-
1
-
-
2542463869
-
Genome-wide identification of high-affinity estrogen response elements in human and mouse
-
Bourdeau V, Deschenes J, Metivier R, Nagai Y, Nguyen D, Bretschneider N, Gannon F, White JH, Mader S 2004 Genome-wide identification of high-affinity estrogen response elements in human and mouse. Mol Endocrinol 18:1411-1427
-
(2004)
Mol Endocrinol
, vol.18
, pp. 1411-1427
-
-
Bourdeau, V.1
Deschenes, J.2
Metivier, R.3
Nagai, Y.4
Nguyen, D.5
Bretschneider, N.6
Gannon, F.7
White, J.H.8
Mader, S.9
-
2
-
-
22144486551
-
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
-
Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M 2005 Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122:33-43
-
(2005)
Cell
, vol.122
, pp. 33-43
-
-
Carroll, J.S.1
Liu, X.S.2
Brodsky, A.S.3
Li, W.4
Meyer, C.A.5
Szary, A.J.6
Eeckhoute, J.7
Shao, W.8
Hestermann, E.V.9
Geistlinger, T.R.10
Fox, E.A.11
Silver, P.A.12
Brown, M.13
-
3
-
-
0032580207
-
Allosteric effects of DNA on transcriptional regulators
-
Lefstin JA, Yamamoto KR 1998 Allosteric effects of DNA on transcriptional regulators. Nature 392:885-888
-
(1998)
Nature
, vol.392
, pp. 885-888
-
-
Lefstin, J.A.1
Yamamoto, K.R.2
-
4
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
-
Solomon MJ, Larsen PL, Varshavsky A 1988 Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937-947
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
Larsen, P.L.2
Varshavsky, A.3
-
5
-
-
33845925394
-
Chromatin immunoprecipitation and microarray-based analysis of protein location
-
Lee TI, Johnstone SE, Young RA 2006 Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1:729-748
-
(2006)
Nat Protoc
, vol.1
, pp. 729-748
-
-
Lee, T.I.1
Johnstone, S.E.2
Young, R.A.3
-
6
-
-
0037177857
-
Reciprocal recruitment of DRIP/Mediator and p160 coactivator complexes in vivo by estrogen receptor
-
Burakov D, Crofts LA, Chang CP, Freedman LP 2002 Reciprocal recruitment of DRIP/Mediator and p160 coactivator complexes in vivo by estrogen receptor. J Biol Chem 277:14359-14362
-
(2002)
J Biol Chem
, vol.277
, pp. 14359-14362
-
-
Burakov, D.1
Crofts, L.A.2
Chang, C.P.3
Freedman, L.P.4
-
7
-
-
0036208492
-
Formation of the androgen receptor transcription complex
-
Shang Y, Myers M, Brown M 2002 Formation of the androgen receptor transcription complex. Mol Cell 9:601-610
-
(2002)
Mol Cell
, vol.9
, pp. 601-610
-
-
Shang, Y.1
Myers, M.2
Brown, M.3
-
8
-
-
0033637703
-
Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription
-
Shang Y, Hu X, DiRenzo J, Lazar MA, Brown M 2000 Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell 103:843-852
-
(2000)
Cell
, vol.103
, pp. 843-852
-
-
Shang, Y.1
Hu, X.2
DiRenzo, J.3
Lazar, M.A.4
Brown, M.5
-
9
-
-
20844451181
-
Transcriptional complexes engaged by apo-estrogen receptor-α isoforms have divergent outcomes
-
Metivier R, Penot G, Carmouche RP, Hubner MR, Reid G, Denger S, Manu D, Brand H, Kos M, Benes V, Gannon F 2004 Transcriptional complexes engaged by apo-estrogen receptor-α isoforms have divergent outcomes. EMBO J 23:3653-3666
-
(2004)
EMBO J
, vol.23
, pp. 3653-3666
-
-
Metivier, R.1
Penot, G.2
Carmouche, R.P.3
Hubner, M.R.4
Reid, G.5
Denger, S.6
Manu, D.7
Brand, H.8
Kos, M.9
Benes, V.10
Gannon, F.11
-
10
-
-
2642544592
-
Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter
-
Metivier R, Penot G, Hubner MR, Reid G, Brand H, Kos M, Gannon F 2003 Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115:751-763
-
(2003)
Cell
, vol.115
, pp. 751-763
-
-
Metivier, R.1
Penot, G.2
Hubner, M.R.3
Reid, G.4
Brand, H.5
Kos, M.6
Gannon, F.7
-
11
-
-
24044540381
-
Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking
-
Wang Q, Carroll JS, Brown M 2005 Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell 19:631-642
-
(2005)
Mol Cell
, vol.19
, pp. 631-642
-
-
Wang, Q.1
Carroll, J.S.2
Brown, M.3
-
12
-
-
30344478870
-
A global map of p53 transcription-factor binding sites in the human genome
-
Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y 2006 A global map of p53 transcription-factor binding sites in the human genome. Cell 124:207-219
-
(2006)
Cell
, vol.124
, pp. 207-219
-
-
Wei, C.L.1
Wu, Q.2
Vega, V.B.3
Chiu, K.P.4
Ng, P.5
Zhang, T.6
Shahab, A.7
Yong, H.C.8
Fu, Y.9
Weng, Z.10
Liu, J.11
Zhao, X.D.12
Chew, J.L.13
Lee, Y.L.14
Kuznetsov, V.A.15
Sung, W.K.16
Miller, L.D.17
Lim, B.18
Liu, E.T.19
Yu, Q.20
Ng, H.H.21
Ruan, Y.22
more..
