PromoterPlot: A graphical display of promoter similarities by pattern recognition

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Di Cara, Alessandro ^a   Schmidt, Karsten ^a,b   Hemmings, Brian A ^a   Oakeley, Edward J ^a  

^a FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; CLIENT SERVER APPLICATION; COMPUTER GRAPHICS; COMPUTER PREDICTION; MAMMAL; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEOMICS; ANIMAL; BINDING SITE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE EXPRESSION REGULATION; GENOMICS; HUMAN; INTERNET; METABOLISM; METHODOLOGY; MOUSE; RAT; COMPUTER MODEL; DNA MICROARRAY; GENETIC ALGORITHM; PREDICTION; PROTEIN EXPRESSION; SEARCH ENGINE;

MAMMALIA;

ALGORITHMS; ANIMALS; BINDING SITES; COMPUTER GRAPHICS; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; INTERNET; MICE; PROMOTER REGIONS (GENETICS); RATS; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 23144434533     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki413     Document Type: Article

References (16)

1. Figeys,D. (2004) Combining different 'omics' technologies to map and validate protein-protein interactions in humans. Brief. Funct. Genomic Proteomic, 2, 357-365.
2. Werner,T. (1999) Models for prediction and recognition of eukaryotic promoters. Mamm. Genome, 10, 168-175.
3. Werner,T. (2002) Finding and decrypting of promoters contributes to the elucidation of gene function. In Silico Biol., 2, 23.
4. Maruyama,K. and Sugano,S. (1994) Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene, 138, 171-174.
5. Perier,R.C., Praz,V., Junier,T., Bonnard,C. and Bucher,P. (2000) The eukaryotic promoter database. Nucleic Acids Res, 28, 302-303.
6. 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, 14-17 August, Stanford, CA. AAAI Press, Menlo Park, CA, pp. 28-36.
7. 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.
8. Werner,T. (2000) Identification and functional modeling of DNA sequence elements of transcription. Brief Bioinform., 1, 372-380.
9. Frech,K., Quandt,K. and Werner,T. (1997) Finding protein-binding sites in DNA sequences: The next generation. Trends Biochem. Sci., 22, 103-104.
10. Christoffels,V.M., Grange,T., Kaestner,K.H., Cole,T.J., Darlington,G.J., Croniger,C.M. and Lamers,W.H. (1998) Glucocorticoid receptor, C/EBP, HNF3 and protein kinase A coordinately activate the glucocorticoid response unit of the carbamoylphosphate synthase I gene. Mol. Cell. Biol., 18, 6305-6315.
11. Klingenhoff,A., Frech,K., Quandt,K. and Werner,T. (1999) Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics, 15, 180-186.
12. Klingenhoff,A., Frech,K. and Werner,T. (2000) Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach. In Silico Biol., 2, S17-S26.
13. Kel,A., Kel-Margoulis,O., Babenko,V. and Wingender,E. (1999) Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells. J. Mol. Biol., 288, 353-376.
14. Kel,A., Reymann,S., Matys,V., Nettesheim,P., Wingender,E. and Borlak,J. (2004) A novel computational approach for the prediction of networked transcription factors of aryl hydrocarbon-receptor-regulated genes. Mol. Pharmacol., 66, 1557-1572.
15. Fisher,S. (1962) Use of chi-square in simple cross-over designs. J. Ment. Sci, 108, 406-410.
16. Kel,A.E., Gossling,E., Reuter,I., Cheremushkin,E., Kel-Margoulis,O.V. and Wingender,E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.