McDonnell DP, Norris JD: Connections and regulation of the human estrogen receptor. Science. 2002, 296: 1642-1644. 10.1126/science.1071884
Article
CAS
PubMed
Google Scholar
Ali S, Coombes RC: Estrogen receptor alpha in human breast cancer: occurence and significance. Journal of Mammary Gland Biologic Neoplasia. 2000, 5: 271-281. 10.1023/A:1009594727358.
Article
CAS
Google Scholar
Bjormstrom L, Sjoberg M: Mechanisms of estrogen receptor signaling: convergence of genomic and non-genomic actions on target genes. Molecular Endocrinology. 2005, 19 (4): 833-842. 10.1210/me.2004-0486
Article
Google Scholar
DeNardo DG, Kim H, Hilsenbeck S, Cuba V, Tsimelzon A, Brown P: Global gene expression analysis of estrogen receptor transcription factor cross talk in breast cancer: identification of estrogen-induced/activator protein-1-dependent genes. Molecular Endocrinology. 2005, 19 (2): 362-378.
Article
CAS
PubMed
Google Scholar
Hall JM, Couse JF, Korach KS: The multifaceted mechanisms of estradiol and estrogen receptor signaling. The Journal of Biological Chemistry. 2001, 276: 36869-36872. 10.1074/jbc.R100029200
Article
CAS
PubMed
Google Scholar
Inoue A, Yoshida N, Omoto Y, Oguchi S, Yamori T, Kiyama R, Hayashi S: Development of cDNA microarray for expression profiling of estrogen-responsive genes. Journal of Molecular Endocrinology. 2002, 29: 175-192. 10.1677/jme.0.0290175
Article
CAS
PubMed
Google Scholar
Frasor J, Danes JM, Komm B, Chang KCN, Lyttle R, Katzenellenbogen BS: Profiling of estrogen up- and down-regulated gene expression in human breast cancer cells: insights into gene networks and pathways underlying estrogenic control of proliferation and cell phenotype. Endocrinology. 2003, 144: 4562-4574. 10.1210/en.2003-0567
Article
CAS
PubMed
Google Scholar
Carroll JSMC, 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
Cheung EKW: Genomic analyses of hormone signaling and gene regulation. Annu Rev Physiol. 2010, 72: 191-218. 10.1146/annurev-physiol-021909-135840
Article
CAS
PubMed
Google Scholar
Bar-Joseph ZGG, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK: Computational discovery of gene modules and regulatory networks. Nature Biotechnology. 2003, 21: 1337-1342. 10.1038/nbt890
Article
CAS
PubMed
Google Scholar
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004, 431: 308-312. 10.1038/nature02782
Article
CAS
PubMed
Google Scholar
Sun NCR, Zhao H: Bayesian error analysis model for reconstructing transcriptional regulatory networks. PNAS. 2006, 103: 7988-7993. 10.1073/pnas.0600164103
Article
PubMed Central
CAS
PubMed
Google Scholar
Yu T, Li KC: Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics. 2005, 21: 4033-4038. 10.1093/bioinformatics/bti656
Article
CAS
PubMed
Google Scholar
Xing B, van der Laan M: A causal inference approach for constructing transcriptional regulatory networks. Bioinformatics. 2005, 21: 4007-4013. 10.1093/bioinformatics/bti648
Article
CAS
PubMed
Google Scholar
Xing B, van der Laan M: A statistical method for constructing transcriptional regulatory networks using gene expression and sequence data. Journal of Computational Biology. 2005, 12: 229-246. 10.1089/cmb.2005.12.229
Article
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 Research. 2006, 66 (24): 11954-11966. 10.1158/0008-5472.CAN-06-1666
Article
CAS
PubMed
Google Scholar
Lim YCLL, Desta Z, Zhao Q, Rae JM, Flockhart DA, Skaar TC: Endoxifen, a secondary metabolite of tamoxifen, and 4-OH-tamoxifen induce similar changes in global gene expression patterns in MCF-7 breast cancer cells. J Pharm Exp Ther. 2006, 318: 503-512. 10.1124/jpet.105.100511.
Article
CAS
Google Scholar
Frasor J, Stossi F, Danes JM, Komm B, Lyttle CR, Katzenellenbogen BS: Discrimination of Agonistic versus Antagonistic Activities by Gene Expression Profiling in Breast Cancer Cells. Cancer Research. 2004, 164: 1522-1533.