-
13
-
-
8644281106
-
A common set of gene regulatory networks links metabolism and growth inhibition
-
Cam H, Balciunaite E, Blais A, Spektor A, Scarpulla RC, Young R, Kluger Y, Dynlacht BD 2004 A common set of gene regulatory networks links metabolism and growth inhibition. Mol Cell 16:399-411
-
(2004)
Mol Cell
, vol.16
, pp. 399-411
-
-
Cam, H.1
Balciunaite, E.2
Blais, A.3
Spektor, A.4
Scarpulla, R.C.5
Young, R.6
Kluger, Y.7
Dynlacht, B.D.8
-
14
-
-
0037080483
-
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints
-
Ren B, Cam H, Takahashi Y, Volkert T, Terragni J, Young RA, Dynlacht BD 2002 E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev 16:245-256
-
(2002)
Genes Dev
, vol.16
, pp. 245-256
-
-
Ren, B.1
Cam, H.2
Takahashi, Y.3
Volkert, T.4
Terragni, J.5
Young, R.A.6
Dynlacht, B.D.7
-
15
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA 2000 Genome-wide location and function of DNA binding proteins. Science 290:2306-2309
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
16
-
-
0037080674
-
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
-
Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ 2002 Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16:235-244
-
(2002)
Genes Dev
, vol.16
, pp. 235-244
-
-
Weinmann, A.S.1
Yan, P.S.2
Oberley, M.J.3
Huang, T.H.4
Farnham, P.J.5
-
17
-
-
33745140886
-
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
-
Bieda M, Xu X, Singer MA, Green R, Farnham PJ 2006 Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 16:595-605
-
(2006)
Genome Res
, vol.16
, pp. 595-605
-
-
Bieda, M.1
Xu, X.2
Singer, M.A.3
Green, R.4
Farnham, P.J.5
-
18
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B 2005 A high-resolution map of active promoters in the human genome. Nature 436:876-880
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
Barrera, L.O.2
Zheng, M.3
Qu, C.4
Singer, M.A.5
Richmond, T.A.6
Wu, Y.7
Green, R.D.8
Ren, B.9
-
19
-
-
34447098370
-
A chromatin landmark and transcription initiation at most promoters in human cells
-
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA 2007 A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77-88
-
(2007)
Cell
, vol.130
, pp. 77-88
-
-
Guenther, M.G.1
Levine, S.S.2
Boyer, L.A.3
Jaenisch, R.4
Young, R.A.5
-
20
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B 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
Wang, W.11
Weng, Z.12
Green, R.D.13
Crawford, G.E.14
Ren, B.15
-
21
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE 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
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
22
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA 2004 Control of pancreas and liver gene expression by HNF transcription factors. Science 303:1378-1381
-
(2004)
Science
, vol.303
, pp. 1378-1381
-
-
Odom, D.T.1
Zizlsperger, N.2
Gordon, D.B.3
Bell, G.W.4
Rinaldi, N.J.5
Murray, H.L.6
Volkert, T.L.7
Schreiber, J.8
Rolfe, P.A.9
Gifford, D.K.10
Fraenkel, E.11
Bell, G.I.12
Young, R.A.13
-
23
-
-
34147173677
-
Expansion of adult β-cell mass in response to increased metabolic demand is dependent on HNF-4α
-
