Genome Research

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


     

Published online before print December 12, 2003, 10.1101/gr.1739204
Genome Res. 14:99-108, 2004
©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04 $5.00
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow HTML Page - index.htslp
Right arrow All Versions of this Article:
1739204v1
14/1/99    most recent
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 Pritsker, M.
Right arrow Articles by Tavazoie, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pritsker, M.
Right arrow Articles by Tavazoie, S.
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?

Letter

Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation

Moshe Pritsker1, Yir-Chung Liu1,2, Michael A. Beer1,2 and Saeed Tavazoie1,2,3

1 Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA 2 The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA

Comprehensive identification of DNA cis-regulatory elements is crucial for a predictive understanding of transcriptional network dynamics. Strong evidence suggests that these DNA sequence motifs are highly conserved between related species, reflecting strong selection on the network of regulatory interactions that underlie common cellular behavior. Here, we exploit a systems-level aspect of this conservation—the network-level topology of these interactions—to map transcription factor (TF) binding sites on a genomic scale. Using network-level conservation as a constraint, our algorithm finds 71% of known TF binding sites in the yeast Saccharomyces cerevisiae, using only 12% of the sequence of a phylogenetic neighbor. Most of the novel predicted motifs show strong features of known TF binding sites, such as functional category and/or expression profile coherence of their corresponding genes. Network-level conservation should provide a powerful constraint for the systematic mapping of TF binding sites in the larger genomes of higher eukaryotes.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1739204. Article published online before print in December 2003.

3 Corresponding author.
E-MAIL tavazoie{at}princeton.edu; FAX (609) 258-1701.

[Supplemental material is available online at www.genome.org.]


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
 BioinformaticsHome page
L. D. Ward and H. J. Bussemaker
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
Bioinformatics, July 1, 2008; 24(13): i165 - i171.
[Abstract] [PDF]

Home page
 BioinformaticsHome page
S. Hannenhalli
Eukaryotic transcription factor binding sites--modeling and integrative search methods
Bioinformatics, June 1, 2008; 24(11): 1325 - 1331.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
D. Ju, X. Wang, H. Xu, and Y. Xie
Genome-Wide Analysis Identifies MYND-Domain Protein Mub1 as an Essential Factor for Rpn4 Ubiquitylation
Mol. Cell. Biol., February 15, 2008; 28(4): 1404 - 1412.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Yang, P.T. Foteinou, K.R. King, M.L. Yarmush, and I.P. Androulakis
A novel non-overlapping bi-clustering algorithm for network generation using living cell array data
Bioinformatics, September 1, 2007; 23(17): 2306 - 2313.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Segal, M. Lapidot, Z. Solan, E. Ruppin, Y. Pilpel, and D. Horn
Nucleotide variation of regulatory motifs may lead to distinct expression patterns
Bioinformatics, July 1, 2007; 23(13): i440 - i449.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. H. Cheung, K. K. B. Barthel, Y. L. Kwan, and X. Liu
Identifying pattern-defined regulatory islands in mammalian genomes
PNAS, June 12, 2007; 104(24): 10116 - 10121.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
L.-C. Lai, A. L. Kosorukoff, P. V. Burke, and K. E. Kwast
Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae.
Eukaryot. Cell, September 1, 2006; 5(9): 1468 - 1489.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. GuhaThakurta
Computational identification of transcriptional regulatory elements in DNA sequence
Nucleic Acids Res., July 19, 2006; 34(12): 3585 - 3598.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
A. A. Sharov, D. B. Dudekula, and M. S. H. Ko
CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome
DNA Res, January 1, 2006; 13(3): 123 - 134.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
K. Dolinski and D. Botstein
Changing perspectives in yeast research nearly a decade after the genome sequence
Genome Res., December 1, 2005; 15(12): 1611 - 1619.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. Wang and G. D. Stormo
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
PNAS, November 29, 2005; 102(48): 17400 - 17405.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
X. Li, S. Zhong, and W. H. Wong
Reliable prediction of transcription factor binding sites by phylogenetic verification
PNAS, November 22, 2005; 102(47): 16945 - 16950.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Yu and K.-C. Li
Inference of transcriptional regulatory network by two-stage constrained space factor analysis
Bioinformatics, November 1, 2005; 21(21): 4033 - 4038.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. A. Notebaart, M. A. Huynen, B. Teusink, R. J. Siezen, and B. Snel
Correlation between sequence conservation and the genomic context after gene duplication
Nucleic Acids Res., October 27, 2005; 33(19): 6164 - 6171.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
G. Balazsi, A.-L. Barabasi, and Z. N. Oltvai
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
PNAS, May 31, 2005; 102(22): 7841 - 7846.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
A. Tanay, A. Regev, and R. Shamir
Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
PNAS, May 17, 2005; 102(20): 7203 - 7208.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
L.-C. Lai, A. L. Kosorukoff, P. V. Burke, and K. E. Kwast
Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae: Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media
Mol. Cell. Biol., May 15, 2005; 25(10): 4075 - 4091.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
C.-S. Chin, J. H. Chuang, and H. Li
Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence
Genome Res., February 1, 2005; 15(2): 205 - 213.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.
Copyright © 2004 by Cold Spring Harbor Laboratory Press.