Skip Navigation

Nucleic Acids Research 2004 32(22):6627-6635; doi:10.1093/nar/gkh1005
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (280K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (20)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Jin, V. X.
Right arrow Articles by Davuluri, R. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jin, V. X.
Right arrow Articles by Davuluri, R. V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 17 December 2004

Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved

Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray

Victor X. Jin, Yu-Wei Leu, Sandya Liyanarachchi, Hao Sun, Meiyun Fan1, Kenneth P. Nephew1, Tim H.-M. Huang and Ramana V. Davuluri*

Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA and 1 Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA

* To whom correspondence should be addressed. Tel: +1 614 688 3088; Fax: +1 614 688 4006; Email: davuluri-1{at}medctr.osu.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received September 24, 2004; Revised November 8, 2004; Accepted November 29, 2004

The estrogen receptor {alpha} (ER{alpha}) regulates gene expression by either direct binding to estrogen response elements or indirect tethering to other transcription factors on promoter targets. To identify these promoter sequences, we conducted a genome-wide screening with a novel microarray technique called ChIP-on-chip. A set of 70 candidate ER{alpha} loci were identified and the corresponding promoter sequences were analyzed by statistical pattern recognition and comparative genomics approaches. We found mouse counterparts for 63 of these loci and classified 42 (67%) as direct ER{alpha} targets using classification and regression tree (CART) statistical model, which involves position weight matrix and human-mouse sequence similarity scores as model parameters. The remaining genes were considered to be indirect targets. To validate this computational prediction, we conducted an additional ChIP-on-chip assay that identified acetylated chromatin components in active ER{alpha} promoters. Of the 27 loci upregulated in an ER{alpha}-positive breast cancer cell line, 20 having mouse counterparts were correctly predicted by CART. This integrated approach, therefore, sets a paradigm in which the iterative process of model refinement and experimental verification will continue until an accurate prediction of promoter target sequences is derived.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
B. Tokovenko, R. Golda, O. Protas, M. Obolenskaya, and A. El'skaya
COTRASIF: conservation-aided transcription-factor-binding site finder
Nucleic Acids Res., April 1, 2009; 37(7): e49 - e49.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
G. Deblois and V. Giguere
Nuclear Receptor Location Analyses in Mammalian Genomes: From Gene Regulation to Regulatory Networks
Mol. Endocrinol., September 1, 2008; 22(9): 1999 - 2011.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
L. Bethke, A. Murray, E. Webb, M. Schoemaker, K. Muir, P. McKinney, S. Hepworth, P. Dimitropoulou, A. Lophatananon, M. Feychting, et al.
Comprehensive Analysis of DNA Repair Gene Variants and Risk of Meningioma
J Natl Cancer Inst, February 20, 2008; 100(4): 270 - 276.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
N. Levy, D. Tatomer, C. B. Herber, X. Zhao, H. Tang, T. Sargeant, L. J. Ball, J. Summers, T. P. Speed, and D. C. Leitman
Differential Regulation of Native Estrogen Receptor-Regulatory Elements by Estradiol, Tamoxifen, and Raloxifene
Mol. Endocrinol., February 1, 2008; 22(2): 287 - 303.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
M. Kininis, B. S. Chen, A. G. Diehl, G. D. Isaacs, T. Zhang, A. C. Siepel, A. G. Clark, and W. L. Kraus
Genomic Analyses of Transcription Factor Binding, Histone Acetylation, and Gene Expression Reveal Mechanistically Distinct Classes of Estrogen-Regulated Promoters
Mol. Cell. Biol., July 15, 2007; 27(14): 5090 - 5104.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
R. Kulshreshtha, M. Ferracin, S. E. Wojcik, R. Garzon, H. Alder, F. J. Agosto-Perez, R. Davuluri, C.-G. Liu, C. M. Croce, M. Negrini, et al.
A MicroRNA Signature of Hypoxia
Mol. Cell. Biol., March 1, 2007; 27(5): 1859 - 1867.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L. Elnitski, V. X. Jin, P. J. Farnham, and S. J.M. Jones
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
Genome Res., December 1, 2006; 16(12): 1455 - 1464.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
V. X. Jin, A. Rabinovich, S. L. Squazzo, R. Green, and P. J. Farnham
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1
Genome Res., December 1, 2006; 16(12): 1585 - 1595.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Li, A. S. L. Cheng, V. X. Jin, H. H. Paik, M. Fan, X. Li, W. Zhang, J. Robarge, C. Balch, R. V. Davuluri, et al.
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-{alpha}
Bioinformatics, September 15, 2006; 22(18): 2210 - 2216.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
J. A. Fretz, L. A. Zella, S. Kim, N. K. Shevde, and J. W. Pike
1,25-Dihydroxyvitamin D3 Regulates the Expression of Low-Density Lipoprotein Receptor-Related Protein 5 via Deoxyribonucleic Acid Sequence Elements Located Downstream of the Start Site of Transcription
Mol. Endocrinol., September 1, 2006; 20(9): 2215 - 2230.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L.-W. Chang, R. Nagarajan, J. A. Magee, J. Milbrandt, and G. D. Stormo
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles
Genome Res., March 1, 2006; 16(3): 405 - 413.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Sun, S. K. Palaniswamy, T. T. Pohar, V. X. Jin, T. H.-M. Huang, and R. V. Davuluri
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D98 - D103.
[Abstract] [Full Text] [PDF]

Home page
 J Mol EndocrinolHome page
V X Jin, H Sun, T T Pohar, S Liyanarachchi, S K Palaniswamy, T H-M Huang, and R V Davuluri
ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes
J. Mol. Endocrinol., October 1, 2005; 35(2): 225 - 230.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.