POBO, transcription factor binding site verification with bootstrapping

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Kankainen, Matti ^a   Holm, Liisa ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; BINDING SITE; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; DOWN REGULATION; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; HUMAN; NONHUMAN; ONLINE SYSTEM; PLANT GENETICS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MICROARRAY; PROTEIN MOTIF; PUBLISHING; RELIABILITY; STATISTICAL ANALYSIS; TRANSGENE; UPREGULATION;

BINDING SITES; GENE EXPRESSION REGULATION; INTERNET; PROMOTER REGIONS (GENETICS); REPRODUCIBILITY OF RESULTS; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 3242887158     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh463     Document Type: Article

References (25)

1. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
2. Lipshutz,R.J., Fodor,S.P.A., Gingeras,T.R. and Lockhart,D.J. (1999) High density synthetic oligonucleotide arrays. Nature Genet., 21, 20-24.
3. Meyer,P. (2001) Chromatin remodeling. Curr. Opin. Plant Biol., 4, 457-462.
4. Meyer,P. (2000) Transcriptional transgene silencing and chromatin components. Plant Mol. Biol., 43, 221-234.
5. Ping,Q. (2003) Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem. Biophys. Res. Commu., 309, 495-501.
6. Kornberg,R.D. (1999) Eukaryotic transcriptional control. Trends Genetics, 15, 46-49.
7. Boardman,P.E., Oliver,S.G. and Hubbard,S.J. (2003) SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences. Nucleic Acids Res., 31, 3572-3575.
8. Thijs,G., Lescot,M., Marchal,K., Rombauts,S., De Moor,B., Rouzé,P. and Moreau Y. (2001) A higher order background model improves the detection of regulatory elements by Gibbs Sampling. Bioinformatics, 17, 1113-1122.
9. Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
10. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, pp. 28-36.
11. Fujibuchi,W., Anderson,J.S. and Landsman,D. (2001) PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches. Nucleic Acids Res., 29, 3988-3996.
12. Vilo,J. (2002) Pattern discovery from biosequences. PhD Thesis, Department of Computer Science, University of Helsinki, Finland. Series of Publications A, Report A-2002-3 Helsinki.
13. van Helden,J., André,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
14. Kreps,J., Budwoth,P., Goff,S. and Wang,R. (2003) Identification of putative plant cold responsive regulatory elements by gene expression profiling and pattern enumeration algorithm. Plant Biotechnol. J., 1, 345-352.
15. Efron,B. and Tibshirani,R.J. (1993) An Introduction to the BootStrap. Chapman & Hall/CRC, New York.
16. Petruccelli,J.D., Nandram,B. and Chen,M. (1999) Applied Statistics for Engineers and Scientists. Prentice-Hall inc, Upper Saddle River, NJ.
17. Huala,E., Dickerman,A.W., Garcia-Hernandez,M., Weems,D., Reiser,L., LaFond,F., Hanley,D., Kiphart,D., Zhuang,M., Huang,W. et al. (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res., 29, 102-105.
18. van helden,J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
19. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
20. Wingender,E., Chen,X., Fricke,E., Geffers,R., Hehl,R., Liebich,I., Krull,M., Matys,V., Michael,H., Ohnhäuser,R., Pruss,M., Schacherer,F., Thiele,S. and Urbach,S. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.
21. Higo,K., Ugawa,Y., Iwamoto,M. and Korenaga,T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res., 27, 297-300.
22. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
23. Eulgem,T., Rushton,P.J., Robatzek,S. and Somssich,I.E. (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci., 5, 199-206.
24. Maleck,K., Levine,A., Eulgem,T., Morgan,A., Schmid,J., Lawton,K.A., Dangl,J.L. and Dietrich,R.A. (2000) The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genet., 26, 403-410.
25. Li,J., Brader,G. and Palva,E.T. (2004) The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell, 16, 319-331.