genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
PATHOGEN GENE EXPRESSION PROFILING
Growth Media Comparison Study
Reproducibility of replicates and clustering of experimental condition groups
Cultivation of S. aureus RN1HG in pMEM medium was performed in triplicate. In the tiling
array analysis of the sample points exponential growth, stationary phase t 2 , and stationary
phase t 4 , the replicates of each group were arranged together in a cluster. As expected, for the
stationary t 4 time point, which is defined as 4 h after entry into stationary phase, a higher
similarity to the t 2 samples, which were harvested 2 h earlier, than to the exponential growth
samples was detected. This similarity was especially visible for the t 4 biological replicates 2 and 1,
whereas the replicate 3 held more distance to the other samples (Fig. R.5.1).
exponentialgrowth
stationary phase t 2
stationary phase t 4
biological replicate 1
biological replicate 2
biological replicate 3
Fig. R.5.1: Hierarchical clustering of 9 tiling array data sets from growth in pMEM medium.
The following clustering algorithms were applied on z-score-transformed data: Agglomerative clustering with average linkage using
cosine correlation as similarity measure. All sequences were included in the cluster analysis.
Three major classes according to the sample points during growth were discernible: 1) exponential growth, 2) stationary phase t 2, and
3) stationary phase t 4. As expected for the stationary t 4 time point, a higher similarity to the t 2 samples than to the exponential growth
samples was detected. This similarity was especially visible for the t 4 biological replicates 2 and 1, whereas the replicate 3 held more
distance to the other samples.
Comparison of experimental condition groups and assessment of differentially regulated genes
The consumption of medium components and the reduction of growth rate after beginning of
stationary phase was accompanied by a substantial change of gene expression. This change was
visualized by the strong scattering when comparing stationary phase t 2 and stationary phase t 4
samples to the exponential growth in scatter plots (Fig. R.5.2).
The comparison of stationary phase samples with exponential growth samples by statistical
testing resulted in 2243 and 1399 sequences, which exhibited a significant difference to
exponential growth at the t 2 and the t 4 time point, respectively. Of these, 1423 sequences
exceeded an absolute fold change of 2 in the t 2 samples, and 1086 sequences passed the cutoff in
the 2 h later samples of the t 4 time point (Table R.5.1).
131