- Article -
| In Silico Biology 3, 0007 (2003); ©2002, Bioinformation Systems e.V. |
Prediction of potential C/EBP/NF-
B composite elements using matrix-based search methods
Ekaterina Shelest 1,3,*, Alexander Kel 2, Ellen Gößling 2 and Edgar Wingender 1, 2
1 GBF German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany;
2 BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany;
3 permanent address: Institute of Cytology and Genetics SB RAN, Lavrentyev pr.,10, 630090, Novosibirsk, Russia
Email: ksl@gbf.de
* corresponding author
Edited by N. Mermod; received September 23, 2002; revised and accepted November 19, 2002; published December 08,2002
Abstract
Bacterial infections trigger a wide range of host cell responses. For the interaction of Pseudomonas aeruginosa and epithelial cells it is known that transcription factor NF-
B plays a central role, but its effects have to be specified by cooperation with additional factors. NF-B containing composite elements, e. g. with C/EBP, may be appropriate indicators for new antibacterial response genes. We refined matrix-based search methods for C/EBP, which was necessary because of weak consensi of the previosly existing C/EBP matrices, established a model for C/EBP/ NF-B composite element, used it for scanning all known human 5'-flanking sequences and identified 135 new candidate genes. The newly constructed C/EBP binding patterns will be available with one of the next releases of the TRANSFAC database (http://www.gene-regulation.de).
Key words: promoters, regulatory sequence signals, transcription factors, transcription factor binding sites, composite elements, antibacterial response