Construction of predictive promoter models on the example of antibacterial response of human epithelial cells : Research / Ekaterina Shelest and Edgar Wingender

Background: Binding of a bacteria to a eukaryotic cell triggers a complex network of interactions in and between both cells. P. aeruginosa is a pathogen that causes acute and chronic lung infections by interacting with the pulmonary epithelial cells. We use this example for examining the ways of triggering the response of the eukaryotic cell(s), leading us to a better understanding of the details of the inflammatory process in general.Results: Considering a set of genes co-expressed during the antibacterial response of human lung epithelial cells, we constructed a promoter model for the search of additional target genes potentially involved in the same cell response. The model construction is based on the consideration of pair-wise combinations of transcription factor binding sites (TFBS). It has been shown that the antibacterial response of human epithelial cells is triggered by at least two distinct pathways. We therefore supposed that there are two subsets of promoters activated by each of them. Optimally, they should be "complementary" in the sense of appearing in complementary subsets of the (+)-training set. We developed the concept of complementary pairs, i.e., two mutually exclusive pairs of TFBS, each of which should be found in one of the two complementary subsets.

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Persons: Shelest, Ekaterina [Other]; Wingender, Edgar [Other]
Format: eArticle
Part of:Theoretical biology and medical modelling 2(2005), 2, Seite 1-19
Physical description:Online-Ressource (PDF-Datei: 19 S., 443,32 KB)