Gupta RK, Gao N, Gorski RK, White P, Hardy OT, Rafiq K, Brestelli JE, Chen G, Stoeckert Jr CJ, Kaestner KH 2007 Expansion of adult β-cell mass in response to increased metabolic demand is dependent on HNF-4α. Genes Dev 21:756-769
-
(2007)
Genes Dev
, vol.21
, pp. 756-769
-
-
Gupta, R.K.1
Gao, N.2
Gorski, R.K.3
White, P.4
Hardy, O.T.5
Rafiq, K.6
Brestelli, J.E.7
Chen, G.8
Stoeckert Jr, C.J.9
Kaestner, K.H.10
-
24
-
-
0242558354
-
Nuclear receptor target gene discovery using high throughput chromatin immunoprecipitation
-
Russell DW, Mangelsdorf DJ, eds, San Diego: Academic Press;
-
Laganière J, Deblois G, Giguère V 2003 Nuclear receptor target gene discovery using high throughput chromatin immunoprecipitation. In: Russell DW, Mangelsdorf DJ, eds. Methods in enzymology. San Diego: Academic Press; 339-350
-
(2003)
Methods in enzymology
, pp. 339-350
-
-
Laganière, J.1
Deblois, G.2
Giguère, V.3
-
25
-
-
22344438888
-
Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor α1 gene in breast cancer cells
-
Laganière J, Deblois G, Giguère V 2005 Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor α1 gene in breast cancer cells. Mol Endocrinol 19:1584-1592
-
(2005)
Mol Endocrinol
, vol.19
, pp. 1584-1592
-
-
Laganière, J.1
Deblois, G.2
Giguère, V.3
-
26
-
-
0028819989
-
Estradiol regulation of the human retinoic acid receptor α gene in human breast carcinoma cells is mediated via an imperfect half-palindromic estrogen response element and Sp1 motifs
-
Rishi AK, Shao ZM, Baumann RG, Li XS, Sheikh MS, Kimura S, Bashirelahi N, Fontana JA 1995 Estradiol regulation of the human retinoic acid receptor α gene in human breast carcinoma cells is mediated via an imperfect half-palindromic estrogen response element and Sp1 motifs. Cancer Res 55:4999-5006
-
(1995)
Cancer Res
, vol.55
, pp. 4999-5006
-
-
Rishi, A.K.1
Shao, Z.M.2
Baumann, R.G.3
Li, X.S.4
Sheikh, M.S.5
Kimura, S.6
Bashirelahi, N.7
Fontana, J.A.8
-
27
-
-
0032230246
-
Estrogen-induced retinoic acid receptor α 1 gene expression: Role of estrogen receptor-Sp1 complex
-
Sun G, Porter W, Safe S 1998 Estrogen-induced retinoic acid receptor α 1 gene expression: role of estrogen receptor-Sp1 complex. Mol Endocrinol 12:882-890
-
(1998)
Mol Endocrinol
, vol.12
, pp. 882-890
-
-
Sun, G.1
Porter, W.2
Safe, S.3
-
28
-
-
33847330324
-
Estrogen receptor regulates expression of the breast cancer 1 associated ring domain 1 (BARD1) gene through intronic DNA sequence
-
Creekmore AL, Ziegler YS, Boney JL, Nardulli AM 2007 Estrogen receptor regulates expression of the breast cancer 1 associated ring domain 1 (BARD1) gene through intronic DNA sequence. Mol Cell Endocrinol 267:106-115
-
(2007)
Mol Cell Endocrinol
, vol.267
, pp. 106-115
-
-
Creekmore, A.L.1
Ziegler, Y.S.2
Boney, J.L.3
Nardulli, A.M.4
-
29
-
-
34250363896
-
Novel estrogen receptor-α binding sites and estradiol target genes identified by chromatin immunoprecipitation cloning in breast cancer
-
Lin Z, Reierstad S, Huang CC, Bulun SE 2007 Novel estrogen receptor-α binding sites and estradiol target genes identified by chromatin immunoprecipitation cloning in breast cancer. Cancer Res 67:5017-5024
-
(2007)
Cancer Res
