Kim TH, Barrera LO, Zheng M, Qu CX, Singer MA, Richmond TA, Wu YN, Green RD, Ren B: A high-resolution map of active promoters in the human genome. Nature. 2005, 436: 876-880. 10.1038/nature03877
Article
PubMed Central
CAS
PubMed
Google Scholar
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: Genome-wide location and function of DNA binding proteins. Science. 2000, 290: 2306-2309. 10.1126/science.290.5500.2306
Article
CAS
PubMed
Google Scholar
Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ: Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 2002, 16: 235-244. 10.1101/gad.943102
Article
PubMed Central
CAS
PubMed
Google Scholar
Wu J, Smith LT, Plass C, Huang TH: ChIP-on-chip comes of age for genome-wide functional analysis. Cancer Res. 2006, 66: 6899-6902. 10.1158/0008-5472.CAN-06-0276
Article
CAS
PubMed
Google Scholar
Roh TY, Cuddapah S, Cui K, Zhao K: The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci USA. 2006, 103: 15782-15787. 10.1073/pnas.0607617103
Article
PubMed Central
CAS
PubMed
Google Scholar
Loh Y-H, Wu Q, Chew J-J, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong K-Y, Sung KW, Lee CWH, Zhao X-D, Chiu K-P, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei C-L, Ruan Y, Lim B, Ng H-H: The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics. 2006, 38: 431-440. 10.1038/ng1760
Article
CAS
PubMed
Google Scholar
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007, 4: 651-657. 10.1038/nmeth1068
Article
CAS
PubMed
Google Scholar
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K: High-resolution profiling of histone methylations in the human genome. Cell. 2007, 129: 823-837. 10.1016/j.cell.2007.05.009
Article
CAS
PubMed
Google Scholar
Johnson DS, Mortazavi A, Myers RM, Wold B: Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007, 316: 1497-1502. 10.1126/science.1141319
Article
CAS
PubMed
Google Scholar
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: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007, 448: 553-560. 10.1038/nature06008
Article
PubMed Central
CAS
PubMed
Google Scholar
Osborne CK, Schiff R: Estrogen-receptor biology: continuing progress and therapeutic implications. J Clin Oncol. 2005, 23: 1616-1622. 10.1200/JCO.2005.10.036
Article
CAS
PubMed
Google Scholar
Klinge CM: Estrogen receptor interaction with co-activators and co-repressors. Steroids. 2000, 65: 227-251. 10.1016/S0039-128X(99)00107-5
Article
CAS
PubMed
Google Scholar
Jakacka M, Ito M, Weiss J, Chien PY, Gehm BD, Jameson JL: Estrogen Receptor Binding to DNA Is Not Required for Its Activity through the Nonclassical AP1 Pathway. J Biol Chem. 2001, 276: 13615-13621.
CAS
PubMed
Google Scholar
Speir E, Yu ZX, Takeda K, Ferrans VJ, Cannon RO: Competition for p300 regulates transcription by estrogen receptors and nuclear factor-kappaB in human coronary smooth muscle cells. Circ Res. 2000, 87: 1006-1011.
