Genome Research International Con Genetics

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Research Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Halfon, M. S.
Right arrow Articles by Michelson, A. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Halfon, M. S.
Right arrow Articles by Michelson, A. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 7, 1019-1028, July 2002

Computation-Based Discovery of Related Transcriptional Regulatory Modules and Motifs Using an Experimentally Validated Combinatorial Model

Marc S. Halfon,1,4 Yonatan Grad,2,4 George M. Church,2 and Alan M. Michelson1,3

1 Howard Hughes Medical Institute and Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; 2 Department of Genetics and Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

Gene expression is regulated by transcription factors that interact with cis-regulatory elements. Predicting these elements from sequence data has proven difficult. We describe here a successful computational search for elements that direct expression in a particular temporal-spatial pattern in the Drosophila embryo, based on a single well characterized enhancer model. The fly genome was searched to identify sequence elements containing the same combination of transcription factors as those found in the model. Experimental evaluation of the search results demonstrates that our method can correctly predict regulatory elements and highlights the importance of functional testing as a means of identifying false-positive results. We also show that the search results enable the identification of additional relevant sequence motifs whose functions can be empirically validated. This approach, combined with gene expression and phylogenetic sequence data, allows for genome-wide identification of related regulatory elements, an important step toward understanding the genetic regulatory networks involved in development.

[Sequence data reported in this paper have been deposited in GenBank with accession nos. AF513981 (Eve MHE) and AF513982 (Hbr DME). Supplementary material is available online at http://www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: R. Blackman]

3 Corresponding author.

4 These authors contributed equally to this work.

12:1019-1028 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. Hu, H. Hu, and X. Li
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs
Nucleic Acids Res., July 7, 2008; (2008) gkn407v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Gotea and I. Ovcharenko
DiRE: identifying distant regulatory elements of co-expressed genes
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W133 - W139.
[Abstract] [Full Text] [PDF]

Home page
 DevelopmentHome page
L. Dubois, J. Enriquez, V. Daburon, F. Crozet, G. Lebreton, M. Crozatier, and A. Vincent
collier transcription in a single Drosophila muscle lineage: the combinatorial control of muscle identity
Development, December 15, 2007; 134(24): 4347 - 4355.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. L. Maeder, B. J. Polansky, B. E. Robson, and D. A. Eastman
Phylogenetic Footprinting Analysis in the Upstream Regulatory Regions of the Drosophila Enhancer of split Genes
Genetics, November 1, 2007; 177(3): 1377 - 1394.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. W. Siggers and B. Honig
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry
Nucleic Acids Res., February 28, 2007; 35(4): 1085 - 1097.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Chowdhary, S. L. Tan, R. A. Ali, B. Boerlage, L. Wong, and V. B Bajic
Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures
Bioinformatics, September 15, 2006; 22(18): 2310 - 2312.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Sinha, Y. Liang, and E. Siggia
Stubb: a program for discovery and analysis of cis-regulatory modules.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W555 - W559.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. D. Cohen, A. Klingenhoff, A. Boucherot, A. Nitsche, A. Henger, B. Brunner, H. Schmid, M. Merkle, M. A. Saleem, K.-P. Koller, et al.
Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins
PNAS, April 11, 2006; 103(15): 5682 - 5687.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
E. J. Ostrin, Y. Li, K. Hoffman, J. Liu, K. Wang, L. Zhang, G. Mardon, and R. Chen
Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless
Genome Res., April 1, 2006; 16(4): 466 - 476.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
G. Junion, T. Jagla, S. Duplant, R. Tapin, J.-P. Da Ponte, and K. Jagla
Mapping Dmef2-binding regulatory modules by using a ChIP-enriched in silico targets approach
PNAS, December 20, 2005; 102(51): 18479 - 18484.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Qian, N. Esumi, Y. Chen, Q. Wang, I. Chowers, and D. J. Zack
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation
Nucleic Acids Res., June 20, 2005; 33(11): 3479 - 3491.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. Levine and E. H. Davidson
From the Cover@;DELIM@;Gene Regulatory Networks Special Feature: Gene regulatory networks for development
PNAS, April 5, 2005; 102(14): 4936 - 4942.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. Sinha and E. D. Siggia
Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila
Mol. Biol. Evol., April 1, 2005; 22(4): 874 - 885.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. D. Buchanan, P. E. Klein, and J. E. Mullet
Phylogenetic Analysis of 5'-Noncoding Regions From the ABA-Responsive rab16/17 Gene Family of Sorghum, Maize and Rice Provides Insight Into the Composition, Organization and Function of cis-Regulatory Modules
Genetics, November 1, 2004; 168(3): 1639 - 1654.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. L. Smith, W. J. Freebern, I. Collins, A. De Siervi, I. Montano, C. M. Haggerty, M. C. McNutt, W. G. Butscher, I. Dzekunova, D. W. Petersen, et al.
Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment
PNAS, August 10, 2004; 101(32): 11554 - 11559.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Kreiman
Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes
Nucleic Acids Res., May 20, 2004; 32(9): 2889 - 2900.
[Abstract] [Full Text] [PDF]

Home page
 DevelopmentHome page
M. Markstein, R. Zinzen, P. Markstein, K.-P. Yee, A. Erives, A. Stathopoulos, and M. Levine
A regulatory code for neurogenic gene expression in the Drosophila embryo
Development, May 15, 2004; 131(10): 2387 - 2394.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. W. Tullai, M. E. Schaffer, S. Mullenbrock, S. Kasif, and G. M. Cooper
Identification of Transcription Factor Binding Sites Upstream of Human Genes Regulated by the Phosphatidylinositol 3-Kinase and MEK/ERK Signaling Pathways
J. Biol. Chem., May 7, 2004; 279(19): 20167 - 20177.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. L. Bulyk, A. M. McGuire, N. Masuda, and G. M. Church
A Motif Co-Occurrence Approach for Genome-Wide Prediction of Transcription-Factor-Binding Sites in Escherichia coli
Genome Res., February 1, 2004; 14(2): 201 - 208.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. M. Gutierrez-Rios, D. A. Rosenblueth, J. A. Loza, A. M. Huerta, J. D. Glasner, F. R. Blattner, and J. Collado-Vides
Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles
Genome Res., November 1, 2003; 13(11): 2435 - 2443.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh
Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells
Genome Res., May 1, 2003; 13(5): 773 - 780.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Zheng, J. Wu, and Z. Sun
An approach to identify over-represented cis-elements in related sequences
Nucleic Acids Res., April 1, 2003; 31(7): 1995 - 2005.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. P. Lifanov, V. J. Makeev, A. G. Nazina, and D. A. Papatsenko
Homotypic Regulatory Clusters in Drosophila
Genome Res., April 1, 2003; 13(4): 579 - 588.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Aerts, G. Thijs, B. Coessens, M. Staes, Y. Moreau, and B. D. Moor
Toucan: deciphering the cis-regulatory logic of coregulated genes
Nucleic Acids Res., March 15, 2003; 31(6): 1753 - 1764.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
P. Sudarsanam, Y. Pilpel, and G. M. Church
Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA Transcription Motifs in Saccharomyces cerevisiae
Genome Res., November 1, 2002; 12(11): 1723 - 1731.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
M. S. Halfon and A. M. Michelson
Exploring genetic regulatory networks in metazoan development: methods and models
Physiol Genomics, September 3, 2002; 10(3): 131 - 143.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.