, vol.67
, pp. 5017-5024
-
-
Lin, Z.1
Reierstad, S.2
Huang, C.C.3
Bulun, S.E.4
-
30
-
-
38749099022
-
Differential regulation of native estrogen receptor regulatory elements by estradiol, tamoxifen, and raloxifene
-
Levy N, Tatomer D, Herber CB, Zhao X, Tang H, Sargeant T, Ball LJ, Summers J, Speed TP, Leitman DC 2008 Differential regulation of native estrogen receptor regulatory elements by estradiol, tamoxifen, and raloxifene. Mol Endocrinol 22:287-303
-
(2008)
Mol Endocrinol
, vol.22
, pp. 287-303
-
-
Levy, N.1
Tatomer, D.2
Herber, C.B.3
Zhao, X.4
Tang, H.5
Sargeant, T.6
Ball, L.J.7
Summers, J.8
Speed, T.P.9
Leitman, D.C.10
-
31
-
-
33748900285
-
Chromatin immunoprecipitation-mediated target identification proved aquaporin 5 is regulated directly by estrogen in the uterus
-
Kobayashi M, Takahashi E, Miyagawa S, Watanabe H, Iguchi T 2006 Chromatin immunoprecipitation-mediated target identification proved aquaporin 5 is regulated directly by estrogen in the uterus. Genes Cells 11:1133-1143
-
(2006)
Genes Cells
, vol.11
, pp. 1133-1143
-
-
Kobayashi, M.1
Takahashi, E.2
Miyagawa, S.3
Watanabe, H.4
Iguchi, T.5
-
32
-
-
23844485897
-
Location analysis of estrogen receptor α target promoters reveals that FOXA1 defines a domain of the estrogen response
-
Laganière J, Deblois G, Lefebvre C, Bataille AR, Robert F, Giguère V 2005 Location analysis of estrogen receptor α target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci USA 102:11651-11656
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 11651-11656
-
-
Laganière, J.1
Deblois, G.2
Lefebvre, C.3
Bataille, A.R.4
Robert, F.5
Giguère, V.6
-
33
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH 2002 Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530-536
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
van't Veer, L.J.1
Dai, H.2
van de Vijver, M.J.3
He, Y.D.4
Hart, A.A.5
Mao, M.6
Peterse, H.L.7
van der Kooy, K.8
Marton, M.J.9
Witteveen, A.T.10
Schreiber, G.J.11
Kerkhoven, R.M.12
Roberts, C.13
Linsley, P.S.14
Bernards, R.15
Friend, S.H.16
-
34
-
-
33750442923
-
Genomewide analysis of estrogen receptor binding sites
-
Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M 2006 Genomewide analysis of estrogen receptor binding sites. Nat Genet 38:1289-1297
-
(2006)
Nat Genet
, vol.38
, pp. 1289-1297
-
-
Carroll, J.S.1
Meyer, C.A.2
Song, J.3
Li, W.4
Geistlinger, T.R.5
Eeckhoute, J.6
Brodsky, A.S.7
Keeton, E.K.8
Fertuck, K.C.9
Hall, G.F.10
Wang, Q.11
Bekiranov, S.12
Sementchenko, V.13
Fox, E.A.14
Silver, P.A.15
Gingeras, T.R.16
Liu, X.S.17
Brown, M.18
-
35
-
-
34347345081
-
Whole-genome cartography of estrogen receptor α binding sites
-
Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET 2007 Whole-genome cartography of estrogen receptor α binding sites. PLoS Genet 3:e87
-
(2007)
PLoS Genet
, vol.3
-
-
Lin, C.Y.1
Vega, V.B.2
Thomsen, J.S.3
Zhang, T.4
Kong, S.L.5
Xie, M.6
Chiu, K.P.7
Lipovich, L.8
Barnett, D.H.9
Stossi, F.10
Yeo, A.11
George, J.12
Kuznetsov, V.A.13
Lee, Y.K.14
Charn, T.H.15
Palanisamy, N.16
Miller, L.D.17
Cheung, E.18
Katzenellenbogen, B.S.19
Ruan, Y.20
Bourque, G.21
Wei, C.L.22
Liu, E.T.23
more..
