-
1
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009).
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
2
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
DOI 10.1038/ng1966, PII NG1966
-
Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the humangenome. Nature Genet.39, 311-318 (2007). (Pubitemid 46328487)
-
(2007)
Nature Genetics
, vol.39
, Issue.3
, 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
Wang, W.11
Weng, Z.12
Green, R.D.13
Crawford, G.E.14
Ren, B.15
-
3
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
DOI 10.1038/nature05295, PII NATURE05295
-
Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502 (2006). (Pubitemid 44809068)
-
(2006)
Nature
, vol.444
, Issue.7118
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
Minovitsky, S.7
Dubchak, I.8
Holt, A.9
Lewis, K.D.10
Plajzer-Frick, I.11
Akiyama, J.12
De Val, S.13
Afzal, V.14
Black, B.L.15
Couronne, O.16
Eisen, M.B.17
Visel, A.18
Rubin, E.M.19
-
4
-
-
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
-
5
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
-
6
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
7
-
-
0034507632
-
Transcription of eukaryotic protein-coding genes
-
DOI 10.1146/annurev.genet.34.1.77
-
Lee, T. I. & Young, R. A. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34, 77-137 (2000). (Pubitemid 32065917)
-
(2000)
Annual Review of Genetics
, vol.34
, pp. 77-137
-
-
Ihn Lee, T.1
Young, R.A.2
-
8
-
-
33744792310
-
Sensors and signals: A coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response
-
DOI 10.1101/gad.1424806
-
Rosenfeld, M. G., Lunyak, V. V. & Glass, C. K. Sensors and signals: a coactivator/ corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. Genes Dev. 20, 1405-1428 (2006). (Pubitemid 43830648)
-
(2006)
Genes and Development
, vol.20
, Issue.11
, pp. 1405-1428
-
-
Rosenfeld, M.G.1
Lunyak, V.V.2
Glass, C.K.3
-
9
-
-
40849085514
-
FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription
-
DOI 10.1016/j.cell.2008.01.018, PII S0092867408001189
-
Lupien, M. et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132, 958-970 (2008). (Pubitemid 351391952)
-
(2008)
Cell
, vol.132
, Issue.6
, 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
-
10
-
-
24344447360
-
Forkhead box A1 regulates prostate ductal morphogenesis and promotes epithelial cell maturation
-
DOI 10.1242/dev.01917
-
Gao, N. et al. Forkhead box A1 regulates prostate ductal morphogenesis and promotes epithelial cell maturation. Development 132, 3431-3443 (2005). (Pubitemid 41246118)
-
(2005)
Development
, vol.132
, Issue.15
, pp. 3431-3443
-
-
Gao, N.1
Ishii, K.2
Mirosevich, J.3
Kuwajima, S.4
Oppenheimer, S.R.5
Roberts, R.L.6
Jiang, M.7
Yu, X.8
Shapell, S.B.9
Caprioli, R.M.10
Stoffel, M.11
Hayward, S.W.12
Matusik, R.J.13
-
11
-
-
13544276537
-
Expression of Foxa transcription factors in the developing and adult murine prostate
-
DOI 10.1002/pros.20131
-
Mirosevich, J.,Gao, N. & Matusik, R. J. Expressionof Foxa transcriptionfactors in the developing and adult murine prostate. Prostate 62, 339-352 (2005). (Pubitemid 40224139)
-
(2005)
Prostate
, vol.62
, Issue.4
, pp. 339-352
-
-
Mirosevich, J.1
Gao, N.2
Matusik, R.J.3
-
12
-
-
8344272750
-
Coregulator recruitment and histone modifications in transcriptional regulation by the androgen receptor
-
DOI 10.1210/me.2004-0245
-
Kang, Z., Janne, O. A. & Palvimo, J. J. Coregulator recruitment and histone modifications in transcriptional regulation by the androgen receptor. Mol. Endocrinol. 18, 2633-2648 (2004). (Pubitemid 39482054)
-
(2004)
Molecular Endocrinology
, vol.18
, Issue.11
, pp. 2633-2648
-
-
Kang, Z.1
Janne, O.A.2
Palvimo, J.J.3
-
13
-
-
0344778475
-