Article
Google Scholar
Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, Zinser C, Chiusano ML, Traini A, De Bortoli M, Weisz A: Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. American Journal of Pathology. 2010, 176 (5): 2113-2130. 10.2353/ajpath.2010.090837
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002, 298: 799-804. 10.1126/science.1075090
Article
CAS
PubMed
Google Scholar
Neve RMCK, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW: A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 2006, 10: 515-527. 10.1016/j.ccr.2006.10.008
Article
PubMed Central
CAS
PubMed
Google Scholar
Li LCA, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP: A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics. 2006, 22: 2210-2216. 10.1093/bioinformatics/btl329
Article
CAS
PubMed
Google Scholar
Lin ZRS, Huang CC, Bulun SE: Novel estrogen receptor-alpha binding sites and estradiol target genes identified by chromatin immunoprecipitation cloning in breast cancer. 2007, 67: 5017-5024.
CAS
Google Scholar
Lin CY, Ström A, Vega VB, Li KS, Li YA, Thomsen JS, Chan WC, Doray B, Bangarusamy DK, Ramasamy A, Vergara LA, Tang S, Chong A, Bajic VB, Miller LD, Gustafsson J, Liu ET: Discovery of estrogen receptor α target genes and response elements in breast tumor cells. Genome Biology. 2004, 5: R66- 10.1186/gb-2004-5-9-r66
Article
PubMed Central
PubMed
Google Scholar
Cicatiello LMM, Grober OM, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, Zinser C, Chiusano ML, Traini A, De Bortoli M, Weisz A: Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am J Pathol. 2010, 176: 2113-2130. 10.2353/ajpath.2010.090837
Article
PubMed Central
CAS
PubMed
Google Scholar
Welboren W, van Driel MA, Janssen-Megens EM, Sweep FC, Span PN, Stunnenberg HG: ChIP-Seq of ERa and RNA polymerase II defines genes differentially responding to ligands. The EMBO Journal. 2009, 28: 1418-1428. 10.1038/emboj.2009.88
Article
PubMed Central
CAS
PubMed
Google Scholar
Kwon YS G-BI, 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: Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci. 2007, 104: 4852-4857. 10.1073/pnas.0700715104
Article
PubMed Central
CAS
PubMed
Google Scholar
Hua S, Kittler R, White KP: Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer. Cell. 2009, 137: 1259-1271. 10.1016/j.cell.2009.04.043
Article
PubMed Central
PubMed
Google Scholar
De Luca A, Sacchetta P, Nieddu M, Di Ilio C, Favaloro B: Important roles of multiple Sp1 binding sites and epigenetic modifications in the regulation of the methionine sulfoxide reductase B1 (MsrB1) promoter. BMC Molecular Biology. 2007, 8: 39- 10.1186/1471-2199-8-39
Article
PubMed Central
PubMed
Google Scholar
Asangani IARS, Leupold JH, Post S, Allgayer H: NRF-1, and AP-1 regulate the promoter of the human calpain small subunit 1 (CAPNS1) gene. Gene. 2008, 410 (1): 197-206. 10.1016/j.gene.2007.12.009
Article
CAS
PubMed
Google Scholar
Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ: A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Research. 2006, 16 (12): 1585-1596. 10.1101/gr.5520206
Article
PubMed Central
CAS
PubMed
Google Scholar
Wenzel K, Daskalow K, Herse F, Seitz S, Zacharias U, Schenk JA, Schulz H, Hubner N, Micheel B, Schlag PM, Osterziel KJ, Ozcelik C, Scherneck S, Jandrig B: Expression of the protein phosphatase 1 inhibitor KEPI is downregulated in breast cancer cell lines and tissues and involved in the regulation of the tumor suppressor EGR1 via the MEK-ERK pathway. Biological Chemistry. 2007, 388 (5): 489-495. 10.1515/BC.2007.062
Article
CAS
PubMed
Google Scholar
Deblois G, Giguere V: Nuclear Receptor Location Analyses in Mammalian Genomes: From Gene Regulation to Regulatory Networks. Molecular Endocrinology. 2008, 22 (9): 1999-2011. 10.1210/me.2007-0546
Article
CAS
PubMed
Google Scholar
Kininis M, Kraus WL: A global view of transcriptional regulation by nuclear receptors: gene expression, factor localization, and DNA sequence analysis. Nuclear Receptor Signaling. 2008, 6: e005-
PubMed Central
PubMed
Google Scholar
McGarvey KM, Van Neste L, Cope L, Ohm JE, Herman JG, Van Criekinge W, Schuebel KE, Baylin SB: Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells. Cancer Research. 2008, 68 (14): 5753-5759. 10.1158/0008-5472.CAN-08-0700
Article
PubMed Central
CAS
PubMed
Google Scholar
Lupien MEJ, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M: FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell. 2008, 132 (6): 958-970. 10.1016/j.cell.2008.01.018
Article
PubMed Central
CAS
PubMed
Google Scholar
Bracken APDN, Pasini D, Hansen KH, Helin K: Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 2006, 20: 1123-1136. 10.1101/gad.381706
Article
PubMed Central
CAS
PubMed
Google Scholar
Kondo YSL, Cheng AS, Ahmed S, Boumber Y, Charo C, et al.: Gene silencing in cancer by histone H3lysine 27 trimethylation independent of promoter DNA methylation. Nat Genet. 2008, 2008: 741-750.
