Prediction of potential C/EBP/NF-κB composite elements using matrix-based search methods

In Silico Biology

Volumn 3, Issue 1-2, 2003, Pages 71-79

  Shelest, Ekaterina ^a,c   Kel, Alexander ^b   Gößling, Ellen ^b   Wingender, Edgar ^b,c  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b BIOBASE GMBH   (Germany)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

Antibacterial response; Composite elements; Promoters; Regulatory sequence signals; Transcription factor binding sites; Transcription factors

Indexed keywords

ALPHA1 GAP JUNCTION PROTEIN; ALPHA5 GAP JUNCTION PROTEIN; APOPTOSIS RELATED PROTEIN 1; BACTERIAL PROTEIN; C REACTIVE PROTEIN; ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1; GRANULOCYTE COLONY STIMULATING FACTOR; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERCELLULAR ADHESION MOLECULE 1; INTERLEUKIN 12BETA; INTERLEUKIN 12P40; INTERLEUKIN 1BETA; INTERLEUKIN 2; INTERLEUKIN 6; INTERLEUKIN 8; KILLER CELL LECTIN LIKE RECEPTOR SUBFAMILY D MEMBER 1; LEUKOCYTE ASSOCIATED IMMUNOGLOBULIN LIKE RECEPTOR 1; LEUKOCYTE ASSOCIATED IMMUNOGLOBULIN LIKE RECEPTOR 2; NITRIC OXIDE SYNTHASE; NUCLEOTIDE; PROTEIN BCL 2; SERUM AMYLOID A1 PROTEIN; SERUM AMYLOID A2 PROTEIN; SERUM AMYLOID A3 PROTEIN; TISSUE PLASMINOGEN ACTIVATOR; TRANSCRIPTION FACTOR; TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 6; UNCLASSIFIED DRUG; UNINDEXED DRUG; ZINC FINGER PROTEIN 137; ZINC FINGER PROTEIN 221;

ANTIBACTERIAL ACTIVITY; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL INFECTION; BINDING SITE; CONFERENCE PAPER; DATA BASE; DNA FLANKING REGION; EPITHELIUM CELL; EXTRACELLULAR MATRIX; GENE CONSTRUCT; GENE IDENTIFICATION; GENE SEQUENCE; GENE TARGETING; GENETIC TRANSCRIPTION; HOST CELL; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROMOTER REGION; PSEUDOMONAS AERUGINOSA; RABBIT; SEQUENCE ANALYSIS;

BASE SEQUENCE; BINDING SITES; CCAAT-ENHANCER-BINDING PROTEINS; CONSENSUS SEQUENCE; DNA PRIMERS; EPITHELIAL CELLS; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; NF-KAPPA B; PSEUDOMONAS AERUGINOSA; TRANSCRIPTION, GENETIC;

EID: 0041386167     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (10)

1. DiMango E., Ratner A. J., Bryan R., Tabibi S. and Prince A. (1998). Activation of NF-kB by adherent Pseudomonas aeruginosa in normal and cystic fibrosis Respuratory epithelial cells. J. Clin. Invest. 101, 2598-2606.
2. Fan, J., Ye, R. D. and Malik, A. B. (2001). Transcriptional mechanisms of acute lung injury. Am. J. Lung Cell Mol. Physiol. 281, L1037-L1050.
3. Goessling, 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.
4. Kel-Margoulis, O. V., Romashchenko, A. G., Kolchanov, N. A., Wingender, E. and Kel, A. E. (2000). COMPEL: A database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res. 28, 311-315.
5. Kel-Margoulis, O. V., Kel, A. E., Goessling, E., Hornischer, K., Levicki-Potapov, B., Tchekmenev, D. and Wingender, E. (2002). Composition-sensitive analysis of the human genome for regulatory signals. (submitted to In Silico Biol.).
6. McNamara, N., Khong, A., McKemy, D., Caterina, M., Boyer, J., Julius, D. and Basbaum, C. (2001). ATP transduces signals from ASGM1, a glycolipid that functions as a bacterial receptor. Proc. Natl. Acad. Sci. USA 98, 9086-9091.
7. Shuman, J. D., Cheong, J. and Colligan, J. E. (1997). ATF-2 and C/EBPalpha can form a heterodimeric DNA binding complex in vitro. Functional implications for transcriptional regulation. J. Biol. Chem. 272, 12793-12800.
8. Smith, R. S., Fedyk, E. R., Springer, T. A., Mukaida, N., Iglewski, B. H. and Phipps, R. P. (2001). IL-8 production in human lung fibroblasts and epithelial cells activated by the Pseudomonas aeruginosa autoinducer N-3-oxodododecanoyl homoserine lactone is transcriptionally regulated by NF-kB and activator protein-2. J. Immunol. 167, 366-374.
9. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhaeuser, R., Pruß, M., Schacherer, F., Thiele, S. and Urbach, S. (2001). The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29, 281-283.
10. Zhang, G. and Ghosh, S. (2001). Toll-like receptor-mediated NF-κB activation: A phylogenetically conserved paradigm in innate immunity. J. Clin. Invest. 107, 13-19.