P-Match: Transcription factor binding site search by combining patterns and weight matrices

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Chekmenev, D S ^a   Haid, C ^a,b   Kel, A E ^a  

^a BIOBASE GMBH   (Germany)

^b SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; DNA;

ACCURACY; ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BINDING SITE; COMPARATIVE STUDY; DATA BASE; DNA SEQUENCE; INTERNET; MEASUREMENT ERROR; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; COMPUTER INTERFACE; COMPUTER PROGRAM; EVALUATION; GENE EXPRESSION REGULATION; GENOMICS; METABOLISM; METHODOLOGY; PROMOTER REGION; ANALYTICAL ERROR; FALSE NEGATIVE RESULT; PROTEIN ANALYSIS; PROTEIN DATABASE; SEARCH ENGINE; TISSUE SPECIFICITY;

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

EID: 23144431724     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki441     Document Type: Article

References (19)

1. Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
2. Kel,A., Kel-Margoulis,O., Borlack,J., Tchekmenev,D. and Wingender,E. (2005) Databases and tools for in silico analysis of regulation of gene expression. In Borlak,J. (ed.), Handbook of Toxicogenomics. VCH Weinheim, pp. 253-290 (ISBN 3-527-30342-1).
3. Matys,V., Fricke,E., Geffers,R., Gößling,E., Haubrock,M., Hehl,R., Homischer,K., Karas,D., Kel,A.E., Kel Margoulis,O. et al. (2003) TRANSFAC®: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
4. Prestridge,D.S. (1996) SIGNAL SCAN 4.0: Additional databases and sequence formats. Comput. Appl. Biosci., 12, 157-160.
5. Chen,Q.K., Hertz,G.Z. and Stormo,G.D. (1995) MATRIX SEARCH 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci., 11, 563-566.
6. Stoeckert,C.J.,Jr, Salas,F., Brunk,B. and Overton,G.C. (1999) EpoDB: A prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res., 27, 200-203.
7. Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
8. 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.
9. Pickert,L., Reuter,I., Klawonn,F. and Wingender,E. (1998) Transcription regulatory region analysis using signal detection and fuzzy clustering. Bioinformatics, 14, 244-251.
10. Kel,A.E., Kondrakhin,Y.V., Kolpakov,Ph.A., Kel,O.V., Romashenko,A.G., Wingender,E., Milanesi,L. and Kolchanov,N.A. (1995) Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 197-205.
11. Bucher,P. (1999) Regulatory elements and expression profiles. Curr. Opin. Struct. Biol., 9,400-407.
12. Fickett,J.W. and Wasserman,W.W. (2000) Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol., 11, 19-24.
13. Conkright,M.D., Guzman,E., Flechner,L., Su,A.I., Hogenesch,J.B. and Montminy,M. (2003) Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol. Cell, 11, 1101-1108.
14. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
15. Gößling,E., Kel-Margoulis,O.V., Kel,A.E. and Wingender,E. (2001) MATCHTM - a tool for searching transcription factor binding sites in DNA sequences. Application for the analysis of human chromosomes. In Proceedings of the German Conference on Bioinformatics GCB'01, October 7-10, Braunschweig, Germany, pp. 158-161.
16. Krull,M., Voss,N., Choi,C., Pistor,S., Potapov,A. and Wingender,E. (2003) TRANSPATH®: An integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res., 31, 97-100.
17. Kel-Margoulis,O.V., Kel,A.E., Reuter,I., Deineko,I.V. and Wingender,E. (2002) TRANSCompel®-a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res., 30, 332-334.
18. Michael,H., Chen,X., Fricke,E., Haubrock,M., Ricanek,R. and Wingender,E. (2004) Deriving an ontology for human gene expression sources from the CYTOMER® database on human organs and cell types. In Silico Biol., 5, 0007.
19. Grabe,N. (2000) AliBaba2: Context specific identification of transcription factor binding sites. In Silico Biol., 1, 0019.