-
1
-
-
0034667792
-
Orchestrated response: A symphony of transcription factors for gene control
-
Lemon, B. and Tjian, R. (2000) Orchestrated response: a symphony of transcription factors for gene control. Genes Dev., 14, 2551-2569.
-
(2000)
Genes Dev.
, vol.14
, pp. 2551-2569
-
-
Lemon, B.1
Tjian, R.2
-
2
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S., Mortazavi, A., Myers, R.M. and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
3
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
-
4
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
Wasserman, W.W. and Sandelin, A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
5
-
-
33845341455
-
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
-
Elnitski, L., Jin, V.X., Farnham, P.J. and Jones, S.J. (2006) Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res., 16, 1455-1464.
-
(2006)
Genome Res.
, vol.16
, pp. 1455-1464
-
-
Elnitski, L.1
Jin, V.X.2
Farnham, P.J.3
Jones, S.J.4
-
6
-
-
30044449116
-
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
-
Crawford, G.E., Holt, I.E., Whittle, J., Webb, B.D., Tai, D., Davis, S., Margulies, E.H., Chen, Y., Bernat, J.A., Ginsburg, D. et al. (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res., 16, 123-131.
-
(2006)
Genome Res.
, vol.16
, pp. 123-131
-
-
Crawford, G.E.1
Holt, I.E.2
Whittle, J.3
Webb, B.D.4
Tai, D.5
Davis, S.6
Margulies, E.H.7
Chen, Y.8
Bernat, J.A.9
Ginsburg, D.10
-
7
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle, A.P., Davis, S., Shulha, H.P., Meltzer, P., Margulies, E.H., Weng, Z., Furey, T.S. and Crawford, G.E. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell, 132, 311-322.
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
Davis, S.2
Shulha, H.P.3
Meltzer, P.4
Margulies, E.H.5
Weng, Z.6
Furey, T.S.7
Crawford, G.E.8
-
8
-
-
34250369627
-
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
-
Giresi, P.G., Kim, J., McDaniell, R.M., Iyer, V.R. and Lieb, J.D. (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res., 17, 877-885.
-
(2007)
Genome Res.
, vol.17
, pp. 877-885
-
-
Giresi, P.G.1
Kim, J.2
McDaniell, R.M.3
Iyer, V.R.4
Lieb, J.D.5
-
9
-
-
67649524640
-
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
-
Giresi, P.G. and Lieb, J.D. (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods, 48, 233-239.
-
(2009)
Methods
, vol.48
, pp. 233-239
-
-
Giresi, P.G.1
Lieb, J.D.2
-
10
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
11
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.K.9
Koche, R.P.10
-
12
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
The ENCODE Project Consortium.
-
The ENCODE Project Consortium. (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
-
-
-
13
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
The ENCODE Project Consortium.
-
The ENCODE Project Consortium. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
-
(2011)
PLoS Biol.
, vol.9
-
-
-
14
-
-
58549106607
-
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
-
Whitington, T., Perkins, A.C. and Bailey, T.L. (2009) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res., 37, 14-25.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 14-25
-
-
Whitington, T.1
Perkins, A.C.2
Bailey, T.L.3
-
15
-
-
77950652940
-
Integrating multiple evidence sources to predict transcription factor binding in the human genome
-
Ernst, J., Plasterer, H.L., Simon, I. and Bar-Joseph, Z. (2010) Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res., 20, 526-536.
-
(2010)
Genome Res.
, vol.20
, pp. 526-536
-
-
Ernst, J.1
Plasterer, H.L.2
Simon, I.3
Bar-Joseph, Z.4
-
16
-
-
79952266465
-
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
-
Pique-Regi, R., Degner, J.F., Pai, A.A., Gaffney, D.J., Gilad, Y. and Pritchard, J.K. (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res., 21, 447-455.
-
(2011)
Genome Res.
, vol.21
, pp. 447-455
-
-
Pique-Regi, R.1
Degner, J.F.2
Pai, A.A.3
Gaffney, D.J.4
Gilad, Y.5
Pritchard, J.K.6
-
17
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
18
-
-
4644309196
-
The functions of animal microRNAs
-
Ambros, V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
-
(2004)
Nature
, vol.431
, pp. 350-355
-
-
Ambros, V.1
-
19
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
20
-
-
78651293534
-
MiRBase: Integrating microRNA annotation and deep-sequencing data
-
Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
21
-
-
34250877841
-
A mammalian microRNA expression atlas based on small RNA library sequencing
-
Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A.O., Landthaler, M. et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129, 1401-1414.
