University of Natural Resources and Life Sciences, Vienna (BOKU) - Research portal

Logo BOKU Resarch Portal

Gewählte Master / Diploma Thesis:

Bernd Fuhrmann (2007): Microarray analysis of murine Tyk2-knockout peritoneal macrophages treated with LPS.
Master / Diploma Thesis, BOKU-Universität für Bodenkultur, pp 50. UB BOKU obvsg

Data Source: ZID Abstracts
A database was developed for analysing gene expression data. These were obtained from a microarray experiment, where the gene expression levels of peritoneal macrophages in reaction to lipopolysaccharide (LPS) treatment were compared between wildtype and Tyk2-knockout mice. For each gene in our analysis, a linear regression model was applied to relate the expression data to the effects of the genotype (wildtype vs. Tyk2-knockout), the LPS-treatment (treated vs. untreated) and the interaction between genotype and LPS-treatment. Furthermore, the database contained sequence data and annotation of genes orthologous between human and mouse. These were used for determining conserved putative functional regulatory motifs by a phylogenetic footprinting approach in 5' upstream regions, corresponding to putative transcription factor binding sites, and in 3' untranslated regions, corresponding to putative microRNA binding sites. Additionally, information from the Gene Ontology (GO) database was integrated, which classifies genes according to three organizing principles: "biological process", "molecular function" and "cellular component". The results from the regression model were combined with the data from the motif search and the GO-database to explore the role of transcription factors, 3'UTR regulatory sequences and GO-classes. Both conserved motifs and GO-categories revealed much higher numbers of significant results than expected by chance. Among these some are already known to be affected by the applied treatment, others were newly discovered.


© BOKU Wien Imprint