Article
CAS
PubMed
Google Scholar
Abdelrahim A, Samudio I, Smith R, Burghardt R, Safe S: Small inhibitory RNA duplexes for Sp1 mRNA block basal and estrogen-induced gene expression and cell cycle progression in MCF-7 breast cancer cells. J Biol Chem. 2002, 277: 28815-28822. 10.1074/jbc.M203828200
Article
CAS
PubMed
Google Scholar
Gaub MP, Bellard M, Scheuer I, Chambon P, Sassone-Corsi P: Activation of the ovalbumin gene by the estrogen receptor involves the fos-jun complex. Cell. 1990, 63: 1267-1276. 10.1016/0092-8674(90)90422-B
Article
CAS
PubMed
Google Scholar
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: Genome-wide analysis of estrogen receptor binding sites. Nature Genetics. 2006, 38: 1289-1297. 10.1038/ng1901
Article
CAS
PubMed
Google Scholar
Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FCGJ, Span PN, Stunnenberg HG: ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands. EMBO J. 2009, 28: 1418-1428. 10.1038/emboj.2009.88
Article
PubMed Central
CAS
PubMed
Google Scholar
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EGY, Huang PYH, Welboren WJ, Han YY, Ooi HS, Ariyaratne PN, Vega VB, Luo YQ, Tan PY, Choy PY, Wansa KDSA, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li HX, Desai KV, Thomsen JS, Lee YK: An oestrogen-receptor-α-bound human chromatin interactome. Nature. 2009, 462: 58-64. 10.1038/nature08497
Article
PubMed Central
CAS
PubMed
Google Scholar
Fan M, Yan PS, Hartman-Frey C, Chen L, Paik H, Oyer SL, Salisbury JD, Cheng AS, Li L, Abbosh PH, Huang TH, Nephew KP: Diverse gene expression and DNA methylation profiles correlate with differential adaptation of breast cancer cells to the antiestrogens tamoxifen and fulvestrant. Cancer Res. 2006, 66: 11954-11966. 10.1158/0008-5472.CAN-06-1666
Article
CAS
PubMed
Google Scholar
Cheng AS, Jin VX, Fan M, Smith LT, Liyanarachchi S, Yan PS, Leu YW, Chan MW, Plass C, Nephew KP, Davuluri RV, Huang TH: Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell. 2006, 21: 393-404. 10.1016/j.molcel.2005.12.016
Article
CAS
PubMed
Google Scholar
Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV: Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucleic Acids Res. 2004, 32: 6627-6635. 10.1093/nar/gkh1005
Article
PubMed Central
CAS
PubMed
Google Scholar
Leu YW, Yan PS, Fan M, Jin VX, Liu JC, Curran EM, Welshons WV, Wei SH, Plass C, Nephew KP, Huang TH: Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res. 2004, 64: 8184-8192. 10.1158/0008-5472.CAN-04-2045
Article
CAS
PubMed
Google Scholar
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: Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005, 122: 33-43. 10.1016/j.cell.2005.05.008
Article
CAS
PubMed
Google Scholar
Hurtado A, Holmes KA, Geistlinger TR, Hutcheson IR, Nicholson RI, Brown M, Jiang J, Howat WJ, Ali S, Carroll JS: Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen. Nature. 2008, 456: 663-666. 10.1038/nature07483
Article
PubMed Central
CAS
PubMed
Google Scholar
Laganière J, Deblois G, Giguère V: Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor alpha1 gene in breast cancer cells. Mol Endocrinol. 2005, 19: 1584-1592.
Article
PubMed
Google Scholar
Massarweh S, Osborne CK, Creighton CJ, Qin L, Tsimelzon A, Huang S, Weiss H, Rimawi M, Schiff R: Tamoxifen resistance in breast tumors is driven by growth factor receptor signaling with repression of classic estrogen receptor genomic function. Cancer Res. 2008, 68: 826-833. 10.1158/0008-5472.CAN-07-2707
Article
CAS
PubMed
Google Scholar
Wu M, Soler DR, Abba MC, Nunez MI, Baer R, Hatzis C, Llombart-Cussac A, Llombart-Bosch A, Aldaz CM: CtIP silencing as a novel mechanism of tamoxifen resistance in breast cancer. Mol Cancer Res. 2007, 5: 1285-1295. 10.1158/1541-7786.MCR-07-0126
Article
CAS
PubMed
Google Scholar
Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang TH-M: The functional consequences of alternative promoter use in mammalian genomes. Trends in Genetics. 2008, 24: 168-177. 10.1016/j.tig.2008.01.008.