-
(2007)
Cell
, vol.129
, pp. 1401-1414
-
-
Landgraf, P.1
Rusu, M.2
Sheridan, R.3
Sewer, A.4
Iovino, N.5
Aravin, A.6
Pfeffer, S.7
Rice, A.8
Kamphorst, A.O.9
Landthaler, M.10
-
22
-
-
79959805164
-
MiRWalk-database: Prediction of Possible MiRNA Binding Sites by 'walking' the genes of three genomes
-
Dweep, H., Sticht, C., Pandey, P. and Gretz, N. (2011) miRWalk-database: prediction of possible miRNA binding sites by 'walking' the genes of three genomes. J. Biomed. Inform., 44, 839-847.
-
(2011)
J. Biomed. Inform.
, vol.44
, pp. 839-847
-
-
Dweep, H.1
Sticht, C.2
Pandey, P.3
Gretz, N.4
-
23
-
-
20444479428
-
C-Myc-regulated microRNAs modulate E2F1 expression
-
O'Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V. and Mendell, J.T. (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature, 435, 839-843.
-
(2005)
Nature
, vol.435
, pp. 839-843
-
-
O'Donnell, K.A.1
Wentzel, E.A.2
Zeller, K.I.3
Dang, C.V.4
Mendell, J.T.5
-
24
-
-
35148886434
-
Tumour invasion and metastasis initiated by microRNA-10b in breast cancer
-
Ma, L., Teruya-Feldstein, J. and Weinberg, R.A. (2007) Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature, 449, 682-688.
-
(2007)
Nature
, vol.449
, pp. 682-688
-
-
Ma, L.1
Teruya-Feldstein, J.2
Weinberg, R.A.3
-
25
-
-
37549008310
-
Widespread microRNA repression by Myc contributes to tumorigenesis
-
Chang, T.C., Yu, D., Lee, Y.S., Wentzel, E.A., Arking, D.E., West, K.M., Dang, C.V., Thomas-Tikhonenko, A. and Mendell, J.T. (2008) Widespread microRNA repression by Myc contributes to tumorigenesis. Nat. Genet., 40, 43-50.
-
(2008)
Nat. Genet.
, vol.40
, pp. 43-50
-
-
Chang, T.C.1
Yu, D.2
Lee, Y.S.3
Wentzel, E.A.4
Arking, D.E.5
West, K.M.6
Dang, C.V.7
Thomas-Tikhonenko, A.8
Mendell, J.T.9
-
26
-
-
48449084118
-
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
-
Marson, A., Levine, S.S., Cole, M.F., Frampton, G.M., Brambrink, T., Johnstone, S., Guenther, M.G., Johnston, W.K., Wernig, M., Newman, J. et al. (2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell, 134, 521-533.
-
(2008)
Cell
, vol.134
, pp. 521-533
-
-
Marson, A.1
Levine, S.S.2
Cole, M.F.3
Frampton, G.M.4
Brambrink, T.5
Johnstone, S.6
Guenther, M.G.7
Johnston, W.K.8
Wernig, M.9
Newman, J.10
-
27
-
-
77957954445
-
Liver-enriched transcription factors regulate microRNA-122 that targets CUTL1 during liver development
-
Xu, H., He, J.H., Xiao, Z.D., Zhang, Q.Q., Chen, Y.Q., Zhou, H. and Qu, L.H. (2010) Liver-enriched transcription factors regulate microRNA-122 that targets CUTL1 during liver development. Hepatology, 52, 1431-1442.
-
(2010)
Hepatology
, vol.52
, pp. 1431-1442
-
-
Xu, H.1
He, J.H.2
Xiao, Z.D.3
Zhang, Q.Q.4
Chen, Y.Q.5
Zhou, H.6
Qu, L.H.7
-
28
-
-
75549092303
-
TransmiR: A transcription factor-microRNA regulation database
-
Wang, J., Lu, M., Qiu, C. and Cui, Q. (2010) TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res., 38, D119-D122.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Wang, J.1
Lu, M.2
Qiu, C.3
Cui, Q.4
-
29
-
-
6344281172
-
Identification of mammalian microRNA host genes and transcription units
-
Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L. and Bradley, A. (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res., 14, 1902-1910.