Nucleosome positioning by the winged helix transcription factor HNF3
-
Shim, E. Y.,Woodcock, C. & Zaret, K. S.Nucleosome positioning by the winged helix transcription factor HNF3. Genes Dev. 12, 5-10 (1998). (Pubitemid 28083653)
-
(1998)
Genes and Development
, vol.12
, Issue.1
, pp. 5-10
-
-
Shim, E.Y.1
Woodcock, C.2
Zaret, K.S.3
-
14
-
-
14644415948
-
FoxA1 binding to the MMTV LTR modulates chromatin structure and transcription
-
DOI 10.1016/j.yexcr.2004.12.002
-
Holmqvist, P. H., Belikov, S., Zaret, K. S. & Wrange, O. FoxA1 binding to the MMTV LTR modulates chromatin structure and transcription. Exp. Cell Res. 304, 593-603 (2005). (Pubitemid 40321135)
-
(2005)
Experimental Cell Research
, vol.304
, Issue.2
, pp. 593-603
-
-
Holmqvist, P.-H.1
Belikov, S.2
Zaret, K.S.3
Wrange, O.4
-
15
-
-
0033609935
-
Hepatocyte nuclear factor 3 relieves chromatin-mediated repression of the a-fetoprotein gene
-
Crowe, A. J. et al. Hepatocyte nuclear factor 3 relieves chromatin-mediated repression of the a-fetoprotein gene. J. Biol. Chem. 274, 25113-25120 (1999).
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 25113-25120
-
-
Crowe, A.J.1
-
16
-
-
0036184236
-
Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4
-
DOI 10.1016/S1097-2765(02)00459-8
-
Cirillo, L. A. et al. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 9, 279-289 (2002). (Pubitemid 34195554)
-
(2002)
Molecular Cell
, vol.9
, Issue.2
, pp. 279-289
-
-
Cirillo, L.A.1
Lin, F.R.2
Cuesta, I.3
Friedman, D.4
Jarnik, M.5
Zaret, K.S.6
-
17
-
-
67650758019
-
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer
-
Wang, Q. et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 138, 245-256 (2009).
-
(2009)
Cell
, vol.138
, pp. 245-256
-
-
Wang, Q.1
-
18
-
-
78651250284
-
FOXA1 is a key determinant of estrogen receptor function and endocrine response
-
Hurtado, A., Holmes, K. A., Ross-Innes, C. S., Schmidt, D. & Carroll, J. S. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nature Genet. 43, 27-33 (2011).
-
(2011)
Nature 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
-
19
-
-
76249098305
-
SOX9 elevation in the prostate promotes proliferation and cooperates with PTEN loss to drive tumor formation
-
Thomsen, M. K. et al. SOX9 elevation in the prostate promotes proliferation and cooperates with PTEN loss to drive tumor formation. Cancer Res. 70, 979-987 (2010).
-
(2010)
Cancer Res.
, vol.70
, pp. 979-987
-
-
Thomsen, M.K.1
-
20
-
-
40949145618
-
SOX9 is expressed in human fetal prostate epithelium and enhances prostate cancer invasion
-
DOI 10.1158/0008-5472.CAN-07-5915
-
Wang, H. et al.SOX9is expressedinhumanfetal prostate epitheliumand enhances prostate cancer invasion. Cancer Res. 68, 1625-1630 (2008). (Pubitemid 351416545)
-
(2008)
Cancer Research
, vol.68
, Issue.6
, pp. 1625-1630
-
-
Wang, H.1
Leav, I.2
Ibaragi, S.3
Wegner, M.4
Hu, G.-F.5
Lu, M.L.6
Balk, S.P.7
Yuan, X.8
-
21
-
-
24144465889
-
Molecular determinants of crosstalk between nuclear receptors and toll-like receptors
-
DOI 10.1016/j.cell.2005.06.029, PII S0092867405006483
-
Ogawa, S. et al. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell 122, 707-721 (2005). (Pubitemid 41242636)
-
(2005)
Cell
, vol.122
, Issue.5
, pp. 707-721
-
-
Ogawa, S.1
Lozach, J.2
Benner, C.3
Pascual, G.4
Tangirala, R.K.5
Westin, S.6
Hoffmann, A.7
Subramaniam, S.8
David, M.9
Rosenfeld, M.G.10
Glass, C.K.11
-
22
-
-
38349062191
-
Hepatocyte nuclear factor-3a (HNF-3a) negatively regulates androgen receptor transactivation in prostate cancer cells
-
Lee, H. J., Hwang, M., Chattopadhyay, S., Choi, H. S. & Lee, K. Hepatocyte nuclear factor-3a (HNF-3a) negatively regulates androgen receptor transactivation in prostate cancer cells. Biochem. Biophys. Res. Commun. 367, 481-486 (2008).
