(Suppl. 1), 313-014.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
, pp. 313-014
-
-
Tatarinova, T.1
Brover, V.2
Troukhan, M.3
Alexandrov, N.4
-
42
-
-
25444443669
-
GC-compositional strand bias around transcription start sites in plants and fungi
-
Fujimori,S., Washio,T. and Tomita,M. (2005) GC-compositional strand bias around transcription start sites in plants and fungi. BMC Genomics 6, 26.
-
(2005)
BMC Genomics
, vol.6
, pp. 26
-
-
Fujimori, S.1
Washio, T.2
Tomita, M.3
|