-
36
-
-
33846659953
-
Sensitive ChIP-DSL technology reveals an extensive estrogen receptor α-binding program on human gene promoters
-
Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan JB, Duan L, Glass CK, Rosenfeld MG, Fu XD 2007 Sensitive ChIP-DSL technology reveals an extensive estrogen receptor α-binding program on human gene promoters. Proc Natl Acad Sci USA 104:4852-4857
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 4852-4857
-
-
Kwon, Y.S.1
Garcia-Bassets, I.2
Hutt, K.R.3
Cheng, C.S.4
Jin, M.5
Liu, D.6
Benner, C.7
Wang, D.8
Ye, Z.9
Bibikova, M.10
Fan, J.B.11
Duan, L.12
Glass, C.K.13
Rosenfeld, M.G.14
Fu, X.D.15
-
37
-
-
34447519218
-
Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters
-
Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL 2007 Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol 27:5090-5104
-
(2007)
Mol Cell Biol
, vol.27
, pp. 5090-5104
-
-
Kininis, M.1
Chen, B.S.2
Diehl, A.G.3
Isaacs, G.D.4
Zhang, T.5
Siepel, A.C.6
Clark, A.G.7
Kraus, W.L.8
-
38
-
-
31544465230
-
Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-α responsive promoters
-
Cheng AS, Jin VX, Fan M, Smith LT, Liyanarachchi S, Yan PS, Leu YW, Chan MW, Plass C, Nephew KP, Davuluri RV, Huang TH 2006 Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-α responsive promoters. Mol Cell 21:393-404
-
(2006)
Mol Cell
, vol.21
, pp. 393-404
-
-
Cheng, A.S.1
Jin, V.X.2
Fan, M.3
Smith, L.T.4
Liyanarachchi, S.5
Yan, P.S.6
Leu, Y.W.7
Chan, M.W.8
Plass, C.9
Nephew, K.P.10
Davuluri, R.V.11
Huang, T.H.12
-
39
-
-
38049007472
-
Genome-wide identification of estrogen receptor α binding sites in mouse liver
-
Gao H, Falt S, Sandelin A, Gustafsson JA, Dahlman-Wright K 2008 Genome-wide identification of estrogen receptor α binding sites in mouse liver. Mol Endocrinol 22:10-22
-
(2008)
Mol Endocrinol
, vol.22
, pp. 10-22
-
-
Gao, H.1
Falt, S.2
Sandelin, A.3
Gustafsson, J.A.4
Dahlman-Wright, K.5
-
40
-
-
9144258171
-
Discovery of estrogen receptor a target genes and response elements in breast tumor cells
-
Lin CY, Strom A, Vega VB, Kong SL, Yeo AL, Thomsen JS, Chan WC, Doray B, Bangarusamy DK, Ramasamy A, Vergara LA, Tang S, Chong A, Bajic VB, Miller LD, Gustafsson JA, Liu ET 2004 Discovery of estrogen receptor a target genes and response elements in breast tumor cells. Genome Biol 5:R66
-
(2004)
Genome Biol
, vol.5
-
-
Lin, C.Y.1
Strom, A.2
Vega, V.B.3
Kong, S.L.4
Yeo, A.L.5
Thomsen, J.S.6
Chan, W.C.7
Doray, B.8
Bangarusamy, D.K.9
Ramasamy, A.10
Vergara, L.A.11
Tang, S.12
Chong, A.13
Bajic, V.B.14
Miller, L.D.15
Gustafsson, J.A.16
Liu, E.T.17
-
41
-
-
33745152719
-
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
-
Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefebvre C, Deblois G, Giguère V, Ferretti V, Bergeron D, Coulombe B, Robert F 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
Laganière, J.5
Lefebvre, C.6
Deblois, G.7
Giguère, V.8
Ferretti, V.9
Bergeron, D.10
Coulombe, B.11
Robert, F.12
-
42
-
-
13544265659
-
Identifying estrogen receptor α target genes using integrated computational genomics and chromatin immunoprecipitation microarray
-
Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV 2004 Identifying estrogen receptor α target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucleic Acids Res 32:6627-6635
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6627-6635
-
-
Jin, V.X.1
Leu, Y.W.2
Liyanarachchi, S.3
Sun, H.4
Fan, M.5
Nephew, K.P.6
Huang, T.H.7
Davuluri, R.V.8
-
43
-
-
8144228848
-
Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes
-
Wang JC, Derynck MK, Nonaka DF, Khodabakhsh DB, Ha C, Yamamoto KR 2004 Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes. Proc Natl Acad Sci USA 101:15603-15608
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 15603-15608
-
-
Wang, J.C.1
Derynck, M.K.2
Nonaka, D.F.3
Khodabakhsh, D.B.4
Ha, C.5
Yamamoto, K.R.6
-
44
-
-
34347324118
-
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor
-
So AY, Chaivorapol C, Bolton EC, Li H, Yamamoto KR 2007 Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet 3:e94
-
(2007)
PLoS Genet
, vol.3
-
-
So, A.Y.1
Chaivorapol, C.2
Bolton, E.C.3
Li, H.4
Yamamoto, K.R.5
-
45
-
-
34547214787
-
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth
-
Wang Q, Li W, Liu XS, Carroll JS, Janne OA, Keeton EK, Chinnaiyan AM, Pienta KJ, Brown M 2007 A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell 27:380-392
-
(2007)
Mol Cell
, vol.27
, pp. 380-392
-
-
Wang, Q.1
Li, W.2
Liu, X.S.3
Carroll, J.S.4
Janne, O.A.5
Keeton, E.K.6
Chinnaiyan, A.M.7
Pienta, K.J.8
Brown, M.9
-
46
-
-
34547931715
-
Cell- and gene-specific regulation of primary target genes by the androgen receptor
-
Bolton EC, So AY, Chaivorapol C, Ha CM, Li H, Yamamoto KR 2007 Cell- and gene-specific regulation of primary target genes by the androgen receptor. Genes Dev 21:2005-2017
-
(2007)
Genes Dev
, vol.21
, pp. 2005-2017
-
-
Bolton, E.C.1
So, A.Y.2
Chaivorapol, C.3
Ha, C.M.4
Li, H.5
Yamamoto, K.R.6
-
47
-
-
35548958147
-
New androgen receptor genomic targets show an interaction with the ETS1 transcription factor
-
Massie CE, Adryan B, Barbosa-Morais NL, Lynch AG, Tran MG, Neal DE, Mills IG 2007 New androgen receptor genomic targets show an interaction with the ETS1 transcription factor. EMBO Rep 8:871-878
-
(2007)
EMBO Rep
, vol.8
, pp. 871-878
-
-
Massie, C.E.1
Adryan, B.2
Barbosa-Morais, N.L.3
Lynch, A.G.4
Tran, M.G.5
Neal, D.E.6
Mills, I.G.7
-
48
-
-
34247554887
-
Genone-wide orchestration of cardiac functions by orphan nucler receptors ERRα and γ
-
Dufour CR, Wilson BJ, Huss JM, Kelly DP, Alaynick WA, Downes M, Evans RM, Blanchette M, Giguère V 2007 Genone-wide orchestration of cardiac functions by orphan nucler receptors ERRα and γ. Cell Metab 5:345-356
-
(2007)
Cell Metab
, vol.5
, pp. 345-356
-
-
Dufour, C.R.1
Wilson, B.J.2
Huss, J.M.3
Kelly, D.P.4
Alaynick, W.A.5
Downes, M.6
Evans, R.M.7
Blanchette, M.8
Giguère, V.9
-
49
-
-
34347259219
-
ERRγ directs and maintains the transition to oxidative metabolism in the post-natal heart
-
Alaynick WA, Kondo RP, Xie W, He W, Dufour CR, Downes M, Jonker JW, Giles W, Naviaux RK, Giguère V, Evans RM 2007 ERRγ directs and maintains the transition to oxidative metabolism in the post-natal heart. Cell Metab 6:16-24
-
(2007)
Cell Metab
, vol.6
, pp. 16-24