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.367
, pp. 481-486
-
-
Lee, H.J.1
Hwang, M.2
Chattopadhyay, S.3
Choi, H.S.4
Lee, K.5
-
23
-
-
0042266417
-
The role of hepatocyte nuclear factor-3 (forkhead box A1) and androgen receptor in transcriptional regulation of prostatic genes
-
DOI 10.1210/me.2003-0020
-
Gao, N. et al. The role of hepatocyte nuclear factor-3a (Forkhead Box A1) and androgen receptor in transcriptional regulation of prostatic genes. Mol. Endocrinol. 17, 1484-1507 (2003). (Pubitemid 36930465)
-
(2003)
Molecular Endocrinology
, vol.17
, Issue.8
, pp. 1484-1507
-
-
Gao, N.1
Zhang, J.2
Rao, M.A.3
Case, T.C.4
Mirosevich, J.5
Wang, Y.6
Jin, R.7
Gupta, A.8
Rennie, P.S.9
Matusik, R.J.10
-
24
-
-
77957139539
-
Mediator and cohesin connect gene expression and chromatin architecture
-
Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435 (2010).
-
(2010)
Nature
, vol.467
, pp. 430-435
-
-
Kagey, M.H.1
-
25
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
He, H. H. et al. Nucleosome dynamics define transcriptional enhancers. Nature Genet. 42, 343-347 (2010).
-
(2010)
Nature Genet.
, vol.42
, pp. 343-347
-
-
He, H.H.1
-
26
-
-
0036022071
-
Chromosomal aberrations in prostate cancer xenografts detected by comparative genomic hybridization
-
DOI 10.1002/gcc.10097
-
Laitinen, S., Karhu, R., Sawyers, C. L., Vessella, R. L. & Visakorpi, T. Chromosomal aberrations in prostate cancer xenografts detected by comparative genomic hybridization. Genes Chromosom. Cancer 35, 66-73 (2002). (Pubitemid 34847870)
-
(2002)
Genes Chromosomes and Cancer
, vol.35
, Issue.1
, pp. 66-73
-
-
Laitinen, S.1
Karhu, R.2
Sawyers, C.L.3
Vessella, R.L.4
Visakorpi, T.5
-
27
-
-
58749094283
-
Hormone escape is associated with genomic instability in a human prostate cancer model
-
Legrier, M. E. et al. Hormone escape is associated with genomic instability in a human prostate cancer model. Int. J. Cancer 124, 1103-1111 (2009).
-
(2009)
Int. J. Cancer
, vol.124
, pp. 1103-1111
-
-
Legrier, M.E.1
-
28
-
-
2442637585
-
High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: Impact of copy number on gene expression
-
Wolf, M. et al. High-resolution analysis of gene copy number alterations in human prostate cancer using CGHon cDNAmicroarrays: impact of copy number on gene expression. Neoplasia 6, 240-247 (2004). (Pubitemid 38657080)
-
(2004)
Neoplasia
, vol.6
, Issue.3
, pp. 240-247
-
-
Wolf, M.1
Mousses, S.2
Hautaniemi, S.3
Karhu, R.4
Huusko, P.5
Allinen, M.6
Elkahloun, A.7
Monni, O.8
Chen, Y.9
Kallioniemi, A.10
Kallioniemi, O.-P.11
-
29
-
-
33846690407
-
Histone Methylation-Dependent Mechanisms Impose Ligand Dependency for Gene Activation by Nuclear Receptors
-
DOI 10.1016/j.cell.2006.12.038, PII S0092867407000621
-
Garcia-Bassets, I. et al. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 128, 505-518 (2007). (Pubitemid 46198894)
-
(2007)
Cell
, vol.128
, Issue.3
, pp. 505-518
-
-
Garcia-Bassets, I.1
Kwon, Y.-S.2
Telese, F.3
Prefontaine, G.G.4
Hutt, K.R.5
Cheng, C.S.6
Ju, B.-G.7
Ohgi, K.A.8
Wang, J.9
Escoubet-Lozach, L.10
Rose, DavidW.11
Glass, C.K.12
Fu, X.-D.13
Rosenfeld, M.G.14
-
30
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223 (2009).
