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PubMed · 12762847

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

Ekaterina Shelest·Alexander E Kel·Ellen Göessling·Edgar Wingender
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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).

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Base SequenceBinding SitesCCAAT-Enhancer-Binding ProteinsConsensus SequenceDNA PrimersEpithelial CellsGene Expression RegulationGenome, HumanHumansNF-kappa BPseudomonas aeruginosaTranscription, GeneticJournal ArticleResearch Support, Non-U.S. Gov't

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Ekaterina Shelest, Alexander E Kel, Ellen Göessling, Edgar Wingender. 2002-12-08. Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods.. https://pubmed.ncbi.nlm.nih.gov/12762847/

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