title: Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods.
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-kappaB 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 previously existing C/EBP matrices, established a model for C/EBP/ NF-kappaB 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).
authors.affiliation: GBF German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany. ksl@gbf.de
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Shelest
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Kel
authors.forename: Ellen
authors.initials: E
authors.lastname: Göessling
authors.forename: Edgar
authors.initials: E
authors.lastname: Wingender
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D022762:CCAAT-Enhancer-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D016384:Consensus Sequence; D017931:DNA Primers; D004847:Epithelial Cells / Q000382:microbiology / Q000502:physiology; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D016328:NF-kappa B / Q000235:genetics* / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000472:pathogenicity / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D022762:CCAAT-Enhancer-Binding Proteins; D017931:DNA Primers; D016328:NF-kappa B