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
31
-
-
58049208232
-
Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules
-
Hu, Q. et al. Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc. Natl Acad. Sci. USA 105, 19199-19204 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 19199-19204
-
-
Hu, Q.1
-
32
-
-
0042307325
-
The ErbB2/ErbB3 heterodimer functions as an oncogenic unit: ErbB2 requires ErbB3 to drive breast tumor cell proliferation
-
DOI 10.1073/pnas.1537685100
-
Holbro, T. et al. The ErbB2/ErbB3 heterodimer functions as an oncogenic unit: ErbB2 requires ErbB3 to derive breast tumor cell proliferation. Proc. Natl Acad. Sci. USA 100, 8933-8938 (2003). (Pubitemid 36899201)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.15
, pp. 8933-8938
-
-
Holbro, T.1
Beerli, R.R.2
Maurer, F.3
Koziczak, M.4
Barbas Iii, C.F.5
Hynes, N.E.6
-
33
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
34
-
-
34249026300
-
High-Resolution Profiling of Histone Methylations in the Human Genome
-
DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
-
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007). (Pubitemid 46802390)
-
(2007)
Cell
, vol.129
, Issue.4
, 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
-
35
-
-
46449123335
-
Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
-
DOI 10.1101/gr.076117.108
-
Linhart, C., Halperin, Y. & Shamir, R. Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res. 18, 1180-1189 (2008). (Pubitemid 351931169)
-
(2008)
Genome Research
, vol.18
, Issue.7
, pp. 1180-1189
-
-
Linhart, C.1
Halperin, Y.2
Shamir, R.3
-
36
-
-
34249709906
-
Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process
-
Chandran, U. R. et al. Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process. BMC Cancer 7, 64 (2007).
-
(2007)
BMC Cancer
, vol.7
, pp. 64
-
-
Chandran, U.R.1
-
37
-
-
4344561557
-
Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy
-
DOI 10.1200/JCO.2004.05.158
-
Yu, Y. P. et al. Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J. Clin. Oncol. 22, 2790-2799 (2004). (Pubitemid 41079896)
-
(2004)
Journal of Clinical Oncology
, vol.22
, Issue.14
, pp. 2790-2799
-
-
Yu, Y.P.1
Landsittel, D.2
Jing, L.3
Nelson, J.4
Ren, B.5
Liu, L.6
McDonald, C.7
Thomas, R.8
Dhir, R.9
Finkelstein, S.10
Michalopoulos, G.11
Becich, M.12
Luo, J.-H.13
-
38
-
-
27644506613
-
Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression
-
DOI 10.1016/j.ccr.2005.10.001, PII S1535610805003053
-
Varambally, S. et al. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 8, 393-406 (2005). (Pubitemid 41579834)
-
(2005)
Cancer Cell
, vol.8
, Issue.5
, pp. 393-406
-
-
Varambally, S.1
Yu, J.2
Laxman, B.3
Rhodes, D.R.4
Mehra, R.5
Tomlins, S.A.6
Shah, R.B.7
Chandran, U.8
Monzon, F.A.9
Becich, M.J.10
Wei, J.T.11
Pienta, K.J.12
Ghosh, D.13
Rubin, M.A.14
Chinnaiyan, A.M.15
-
39
-
-
2142717404
-
Gene expression profiling predicts clinical outcome of prostate cancer
-
DOI 10.1172/JCI200420032
-
Glinsky, G. V., Glinskii, A. B., Stephenson, A. J., Hoffman, R. M. & Gerald, W. L. Gene expression profiling predicts clinical outcome of prostate cancer. J. Clin. Invest. 113, 913-923 (2004). (Pubitemid 38544150)
-
(2004)
Journal of Clinical Investigation
, vol.113
, Issue.6
, pp. 913-923
-
-
Glinsky, G.V.1
Glinskii, A.B.2
Stephenson, A.J.3
Hoffman, R.M.4
Gerald, W.L.5
-
40
-
-
77954255681
-
Integrative genomic profiling of human prostate cancer
-
Taylor, B. S. et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22 (2010).
-
(2010)
Cancer Cell
, vol.18
, pp. 11-22
-
-
Taylor, B.S.1
|