-
1
-
-
0034730326
-
Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors
-
Halfon, M.S. et al. Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors. Cell 103, 63-74 (2000).
-
(2000)
Cell
, vol.103
, pp. 63-74
-
-
Halfon, M.S.1
-
2
-
-
84856995675
-
Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly
-
Lettice, L.A. et al. Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly. Dev. Cell 22, 459-467 (2012).
-
(2012)
Dev. Cell
, vol.22
, pp. 459-467
-
-
Lettice, L.A.1
-
3
-
-
84865249952
-
Transcription factors: From enhancer binding to developmental control
-
Spitz, F. & Furlong, E.E. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613-626 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.2
-
4
-
-
55049108856
-
Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein
-
Jeong, Y. et al. Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nat. Genet. 40, 1348-1353 (2008).
-
(2008)
Nat. Genet.
, vol.40
, pp. 1348-1353
-
-
Jeong, Y.1
-
5
-
-
61349104285
-
Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence
-
Benko, S. et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat. Genet. 41, 359-364 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 359-364
-
-
Benko, S.1
-
6
-
-
40749158014
-
A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color
-
Sturm, R.A. et al. A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Am. J. Hum. Genet. 82, 424-431 (2008).
-
(2008)
Am. J. Hum. Genet.
, vol.82
, pp. 424-431
-
-
Sturm, R.A.1
-
7
-
-
79951473520
-
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response
-
Harismendy, O. et al. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature 470, 264-268 (2011).
-
(2011)
Nature
, vol.470
, pp. 264-268
-
-
Harismendy, O.1
-
8
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
9
-
-
84864462544
-
A map of the cis-regulatory sequences in the mouse genome
-
Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
-
(2012)
Nature
, vol.488
, pp. 116-120
-
-
Shen, Y.1
-
10
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
-
11
-
-
77956641239
-
ChIP-Seq identification of weakly conserved heart enhancers
-
Blow, M.J. et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 42, 806-810 (2010).
-
(2010)
Nat. Genet.
, vol.42
, pp. 806-810
-
-
Blow, M.J.1
-
12
-
-
80053539409
-
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
-
Song, L. et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21, 1757-1767 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1757-1767
-
-
Song, L.1
-
13
-
-
44349089659
-
The words of the regulatory code are arranged in a variable manner in highly conserved enhancers
-
Rastegar, S. et al. The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev. Biol. 318, 366-377 (2008).
-
(2008)
Dev. Biol.
, vol.318
, pp. 366-377
-
-
Rastegar, S.1
-
14
-
-
0347765651
-
Information display by transcriptional enhancers
-
Kulkarni, M.M. & Arnosti, D.N. Information display by transcriptional enhancers. Development 130, 6569-6575 (2003).
-
(2003)
Development
, vol.130
, pp. 6569-6575
-
-
Kulkarni, M.M.1
Arnosti, D.N.2
-
15
-
-
34548690542
-
Functional architecture and evolution of transcriptional elements that drive gene coexpression
-
Brown, C.D., Johnson, D.S. & Sidow, A. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 317, 1557-1560 (2007).
-
(2007)
Science
, vol.317
, pp. 1557-1560
-
-
Brown, C.D.1
Johnson, D.S.2
Sidow, A.3
-
17
-
-
0029617947
-
Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome
-
Thanos, D. & Maniatis, T. Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome. Cell 83, 1091-1100 (1995).
-
(1995)
Cell
, vol.83
, pp. 1091-1100
-
-
Thanos, D.1
Maniatis, T.2
-
18
-
-
0034819935
-
A predictive model for regulatory sequences directing liver-specific transcription
-
Krivan, W. & Wasserman, W.W. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res. 11, 1559-1566 (2001).
-
(2001)
Genome Res.
