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Beyond Good and Evil in the Oral Cavity: Insights into Host-Microbe Relationships Derived from Transcriptional Profiling of Gingival Cells

¹ Department of Oral Biology and Center for Molecular Microbiology, College of Dentistry, Box 100424 JHMHSC, and
² Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610-0424, USA

View larger version (57K): [in this window] [in a new window]   Figure 1. Different patterns of gene expression of oral epithelial HIGK cells upon co-culture with oral species. Hierarchical clustering of variance-normalized gene expression data from uninfected human HIGK cells and from cells in co-culture with micro-organisms for 2 hrs before RNA isolation and purification. Expression and variation filters were applied to the dataset before clustering. Probe sets giving hybridization signal intensity at or below background levels on all arrays tested were eliminated from further analysis. The resulting dataset was culled by ranking on the coefficient of variation, and eliminating the bottom half of the dataset to remove probe sets whose expression did not vary between the treatment regimens. The gene expression observations were variance-normalized to a mean of 0 and a standard deviation of 1, and this normalized dataset was subjected to hierarchical cluster analysis with average linkage clustering of the nodes. The variation in gene expression for a given gene is expressed as distance from the mean observation for that gene. Each expression datapoint represents the ratio of the fluorescence intensity of the cRNA from A. actinomycetemcomitans-infected (columns Aa), P. gingivalis-infected (columns Pg), F. nucleatum-infected (column Fn), and S. gordonii-infected (column Sg) to the fluorescence intensity of the cRNA from mock-infected HIGK cells (columns CTRL). The scale adjacent to the dendrogram relates to Pearson’s correlation coefficient. Re-normalized from array data previously reported in Handfield et al.(2005) and Hasegawa et al.(2007), following procedures described in the APPENDIX.

View larger version (61K): [in this window] [in a new window]   Figure 2. Ontology analysis of the regulation of the actin cytoskeleton. BRB ArrayTools was used to generate probe sets differentially regulated at the P < 0.05 level of significance. The geometric mean signal intensity levels for probe sets passing this threshold were analyzed with Pathway Express software to populate known KEGG pathways according to transcriptional profiles obtained from GeneChip experiments. HIGK responses of infected vs. controls for (A) S. gordonii, (B) F. nucleatum, (C) A. actinomycetemcomitans, and (D) P. gingivalis. Genes shown in red are transcriptionally induced compared with the baseline level, while genes in blue are transcriptionally down-regulated. Genes in green are unchanged at the P < 0.05 significance level.

Journal of Dental Research, Vol. 87, No. 3, 203-223 (2008)
DOI: 10.1177/154405910808700302


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