genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Kidney Gene Expression Pattern in an in vivo Infection Model
In this study, the PCA plot was derived from log-transformed intensity data of 24 arrays,
analyzing 2 biological replicates of mice infected with S. aureus RN1HG and RN1HG ΔsigB and one
additional group of sham infection (Fig. R.2.2). The analysis was performed on sequence level
(probe sets). Control sequences and sequences that are absent on all 24 arrays (p > 0.01 on
intensity profile level) were not included.
The biological reproducibility is visualized in the PCA plot by the arrangement of
corresponding data points close to each other. The PCA clearly distinguished two groups:
infection with S. aureus and sham infection / NaCl control (Fig. R.2.2 A). Furthermore, the PCA
depicted that the data sets of infection with S. aureus RN1HG and infection with RN1HG ΔsigB
were highly similar (Fig. R.2.2 A−C).
A view from front B view from right side C view from above
Fig. R.2.2: Visualization of transcriptome data using Principal Component Analysis (PCA).
Log-transformed data were used to derive a PCA plot containing 24 arrays (analyzing 2 biological replicates of 2 groups with different
infecting strains and one additional group of sham infection). Resulting principal components (PC) were set to cover 95 % of total
variation, while the total number of principal components was not limited. The analysis was restricted to non-control probe sets that
were not absent on all 24 arrays, when absence of expression is defined via a p-value > 0.01 on intensity profile level in Rosetta
Resolver.
All 3 images (A-C) belong to the same PCA shown in the normal view from the front in the first image (A). In the second image the
PCA-graph is turned by 90° to the left around the axis of principle component 2 resulting in a view from the right side into the plot (B).
Finally, in the third image the view from above into the graph is achieved by turning the plot by 90° around the axis of principle
component 1 (C).
Arrays of the first biological replicate (BR1) are represented by rhombi () and arrays of the second biological replicate (BR2) by
dots (•). Coloring distinguishes the three treatment groups of infection with S. aureus RN1HG (red), infection with S. aureus
RN1HG ΔsigB (blue) and sham infection / NaCl control (green).
Comparison of treatment groups reveals the same host reaction to infection with S. aureus
RN1HG and its sigB-mutant
Already the PCA had shown a high similarity between the reaction to the two different
infecting strains S. aureus RN1HG and RN1HG ΔsigB. Based on the PCA results the strategy for
statistical testing consisted of four main types of comparison (Fig. R.2.3):
comparison of the two groups with different infecting strains (infection with RN1HG ΔsigB
vs. infection with RN1HG) after combining both biological replicates
comparison of the two groups with different infecting strains for each biological replicate
separately
comparison of the same experimental groups of different biological replicates (infection with
RN1HG: BR1 vs. BR2; infection with RN1HG ΔsigB: BR1 vs. BR2)
comparison of infection with S. aureus and sham infection in the second biological replicate
(infection with RN1HG vs. sham infection; infection with RN1HG ΔsigB vs. sham infection)
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