-
-
Alaynick, W.A.1
Kondo, R.P.2
Xie, W.3
He, W.4
Dufour, C.R.5
Downes, M.6
Jonker, J.W.7
Giles, W.8
Naviaux, R.K.9
Giguère, V.10
Evans, R.M.11
-
50
-
-
34547643550
-
Nuclear receptor ERRα and coactivator PGC-1β are effectors of IFN-γ induced host defense
-
Sonoda J, Laganière J, Mehl IR, Barish GD, Chong LW, Li X, Scheffler IE, Mock DC, Bataille AR, Robert F, Lee C-H, Giguère V, Evans RM 2007 Nuclear receptor ERRα and coactivator PGC-1β are effectors of IFN-γ induced host defense. Genes Dev 21:1909-1920
-
(2007)
Genes Dev
, vol.21
, pp. 1909-1920
-
-
Sonoda, J.1
Laganière, J.2
Mehl, I.R.3
Barish, G.D.4
Chong, L.W.5
Li, X.6
Scheffler, I.E.7
Mock, D.C.8
Bataille, A.R.9
Robert, F.10
Lee, C.-H.11
Giguère, V.12
Evans, R.M.13
-
51
-
-
34347248013
-
The nuclear receptor ERRα is required for the bioenergetic and functional adaption to cardiac pressure overload
-
Huss JM, Imahashi K-I, Dufour C, Weinheimer CJ, Courtois M, Kovacs A, Giguère V, Murphy E, Kelly DP 2007 The nuclear receptor ERRα is required for the bioenergetic and functional adaption to cardiac pressure overload. Cell Metab 6:25-37
-
(2007)
Cell Metab
, vol.6
, pp. 25-37
-
-
Huss, J.M.1
Imahashi, K.-I.2
Dufour, C.3
Weinheimer, C.J.4
Courtois, M.5
Kovacs, A.6
Giguère, V.7
Murphy, E.8
Kelly, D.P.9
-
54
-
-
36549061004
-
RNA polymerase is poised for activation across the genome
-
Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K 2007 RNA polymerase is poised for activation across the genome. Nat Genet 39:1507-1511
-
(2007)
Nat Genet
, vol.39
, pp. 1507-1511
-
-
Muse, G.W.1
Gilchrist, D.A.2
Nechaev, S.3
Shah, R.4
Parker, J.S.5
Grissom, S.F.6
Zeitlinger, J.7
Adelman, K.8
-
55
-
-
36549013619
-
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
-
Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA 2007 RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39:1512-1516
-
(2007)
Nat Genet
, vol.39
, pp. 1512-1516
-
-
Zeitlinger, J.1
Stark, A.2
Kellis, M.3
Hong, J.W.4
Nechaev, S.5
Adelman, K.6
Levine, M.7
Young, R.A.8
-
56
-
-
22344449669
-
Constructing transcriptional regulatory networks
-
Blais A, Dynlacht BD 2005 Constructing transcriptional regulatory networks. Genes Dev 19:1499-1511
-
(2005)
Genes Dev
, vol.19
, pp. 1499-1511
-
-
Blais, A.1
Dynlacht, B.D.2
-
57
-
-
33845311536
-
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
-
Walhout AJ 2006 Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 16:1445-1454
-
(2006)
Genome Res
, vol.16
, pp. 1445-1454
-
-
Walhout, A.J.1
-
58
-
-
34250369629
-
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
-
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigo R, Gingeras TR, Antonarakis SE, Reymond A 2007 Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17:746-759
-
(2007)
Genome Res
, vol.17
, pp. 746-759
-
-
Denoeud, F.1
Kapranov, P.2
Ucla, C.3
Frankish, A.4
Castelo, R.5
Drenkow, J.6
Lagarde, J.7
Alioto, T.8
Manzano, C.9
Chrast, J.10
Dike, S.11
Wyss, C.12
Henrichsen, C.N.13
Holroyd, N.14
Dickson, M.C.15
Taylor, R.16
Hance, Z.17
Foissac, S.18
Myers, R.M.19
Rogers, J.20
Hubbard, T.21
Harrow, J.22
Guigo, R.23
Gingeras, T.R.24
Antonarakis, S.E.25
Reymond, A.26
more..