, vol.11
, pp. 1559-1566
-
-
Krivan, W.1
Wasserman, W.W.2
-
19
-
-
83055181959
-
Discriminative prediction of mammalian enhancers from DNA sequence
-
Lee, D., Karchin, R. & Beer, M.A. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 21, 2167-2180 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 2167-2180
-
-
Lee, D.1
Karchin, R.2
Beer, M.A.3
-
20
-
-
77649259719
-
Genome-wide discovery of human heart enhancers
-
Narlikar, L. et al. Genome-wide discovery of human heart enhancers. Genome Res. 20, 381-392 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 381-392
-
-
Narlikar, L.1
-
21
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
Gotea, V. et al. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res. 20, 565-577 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 565-577
-
-
Gotea, V.1
-
22
-
-
84862002321
-
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
-
Sharon, E. et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat. Biotechnol. 30, 521-530 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 521-530
-
-
Sharon, E.1
-
23
-
-
34548411011
-
Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells
-
Grskovic, M., Chaivorapol, C., Gaspar-Maia, A., Li, H. & Ramalho-Santos, M. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet. 3, e145 (2007).
-
(2007)
PLoS Genet.
, vol.3
-
-
Grskovic, M.1
Chaivorapol, C.2
Gaspar-Maia, A.3
Li, H.4
Ramalho-Santos, M.5
-
24
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz, J., Siggia, E.D. & Cohen, B.A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215-218 (2009).
-
(2009)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
25
-
-
84863229330
-
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
-
Melnikov, A. et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat. Biotechnol. 30, 271-277 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 271-277
-
-
Melnikov, A.1
-
26
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
Patwardhan, R.P. et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 30, 265-270 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 265-270
-
-
Patwardhan, R.P.1
-
27
-
-
79952988266
-
Functional characterization of liver enhancers that regulate drug-associated transporters
-
Kim, M.J. et al. Functional characterization of liver enhancers that regulate drug-associated transporters. Clin. Pharmacol. Ther. 89, 571-578 (2011).
-
(2011)
Clin. Pharmacol. Ther.
, vol.89
, pp. 571-578
-
-
Kim, M.J.1
-
28
-
-
0033166561
-
High levels of foreign gene expression in hepatocytes after tail vein injections of naked plasmid DNA
-
Zhang, G., Budker, V. & Wolff, J.A. High levels of foreign gene expression in hepatocytes after tail vein injections of naked plasmid DNA. Hum. Gene Ther. 10, 1735-1737 (1999).
-
(1999)
Hum. Gene Ther.
, vol.10
, pp. 1735-1737
-
-
Zhang, G.1
Budker, V.2
Wolff, J.A.3
-
29
-
-
33846112470
-
VISTA Enhancer Browser - A database of tissue-specific human enhancers
-
Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L.A. VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Visel, A.1
Minovitsky, S.2
Dubchak, I.3
Pennacchio, L.A.4
-
30
-
-
0024261447
-
A muscle-specific enhancer is located at the 3′ end of the myosin light-chain 1/3 gene locus
-
Donoghue, M., Ernst, H., Wentworth, B., Nadal-Ginard, B. & Rosenthal, N. A muscle-specific enhancer is located at the 3′ end of the myosin light-chain 1/3 gene locus. Genes Dev. 2, 1779-1790 (1988).
-
(1988)
Genes Dev.
, vol.2
, pp. 1779-1790
-
-
Donoghue, M.1
Ernst, H.2
Wentworth, B.3
Nadal-Ginard, B.4
Rosenthal, N.5
-
31
-
-
0027525576
-
The peroxisome proliferator-activated receptor:Retinoid X receptor heterodimer is activated by fatty acids and fibrate hypolipidaemic drugs
-
Issemann, I., Prince, R.A., Tugwood, J.D. & Green, S. The peroxisome proliferator-activated receptor:retinoid X receptor heterodimer is activated by fatty acids and fibrate hypolipidaemic drugs. J. Mol. Endocrinol. 11, 37-47 (1993).
-
(1993)
J. Mol. Endocrinol.
, vol.11
, pp. 37-47
-
-
Issemann, I.1
Prince, R.A.2
Tugwood, J.D.3
Green, S.4
-
32
-
-
0025736199
-
Characterization of a dimerization motif in AP-2 and its function in heterologous DNA-binding proteins
-
Williams, T. & Tjian, R. Characterization of a dimerization motif in AP-2 and its function in heterologous DNA-binding proteins. Science 251, 1067-1071 (1991).