Article
Google Scholar
Carroll JS, Brown M: Estrogen Receptor Target Gene: An Evolving Concept. Molecular Endocrinology. 2006, 20: 1707-1714. 10.1210/me.2005-0334
Article
CAS
PubMed
Google Scholar
Komashko VM, Acevedo LG, Squazzo SL, Iyengar S, Rabinovich A, O'Geen H, Farnham PJ: Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res. 2008, 18: 521-532. 10.1101/gr.074609.107
Article
PubMed Central
CAS
PubMed
Google Scholar
Kinnis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL: Genomic analysis of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Molecular and Cellular Biology. 2007, 27: 5090-5104. 10.1128/MCB.00083-07
Article
Google Scholar
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: Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet. 2007, 3: e87- 10.1371/journal.pgen.0030087
Article
PubMed Central
PubMed
Google Scholar
Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ: Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 2007, 17: 807-817. 10.1101/gr.6006107
Article
PubMed Central
CAS
PubMed
Google Scholar
Jin VX, Apostolos J, Nagisetty NSVR, Farnham PJ: W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics. 2009, 25: 3191-3193. 10.1093/bioinformatics/btp570
Article
PubMed Central
CAS
PubMed
Google Scholar
Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüß M, Reuter I, Schacherer F: TRANSFAC®: an integrated system for gene expression regulation. Nucleic Acids Res. 2000, 28: 316-319. 10.1093/nar/28.1.316
Article
PubMed Central
CAS
PubMed
Google Scholar
Wasserman WW, Sandelin A: Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004, 5: 276-287. 10.1038/nrg1315
Article
CAS
PubMed
Google Scholar
Levy N, Zhao X, Tang H, Jaffe RB, Speed TP, Leitman DC: Multiple transcription factor elements collaborate with estrogen receptor alpha to activate an inducible estrogen response element in the NKG2E gene. Endocrinology. 2007, 148: 3449-3458. 10.1210/en.2006-1632
Article
CAS
PubMed
Google Scholar
Jakacka M, Ito M, Weiss J, Chien PY, Gehm BD, Jameson JL: Estrogen Receptor Binding to DNA Is Not Required for Its Activity through the Nonclassical AP1 Pathway. J Biol Chem. 2001, 276: 13615-13621.
CAS
PubMed
Google Scholar
Carroll JS, Brown M: Estrogen receptor target gene: an evolving concept. Mol Endocrinol. 2006, 20: 1707-1714. 10.1210/me.2005-0334
Article
CAS
PubMed
Google Scholar
Laganière J, Deblois G, Lefebvre C, Bataille AR, Robert F, Giguère V: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci USA. 2005, 102: 11651-11656.
Article
PubMed Central
PubMed
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003, 13: 2498-504. 10.1101/gr.1239303
Article
PubMed Central
CAS
PubMed
Google Scholar
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z: Reconstructing Dynamic Regulatory Maps. Molecular Systems Biology. 2007, 3: 74- 10.1038/msb4100115
Article
PubMed Central
PubMed
Google Scholar
Lemmens K, Dhollander T, Bie TD, Monsieurs P, Engelen K, Smets B, Winderickx J, Moor BD, Marchal K: Inferring transcriptional module networks from ChIP-chip-, motif- and microarray data. Genome Biology. 2006, 7: R37- 10.1186/gb-2006-7-5-r37
Article
PubMed Central
PubMed
Google Scholar
Ross-Innes CS, Stark R, Holmes KA, Schmidt D, Spyrou C, Russell R, Massie CE, Vowler SL, Eldridge M, Carroll JS: Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer. Genes Dev. 2010, 24: 171-182. 10.1101/gad.552910
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009, 4: 44-57. 10.1038/nprot.2008.211.
Article
CAS
Google Scholar
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007, 4: 651-657. 10.1038/nmeth1068
Article
CAS
PubMed
Google Scholar
Frietze S, Lan X, Jin VX, Farnham PJ: Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010, 285: 1393-1403. 10.1074/jbc.M109.063032
Article
PubMed Central
CAS
PubMed
Google Scholar
Fisher RA: On the interpretation of χ2 from contingency tables, and the calculation of P. Journal of the Royal Statistical Society. 1922, 85: 87-94. 10.2307/2340521.
Article
Google Scholar