A steganalysis-based approach to comprehensive ide...[Genome Biol. 2006]

SearchDatabase nameforSearch term

Advanced Search

Your browser version may not work well with NCBI's Web applications. More information here...

Display Show

All: 1

Review: 0

Click to change filter selection through MyNCBI.

1: Genome Biol. 2006;7(6):R49. Links

A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements.

Wang G, Zhang W.

Department of Computer Science and Engineering, Washington University, St, Louis, MO 63130, USA.

The comprehensive identification of cis-regulatory elements on a genome scale is a challenging problem. We develop a novel, steganalysis-based approach for genome-wide motif finding, called WordSpy, by viewing regulatory regions as a stegoscript with cis-elements embedded in 'background' sequences. We apply WordSpy to the promoters of cell-cycle-related genes of Saccharomyces cerevisiae and Arabidopsis thaliana, identifying all known cell-cycle motifs with high ranking. WordSpy can discover a complete set of cis-elements and facilitate the systematic study of regulatory networks.

PMID: 16787547 [PubMed - indexed for MEDLINE]

PMCID: PMC1779545

WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar.
Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W412-6.

[Nucleic Acids Res. 2005]
XcisClique: analysis of regulatory bicliques.
BMC Bioinformatics. 2006 Apr 21; 7:218. Epub 2006 Apr 21.

[BMC Bioinformatics. 2006]
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome.
Proc Natl Acad Sci U S A. 2005 Nov 29; 102(48):17400-5. Epub 2005 Nov 21.

[Proc Natl Acad Sci U S A. 2005]
ReviewIdentification of cis-regulatory elements in gene co-expression networks using A-GLAM.
Methods Mol Biol. 2009; 541:1-22.

[Methods Mol Biol. 2009]
ReviewComputational identification of transcriptional regulatory elements in DNA sequence.
Nucleic Acids Res. 2006; 34(12):3585-98. Epub 2006 Jul 19.

[Nucleic Acids Res. 2006]
» See reviews... | » See all...

Cited by 6 PubMed Central articles

Identification of novel and candidate miRNAs in rice by high throughput sequencing.
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. BMC Plant Biol. 2008 Feb 29; 8:25. Epub 2008 Feb 29.

[BMC Plant Biol. 2008]
Generic eukaryotic core promoter prediction using structural features of DNA.
Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y. Genome Res. 2008 Feb; 18(2):310-23. Epub 2007 Dec 20.

[Genome Res. 2008]
fREDUCE: detection of degenerate regulatory elements using correlation with expression.
Wu RZ, Chaivorapol C, Zheng J, Li H, Liang S. BMC Bioinformatics. 2007 Oct 17; 8:399. Epub 2007 Oct 17.

[BMC Bioinformatics. 2007]
» See all...

Recent Activity

Clear Turn Off Turn On

A steganalysis-based approach to comprehensive identification and characterization of func...A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements.

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Display Show

A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements.

Related articles

Cited by 6 PubMed Central articles

Recent Activity