-
59
-
-
34250322116
-
-
Trinklein ND, Karaoz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z 2007 Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res 17:720-731
-
Trinklein ND, Karaoz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z 2007 Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res 17:720-731
-
-
-
-
60
-
-
34249098071
-
Mammalian RNA polymerase II core promoters: Insights from genome-wide studies
-
Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA 2007 Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 8:424-436
-
(2007)
Nat Rev Genet
, vol.8
, pp. 424-436
-
-
Sandelin, A.1
Carninci, P.2
Lenhard, B.3
Ponjavic, J.4
Hayashizaki, Y.5
Hume, D.A.6
-
61
-
-
0023904316
-
Action at a distance along a DNA
-
Wang JC, Giaever GN 1988 Action at a distance along a DNA. Science 240:300-304
-
(1988)
Science
, vol.240
, pp. 300-304
-
-
Wang, J.C.1
Giaever, G.N.2
-
62
-
-
0028801067
-
Action at a distance: DNA-looping and initiation of transcription
-
Rippe K, von Hippel PH, Langowski J 1995 Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci 20:500-506
-
(1995)
Trends Biochem Sci
, vol.20
, pp. 500-506
-
-
Rippe, K.1
von Hippel, P.H.2
Langowski, J.3
-
63
-
-
0036898580
-
Long-range chromatin regulatory interactions in vivo
-
Carter D, Chakalova L, Osborne CS, Dai YF, 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
-
64
-
-
0030960672
-
Transcriptional activation by recruitment
-
Ptashne M, Gann A 1997 Transcriptional activation by recruitment. Nature 386:569-577
-
(1997)
Nature
, vol.386
, pp. 569-577
-
-
Ptashne, M.1
Gann, A.2
-
65
-
-
29444448047
-
On a chromosome far, far away: LCRs and gene expression
-
Dean A 2006 On a chromosome far, far away: LCRs and gene expression. Trends Genet 22:38-45
-
(2006)
Trends Genet
, vol.22
, pp. 38-45
-
-
Dean, A.1
-
66
-
-
33645887244
-
Chromatin looping and the probability of transcription
-
Li Q, Barkess G, Qian H 2006 Chromatin looping and the probability of transcription. Trends Genet 22:197-202
-
(2006)
Trends Genet
, vol.22
, pp. 197-202
-
-
Li, Q.1
Barkess, G.2
Qian, H.3
-
67
-
-
0042880630
-
Spatial organization of gene expression: The active chromatin hub
-
de Laat W, Grosveld F 2003 Spatial organization of gene expression: the active chromatin hub. Chromosome Res 11:447-459
-
(2003)
Chromosome Res
, vol.11
, pp. 447-459
-
-
de Laat, W.1
Grosveld, F.2
-
68
-
-
33746228114
-
Interchromosomal interactions and olfactory receptor choice
-
Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R 2006 Interchromosomal interactions and olfactory receptor choice. Cell 126:403-413
-
(2006)
Cell
, vol.126
, pp. 403-413
-
-
Lomvardas, S.1
Barnea, G.2
Pisapia, D.J.3
Mendelsohn, M.4
Kirkland, J.5
Axel, R.6
-
70
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
-
Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348-1354
-
(2006)
Nat Genet
, vol.38
, pp. 1348-1354
-
-
Simonis, M.1
Klous, P.2
Splinter, E.3
Moshkin, Y.4
Willemsen, R.5
de Wit, E.6
van Steensel, B.7
de Laat, W.8
-
71
-
-
34248524473
-
Mapping networks of physical interactions between genomic elements using 5C technology
-
Dostie J, Dekker J 2007 Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2:988-1002
-
(2007)
Nat Protoc
, vol.2
, pp. 988-1002
-
-
Dostie, J.1
Dekker, J.2
-
72
-
-
33749400168
-
Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements
-
Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J 2006 Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16:1299-1309
-
(2006)
Genome Res
, vol.16
, pp. 1299-1309
-
-
Dostie, J.1
Richmond, T.A.2
Arnaout, R.A.3
Selzer, R.R.4
Lee, W.L.5
Honan, T.A.6
Rubio, E.D.7
Krumm, A.8
Lamb, J.9
Nusbaum, C.10
Green, R.D.11
Dekker, J.12
-
73
-
-
35748956435
-
An evaluation of 3C-based methods to capture DNA interactions
-
Simonis M, Kooren J, de Laat W 2007 An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4:895-901
-
(2007)
Nat Methods
, vol.4
, pp. 895-901
-
-
Simonis, M.1
Kooren, J.2
de Laat, W.3
-
74
-
-
40849085514
-
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
-
Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, 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
-
75
-
-
40649106738
-
Interaction of the glucocorticoid receptor with the chromatin landscape
-
John S, Sabo PJ, Johnson TA, Sung MH, Biddie SC, Lightman SL, Voss TC, Davis SR, Meltzer PS, Stamatoyannopoulos JA, Hager GL 2008 Interaction of the glucocorticoid receptor with the chromatin landscape. Mol Cell 29:611-624
-
(2008)
Mol Cell
, vol.29
, pp. 611-624
-
-
John, S.1
Sabo, P.J.2
Johnson, T.A.3
Sung, M.H.4
Biddie, S.C.5
Lightman, S.L.6
Voss, T.C.7
Davis, S.R.8
Meltzer, P.S.9
Stamatoyannopoulos, J.A.10
Hager, G.L.11
|