-
(2004)
Genome Res.
, vol.14
, pp. 1902-1910
-
-
Rodriguez, A.1
Griffiths-Jones, S.2
Ashurst, J.L.3
Bradley, A.4
-
30
-
-
13944260434
-
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
-
Baskerville, S. and Bartel, D.P. (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11, 241-247.
-
(2005)
RNA
, vol.11
, pp. 241-247
-
-
Baskerville, S.1
Bartel, D.P.2
-
31
-
-
8144225486
-
MicroRNA genes are transcribed by RNA polymerase II
-
Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H. and Kim, V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051-4060.
-
(2004)
EMBO J.
, vol.23
, pp. 4051-4060
-
-
Lee, Y.1
Kim, M.2
Han, J.3
Yeom, K.H.4
Lee, S.5
Baek, S.H.6
Kim, V.N.7
-
32
-
-
34249817549
-
Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis
-
Chang, T.C., Wentzel, E.A., Kent, O.A., Ramachandran, K., Mullendore, M., Lee, K.H., Feldmann, G., Yamakuchi, M., Ferlito, M., Lowenstein, C.J. et al. (2007) Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol. Cell, 26, 745-752.
-
(2007)
Mol. Cell
, vol.26
, pp. 745-752
-
-
Chang, T.C.1
Wentzel, E.A.2
Kent, O.A.3
Ramachandran, K.4
Mullendore, M.5
Lee, K.H.6
Feldmann, G.7
Yamakuchi, M.8
Ferlito, M.9
Lowenstein, C.J.10
-
33
-
-
75549086270
-
MiRGen 2.0: A database of microRNA genomic information and regulation
-
Alexiou, P., Vergoulis, T., Gleditzsch, M., Prekas, G., Dalamagas, T., Megraw, M., Grosse, I., Sellis, T. and Hatzigeorgiou, A.G. (2010) miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res., 38, D137-D141.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Alexiou, P.1
Vergoulis, T.2
Gleditzsch, M.3
Prekas, G.4
Dalamagas, T.5
Megraw, M.6
Grosse, I.7
Sellis, T.8
Hatzigeorgiou, A.G.9
-
34
-
-
79952198386
-
MIR@NT@N: A framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model
-
Le Bechec, A., Portales-Casamar, E., Vetter, G., Moes, M., Zindy, P.J., Saumet, A., Arenillas, D., Theillet, C., Wasserman, W.W., Lecellier, C.H. et al. (2011) MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinformatics, 12, 67.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 67
-
-
Le Bechec, A.1
Portales-Casamar, E.2
Vetter, G.3
Moes, M.4
Zindy, P.J.5
Saumet, A.6
Arenillas, D.7
Theillet, C.8
Wasserman, W.W.9
Lecellier, C.H.10
-
35
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
-
(2002)
Genome Res.
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
36
-
-
77950820292
-
PuTmiR: A database for extracting neighboring transcription factors of human microRNAs
-
Bandyopadhyay, S. and Bhattacharyya, M. (2010) PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics, 11, 190.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 190
-
-
Bandyopadhyay, S.1
Bhattacharyya, M.2
-
37
-
-
25844498846
-
Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
-
Stone, E.A., Cooper, G.M. and Sidow, A. (2005) Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu. Rev. Genomics Hum. Genet., 6, 143-164.
-
(2005)
Annu. Rev. Genomics Hum. Genet.
, vol.6
, pp. 143-164
-
-
Stone, E.A.1
Cooper, G.M.2
Sidow, A.3
-
38
-
-
56549129538
-
Chromatin structure analyses identify miRNA promoters
-
Ozsolak, F., Poling, L.L., Wang, Z., Liu, H., Liu, X.S., Roeder, R.G., Zhang, X., Song, J.S. and Fisher, D.E. (2008) Chromatin structure analyses identify miRNA promoters. Genes Dev., 22, 3172-3183.
-
(2008)
Genes Dev.
, vol.22
, pp. 3172-3183
-
-
Ozsolak, F.1
Poling, L.L.2
Wang, Z.3
Liu, H.4
Liu, X.S.5
Roeder, R.G.6
Zhang, X.7
Song, J.S.8
Fisher, D.E.9
-
39
-
-
84856799876
-
MiRviewer: A multispecies microRNA homologous viewer
-
Kiezun, A., Artzi, S., Modai, S., Volk, N., Isakov, O. and Shomron, N. (2012) miRviewer: a multispecies microRNA homologous viewer. BMC Res. Notes, 5, 92.