-
(1991)
Science
, vol.251
, pp. 1067-1071
-
-
Williams, T.1
Tjian, R.2
-
33
-
-
57149148250
-
Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors
-
De Val, S. et al. Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell 135, 1053-1064 (2008).
-
(2008)
Cell
, vol.135
, pp. 1053-1064
-
-
De Val, S.1
-
34
-
-
0003772730
-
-
KTK Scientific Publishers, Tokyo
-
Sakamoto, Y., Ishiguro, M. & Kitagawa, G. Akaike Information Criterion Statistics (KTK Scientific Publishers, Tokyo, 1986).
-
(1986)
Akaike Information Criterion Statistics
-
-
Sakamoto, Y.1
Ishiguro, M.2
Kitagawa, G.3
-
35
-
-
34249654609
-
Position dependencies in transcription factor binding sites
-
Tomovic, A. & Oakeley, E.J. Position dependencies in transcription factor binding sites. Bioinformatics 23, 933-941 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 933-941
-
-
Tomovic, A.1
Oakeley, E.J.2
-
36
-
-
40849085514
-
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
-
Lupien, M. et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132, 958-970 (2008).
-
(2008)
Cell
, vol.132
, pp. 958-970
-
-
Lupien, M.1
-
37
-
-
0025690311
-
Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily
-
Sladek, F.M., Zhong, W.M., Lai, E. & Darnell, J.E. Jr. Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily. Genes Dev. 4, 2353-2365 (1990).
-
(1990)
Genes Dev.
, vol.4
, pp. 2353-2365
-
-
Sladek, F.M.1
Zhong, W.M.2
Lai, E.3
Darnell Jr., J.E.4
-
38
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723 (2009).
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
-
39
-
-
34249302025
-
Development of the mammalian liver and ventral pancreas is dependent on GATA4
-
Watt, A.J., Zhao, R., Li, J. & Duncan, S.A. Development of the mammalian liver and ventral pancreas is dependent on GATA4. BMC Dev. Biol. 7, 37 (2007).
-
(2007)
BMC Dev. Biol.
, vol.7
, pp. 37
-
-
Watt, A.J.1
Zhao, R.2
Li, J.3
Duncan, S.A.4
-
40
-
-
1642535393
-
Hepatic erythropoietin gene regulation by GATA-4
-
Dame, C. et al. Hepatic erythropoietin gene regulation by GATA-4. J. Biol. Chem. 279, 2955-2961 (2004).
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 2955-2961
-
-
Dame, C.1
-
41
-
-
84866128726
-
Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules
-
Schwartz, J.J., Lee, C. & Shendure, J. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nat. Methods 9, 913-915 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 913-915
-
-
Schwartz, J.J.1
Lee, C.2
Shendure, J.3
-
42
-
-
84859829017
-
SLiCE: A novel bacterial cell extract-based DNA cloning method
-
Zhang, Y., Werling, U. & Edelmann, W. SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res. 40, e55 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Zhang, Y.1
Werling, U.2
Edelmann, W.3
-
43
-
-
12744253685
-
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
-
Ovcharenko, I. et al. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15, 184-194 (2005).
-
(2005)
Genome Res.
, vol.15
, pp. 184-194
-
-
Ovcharenko, I.1
-
44
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
45
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57, 289-300 (1995).
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
46
-
-
84952094529
-
Detection of influential observation in linear regression
-
Cook, D. Detection of influential observation in linear regression. Technometrics 19, 15-18 (1977).
-
(1977)
Technometrics
, vol.19
, pp. 15-18
-
-
Cook, D.1
-
47
-
-
0031877016
-
Combining evidence using p-values: Application to sequence homology searches
-
Bailey, T.L. & Gribskov, M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54 (1998).
-
(1998)
Bioinformatics
, vol.14
, pp. 48-54
-
-
Bailey, T.L.1
Gribskov, M.2
|