Article
Google Scholar
McGarvey KMVNL, Cope L, Ohm JE, Herman JG, Van Criekinge W, et al.: Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells. Cancer Res. 2008, 68: 5753-5759. 10.1158/0008-5472.CAN-08-0700
Article
PubMed Central
CAS
PubMed
Google Scholar
Schlesinger YSR, Keshet I, Farkash S, Hecht M, Zimmerman J, et al.: Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genetics. 2007, 39: 232-236. 10.1038/ng1950
Article
CAS
PubMed
Google Scholar
Balch CNK, Huang TH, Bapat SA: Epigenetic "bivalently marked" process of cancer stem cell driven tumorigenesis. Bioessays. 2007, 29: 842-845. 10.1002/bies.20619
Article
PubMed
Google Scholar
Li MPH, Balch C, Kim Y, Li L, Huang TH, Nephew KP, Kim S: Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. Bioinformatics. 2008, 24 (16): 1745-1748. 10.1093/bioinformatics/btn256
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee TI, Johnstone SE, Young RA: Chromatin immunoprecipitation and microarray-based analysis of protein location. Nature Protocol. 2006, 1 (2): 729-748. 10.1038/nprot.2006.98.
Article
CAS
Google Scholar
Feng W, Liu Y, Wu J, Nephew KP, Huang TH, Li L: A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology. BMC Genomics. 2008, 9 (suppl 2): S23- 10.1186/1471-2164-9-S2-S23
Article
PubMed Central
PubMed
Google Scholar
Huang YW, Liu JC, Deatherage DE, Luo J, Mutch DG, Goodfellow PJ, Miller DS, Huang TH: Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer. Cancer Research. 2009, 69 (23): 9038-9046. 10.1158/0008-5472.CAN-09-1499
Article
PubMed Central
CAS
PubMed
Google Scholar
Newton MA KCM, Richmond CS, Blattner FR, Tsui KW: On differential variability of expression ratio: improving statistical inference about gene expression changes from microarray data. Journal of Computational Biology. 2001, 8: 37-52. 10.1089/106652701300099074
Article
CAS
PubMed
Google Scholar
Kendziorski CM, Newton MA, Lan H, Gould MN: On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistic in Medicine. 2003, 22: 3899-3914. 10.1002/sim.1548.
Article
CAS
Google Scholar
Newton MA, Noueiry A, Sarkar D, Ahlquist P: Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics. 2004, 5 (2): 155-176. 10.1093/biostatistics/5.2.155
Article
PubMed
Google Scholar
Johnson WE, Li W, Meyer CA, Gottardo R, Brown M, Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. PNAS. 2006, 103 (33): 12457-12462. 10.1073/pnas.0601180103
Article
PubMed Central
CAS
PubMed
Google Scholar
Ohler U, Niemann H: Identification and analysis of eukaryotic promoters: recent computational approaches. Trends in Genetics. 2001, 17: 56-60. 10.1016/S0168-9525(00)02174-0
Article
CAS
PubMed
Google Scholar
Efron B, Tibshirani R, Storey JD, Tusher VG: Empirical Bayes Analysis of a Microarray Experiment. Journal of the American Statistical Association. 2001, 96: 1151-1160. 10.1198/016214501753382129.
Article
Google Scholar