-
(2012)
BMC Res. Notes
, vol.5
, pp. 92
-
-
Kiezun, A.1
Artzi, S.2
Modai, S.3
Volk, N.4
Isakov, O.5
Shomron, N.6
-
40
-
-
70349643725
-
Chromatin poises miRNA-and protein-coding genes for expression
-
Barski, A., Jothi, R., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E. and Zhao, K. (2009) Chromatin poises miRNA-and protein-coding genes for expression. Genome Res., 19, 1742-1751.
-
(2009)
Genome Res.
, vol.19
, pp. 1742-1751
-
-
Barski, A.1
Jothi, R.2
Cuddapah, S.3
Cui, K.4
Roh, T.Y.5
Schones, D.E.6
Zhao, K.7
-
41
-
-
84862330054
-
Beta-Catenin/LEF1 transactivates the microRNA-371-373 cluster that modulates the Wnt/beta-catenin-signaling pathway
-
Zhou, A.D., Diao, L.T., Xu, H., Xiao, Z.D., Li, J.H., Zhou, H. and Qu, L.H. (2012) beta-Catenin/LEF1 transactivates the microRNA-371-373 cluster that modulates the Wnt/beta-catenin-signaling pathway. Oncogene, 31, 2968-2978.
-
(2012)
Oncogene
, vol.31
, pp. 2968-2978
-
-
Zhou, A.D.1
Diao, L.T.2
Xu, H.3
Xiao, Z.D.4
Li, J.H.5
Zhou, H.6
Qu, L.H.7
-
42
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
-
(2005)
Genome Res.
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
-
43
-
-
4143149651
-
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
-
Washietl, S. and Hofacker, I.L. (2004) Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J. Mol. Biol., 342, 19-30.
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 19-30
-
-
Washietl, S.1
Hofacker, I.L.2
-
44
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
45
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
-
46
-
-
75549083247
-
JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar, E., Thongjuea, S., Kwon, A.T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W.W. and Sandelin, A. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
47
-
-
0028353904
-
The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix
-
Overdier, D.G., Porcella, A. and Costa, R.H. (1994) The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix. Mol. Cell Biol., 14, 2755-2766.
-
(1994)
Mol. Cell Biol.
, vol.14
, pp. 2755-2766
-
-
Overdier, D.G.1
Porcella, A.2
Costa, R.H.3
-
48
-
-
0032905924
-
C-Myc target genes involved in cell growth, apoptosis, and metabolism
-
Dang, C.V. (1999) c-Myc target genes involved in cell growth, apoptosis, and metabolism. Mol. Cell Biol., 19, 1-11.
-
(1999)
Mol. Cell Biol.
, vol.19
, pp. 1-11
-
-
Dang, C.V.1
-
49
-
-
55549103719
-
E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
-
Rabinovich, A., Jin, V.X., Rabinovich, R., Xu, X. and Farnham, P.J. (2008) E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res., 18, 1763-1777.
-
(2008)
Genome Res.
, vol.18
, pp. 1763-1777
-
-
Rabinovich, A.1
Jin, V.X.2
Rabinovich, R.3
Xu, X.4
Farnham, P.J.5
-
50
-
-
77951935861
-
Genome-wide MyoD binding in skeletal muscle cells: A potential for broad cellular reprogramming
-
Cao, Y., Yao, Z., Sarkar, D., Lawrence, M., Sanchez, G.J., Parker, M.H., MacQuarrie, K.L., Davison, J., Morgan, M.T., Ruzzo, W.L. et al. (2010) Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev. Cell, 18, 662-674.
