Published online 19 July 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Survey and Summary |
Computational identification of transcriptional regulatory elements in DNA sequence
Research Genetics Division, Rosetta Inpharmatics LLC (a wholly owned subsidiary of Merck & Co., Inc.) 401 Terry Avenue North, Seattle, WA 98109, USA
*Tel: +1 206 802 6430; Fax: +1 206 802 6377; Email: debraj_guhathakurta{at}merck.com
Received March 5, 2006. Accepted April 27, 2006.
Identification and annotation of all the functional elements in the genome, including genes and the regulatory sequences, is a fundamental challenge in genomics and computational biology. Since regulatory elements are frequently short and variable, their identification and discovery using computational algorithms is difficult. However, significant advances have been made in the computational methods for modeling and detection of DNA regulatory elements. The availability of complete genome sequence from multiple organisms, as well as mRNA profiling and high-throughput experimental methods for mapping protein-binding sites in DNA, have contributed to the development of methods that utilize these auxiliary data to inform the detection of transcriptional regulatory elements. Progress is also being made in the identification of cis-regulatory modules and higher order structures of the regulatory sequences, which is essential to the understanding of transcription regulation in the metazoan genomes. This article reviews the computational approaches for modeling and identification of genomic regulatory elements, with an emphasis on the recent developments, and current challenges.
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
G. Li, B. Liu, and Y. Xu Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes Nucleic Acids Res., November 11, 2009; (2009) gkp907v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Miklos, A. Novak, R. Satija, R. Lyngso, and J. Hein Stochastic models of sequence evolution including insertion--deletion events Statistical Methods in Medical Research, October 1, 2009; 18(5): 453 - 485. [Abstract] [PDF] |
||||
![]() |
H. G. Roider, B. Lenhard, A. Kanhere, S. A. Haas, and M. Vingron CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses Nucleic Acids Res., October 1, 2009; 37(19): 6305 - 6315. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. A. F. T. van Hijum, M. H. Medema, and O. P. Kuipers Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation Microbiol. Mol. Biol. Rev., September 1, 2009; 73(3): 481 - 509. [Abstract] [Full Text] [PDF] |
||||
![]() |
U. J. Pape, H. Klein, and M. Vingron Statistical detection of cooperative transcription factors with similarity adjustment Bioinformatics, August 15, 2009; 25(16): 2103 - 2109. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. A. Temiz and C. J. Camacho Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface Nucleic Acids Res., July 1, 2009; 37(12): 4076 - 4088. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Hawkins, C. Grant, W. S. Noble, and T. L. Bailey Assessing phylogenetic motif models for predicting transcription factor binding sites Bioinformatics, June 15, 2009; 25(12): i339 - i347. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Zhang, M. Xu, S. Li, and Z. Su Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes Nucleic Acids Res., June 1, 2009; 37(10): e72 - e72. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Kang, J. H. Chung, and J. Kim Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites Nucleic Acids Res., April 1, 2009; 37(6): 2003 - 2013. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Alon, E. Eisenberg, J. Jacob-Hirsch, G. Rechavi, G. Vatine, R. Toyama, S. L. Coon, D. C. Klein, and Y. Gothilf A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland Bioinformatics, March 1, 2009; 25(5): 559 - 562. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Fauteux, M. Blanchette, and M. V. Stromvik Seeder: discriminative seeding DNA motif discovery Bioinformatics, October 15, 2008; 24(20): 2303 - 2307. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. G. S. da Fonseca, K. S. Guimaraes, and M.-F. Sagot Efficient representation and P-value computation for high-order Markov motifs Bioinformatics, August 15, 2008; 24(16): i160 - i166. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Cordero, M. Botta, and R. A. Calogero Microarray data analysis and mining approaches Brief Funct Genomic Proteomic, January 22, 2008; (2008) elm034v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
X. Wang, J. Gu, M. Q. Zhang, and Y. Li Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species Bioinformatics, January 15, 2008; 24(2): 165 - 171. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Dinkel and H. Sticht A computational strategy for the prediction of functional linear peptide motifs in proteins Bioinformatics, December 15, 2007; 23(24): 3297 - 3303. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. A. Cogburn, T. E. Porter, M. J. Duclos, J. Simon, S. C. Burgess, J. J. Zhu, H. H. Cheng, J. B. Dodgson, and J. Burnside Functional Genomics of the Chicken A Model Organism Poult. Sci., October 1, 2007; 86(10): 2059 - 2094. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. B. Doyon and D. R. Liu Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination Nucleic Acids Res., September 27, 2007; 35(17): 5851 - 5860. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. M. Carlson, A. Chakravarty, C. E. DeZiel, and R. H. Gross SCOPE: a web server for practical de novo motif discovery Nucleic Acids Res., July 13, 2007; 35(suppl_2): W259 - W264. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. Okumura, H. Makiguchi, Y. Makita, R. Yamashita, and K. Nakai Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions Nucleic Acids Res., July 13, 2007; 35(suppl_2): W227 - W231. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Brilli, R. Fani, and P. Lio MotifScorer: using a compendium of microarrays to identify regulatory motifs Bioinformatics, February 15, 2007; 23(4): 493 - 495. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. G. Jegga, J. Chen, S. Gowrisankar, M. A. Deshmukh, R. Gudivada, S. Kong, V. Kaimal, and B. J. Aronow GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs Nucleic Acids Res., January 12, 2007; 35(suppl_1): D116 - D121. [Abstract] [Full Text] [PDF] |
||||