-
(2010)
Dev. Cell
, vol.18
, pp. 662-674
-
-
Cao, Y.1
Yao, Z.2
Sarkar, D.3
Lawrence, M.4
Sanchez, G.J.5
Parker, M.H.6
MacQuarrie, K.L.7
Davison, J.8
Morgan, M.T.9
Ruzzo, W.L.10
-
51
-
-
33748526495
-
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
-
Johnson, R., Gamblin, R.J., Ooi, L., Bruce, A.W., Donaldson, I.J., Westhead, D.R., Wood, I.C., Jackson, R.M. and Buckley, N.J. (2006) Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res., 34, 3862-3877.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3862-3877
-
-
Johnson, R.1
Gamblin, R.J.2
Ooi, L.3
Bruce, A.W.4
Donaldson, I.J.5
Westhead, D.R.6
Wood, I.C.7
Jackson, R.M.8
Buckley, N.J.9
-
52
-
-
54949103985
-
REST regulates distinct transcriptional networks in embryonic and neural stem cells
-
Johnson, R., Teh, C.H., Kunarso, G., Wong, K.Y., Srinivasan, G., Cooper, M.L., Volta, M., Chan, S.S., Lipovich, L., Pollard, S.M. et al. (2008) REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biol., 6, e256.
-
(2008)
PLoS Biol.
, vol.6
-
-
Johnson, R.1
Teh, C.H.2
Kunarso, G.3
Wong, K.Y.4
Srinivasan, G.5
Cooper, M.L.6
Volta, M.7
Chan, S.S.8
Lipovich, L.9
Pollard, S.M.10
-
53
-
-
34547662962
-
Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation
-
Ettwiller, L., Paten, B., Ramialison, M., Birney, E. and Wittbrodt, J. (2007) Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat. Methods, 4, 563-565.
-
(2007)
Nat. Methods
, vol.4
, pp. 563-565
-
-
Ettwiller, L.1
Paten, B.2
Ramialison, M.3
Birney, E.4
Wittbrodt, J.5
-
54
-
-
40849085514
-
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
-
Lupien, M., Eeckhoute, J., Meyer, C.A., Wang, Q., Zhang, Y., Li, W., Carroll, J.S., Liu, X.S. and Brown, M. (2008) FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell, 132, 958-970.
-
(2008)
Cell
, vol.132
, pp. 958-970
-
-
Lupien, M.1
Eeckhoute, J.2
Meyer, C.A.3
Wang, Q.4
Zhang, Y.5
Li, W.6
Carroll, J.S.7
Liu, X.S.8
Brown, M.9
-
55
-
-
76249083492
-
Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq
-
Motallebipour, M., Ameur, A., Reddy Bysani, M.S., Patra, K., Wallerman, O., Mangion, J., Barker, M.A., McKernan, K.J., Komorowski, J. and Wadelius, C. (2009) Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Genome Biol., 10, R129.
-
(2009)
Genome Biol.
, vol.10
-
-
Motallebipour, M.1
Ameur, A.2
Reddy Bysani, M.S.3
Patra, K.4
Wallerman, O.5
Mangion, J.6
Barker, M.A.7
McKernan, K.J.8
Komorowski, J.9
Wadelius, C.10
-
56
-
-
78651250284
-
FOXA1 is a key determinant of estrogen receptor function and endocrine response
-
Hurtado, A., Holmes, K.A., Ross-Innes, C.S., Schmidt, D. and Carroll, J.S. (2011) FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat. Genet., 43, 27-33.
-
(2011)
Nat. Genet.
, vol.43
, pp. 27-33
-
-
Hurtado, A.1
Holmes, K.A.2
Ross-Innes, C.S.3
Schmidt, D.4
Carroll, J.S.5
-
57
-
-
77954355124
-
De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis
-
Boeva, V., Surdez, D., Guillon, N., Tirode, F., Fejes, A.P., Delattre, O. and Barillot, E. (2010) De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res., 38, e126.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Boeva, V.1
Surdez, D.2
Guillon, N.3
Tirode, F.4
Fejes, A.P.5
Delattre, O.6
Barillot, E.7
-
58
-
-
75549084786
-
DeepBase: A database for deeply annotating and mining deep sequencing data
-
Yang, J.H., Shao, P., Zhou, H., Chen, Y.Q. and Qu, L.H. (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 38, D123-D130.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Yang, J.H.1
Shao, P.2
Zhou, H.3
Chen, Y.Q.4
Qu, L.H.5
-
59
-
-
77649193420
-
Ancient animal microRNAs and the evolution of tissue identity
-
Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G.J., Bork, P. and Arendt, D. (2010) Ancient animal microRNAs and the evolution of tissue identity. Nature, 463, 1084-1088.
-
(2010)
Nature
, vol.463
, pp. 1084-1088
-
-
Christodoulou, F.1
Raible, F.2
Tomer, R.3
Simakov, O.4
Trachana, K.5
Klaus, S.6
Snyman, H.7
Hannon, G.J.8
Bork, P.9
Arendt, D.10
-
60
-
-
36749026287
-
Genomic analysis of human microRNA transcripts
-
Saini, H.K., Griffiths-Jones, S. and Enright, A.J. (2007) Genomic analysis of human microRNA transcripts. Proc. Natl Acad. Sci. USA, 104, 17719-17724.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 17719-17724
-
-
Saini, H.K.1
Griffiths-Jones, S.2
Enright, A.J.3
-
61
-
-
59949103192
-
High-resolution human core-promoter prediction with CoreBoost-HM
-
Wang, X., Xuan, Z., Zhao, X., Li, Y. and Zhang, M.Q. (2009) High-resolution human core-promoter prediction with CoreBoost-HM. Genome Res., 19, 266-275.
-
(2009)
Genome Res.
, vol.19
, pp. 266-275
-
-
Wang, X.1
Xuan, Z.2
Zhao, X.3
Li, Y.4
Zhang, M.Q.5
-
62
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman, N.D., Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D., Barrera, L.O., Van Calcar, S., Qu, C., Ching, K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39, 311-318.
-
(2007)
Nat. Genet.
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
-
63
-
-
33744912772
-
The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis
-
Barsyte-Lovejoy, D., Lau, S.K., Boutros, P.C., Khosravi, F., Jurisica, I., Andrulis, I.L., Tsao, M.S. and Penn, L.Z. (2006) The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res., 66, 5330-5337.
-
(2006)
Cancer Res.
, vol.66
, pp. 5330-5337
-
-
Barsyte-Lovejoy, D.1
Lau, S.K.2
Boutros, P.C.3
Khosravi, F.4
Jurisica, I.5
Andrulis, I.L.6
Tsao, M.S.7
Penn, L.Z.8
-
64
-
-
77649275464
-
MiR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis
-
Ma, L., Young, J., Prabhala, H., Pan, E., Mestdagh, P., Muth, D., Teruya-Feldstein, J., Reinhardt, F., Onder, T.T., Valastyan, S. et al. (2010) miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis. Nat. Cell Biol., 12, 247-256.
-
(2010)
Nat. Cell Biol.
, vol.12
, pp. 247-256
-
-
Ma, L.1
Young, J.2
Prabhala, H.3
Pan, E.4
Mestdagh, P.5
Muth, D.6
Teruya-Feldstein, J.7
Reinhardt, F.8
Onder, T.T.9
Valastyan, S.10
-
65
-
-
67349149082
-
MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells
-
Xu, N., Papagiannakopoulos, T., Pan, G., Thomson, J.A. and Kosik, K.S. (2009) MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell, 137, 647-658.
-
(2009)
Cell
, vol.137
, pp. 647-658
-
-
Xu, N.1
Papagiannakopoulos, T.2
Pan, G.3
Thomson, J.A.4
Kosik, K.S.5
-
66
-
-
58149200952
-
UniPROBE: An online database of protein binding microarray data on protein-DNA interactions
-
Newburger, D.E. and Bulyk, M.L. (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res., 37, D77-D82.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Newburger, D.E.1
Bulyk, M.L.2
-
67
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko, P.V., Tolstorukov, M.Y. and Park, P.J. (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol., 26, 1351-1359.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
68
-
-
83255164884
-
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
-
Rhee, H.S. and Pugh, B.F. (2011) Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell, 147, 1408-1419.
-
(2011)
Cell
, vol.147
, pp. 1408-1419
-
-
Rhee, H.S.1
Pugh, B.F.2
-
69
-
-
62549128139
-
A census of human transcription factors: Function, expression and evolution
-
Vaquerizas, J.M., Kummerfeld, S.K., Teichmann, S.A. and Luscombe, N.M. (2009) A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet., 10, 252-263.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 252-263
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
70
-
-
77958096076
-
Determining the specificity of protein-DNA interactions
-
Stormo, G.D. and Zhao, Y. (2010) Determining the specificity of protein-DNA interactions. Nat. Rev. Genet., 11, 751-760.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 751-760
-
-
Stormo, G.D.1
Zhao, Y.2
-
71
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
The modENCODE Consortium, et al.
-
The modENCODE Consortium et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330, 1787-1797.
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
-
72
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
The modENCODE Consortium, et al.
-
The modENCODE Consortium et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science, 330, 1775-1787.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
-
73
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
|