genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Kidney Gene Expression Pattern in an in vivo Infection Model
infection with
RN1HG
BR1
(4 arrays)
3
infection with
RN1HG
BR2
(5 arrays)
4
2
1
2
sham infection
(NaCl)
BR2
(5 arrays)
infection with
RN1HG ΔsigB
BR1
(5 arrays)
3
infection with
RN1HG ΔsigB
BR2
(5 arrays)
4
Fig. R.2.3: Overview on the comparisons between groups in this study that were addressed with statistical testing and visualized with
scatter plots.
The two groups with different infecting strains (infection with RN1HG ΔsigB vs. infection with RN1HG) were compared after
combining both biological replicates () and for each biological replicate separately (). Same experimental groups of different
biological replicates (infection with RN1HG: BR1 vs. BR2; infection with RN1HG ΔsigB: BR1 vs. BR2) were also checked against each
other (). The last comparison focused on infection and sham infection in the second biological replicate (infection with RN1HG vs.
sham infection; infection with RN1HG ΔsigB vs. sham infection; ).
BR – biological replicate.
The comparisons were visualized using scatter plots (Fig. R.2.4). Comparable to the PCA
results, a striking concordance between expression values of kidney after infection with RN1HG
and infection with RN1HG ΔsigB was observed, especially when both biological replicates were
combined (Fig. R.2.4, panel ), but also when the biological replicates were considered
separately (Fig. R.2.4, panel ). In the comparison of the same experimental groups in both
replicates high similarity was observed (Fig. R.2.4, panel ), although the inter-replicate variation
of the same treatment was higher than the intra-replicate variation of the different treatments
for S. aureus infected samples. The inter-replicate variation might be due to the difference of one
day in the sampling time point (d 4 or d 5). Strong effects of S. aureus infection independent of
the infecting strain emerged in the comparison to the sham infected / NaCl control sample group
(Fig. R.2.4, panel ).
The different experimental groups were compared with statistical testing to obtain lists of
differentially expressed genes. Sequences not expressed and control sequences were not
included in statistical testing.
The first statistical test compared kidney samples of mice infected with S. aureus RN1HG ΔsigB
vs. infection with RN1HG in an approach that combined both biological replicates (for
comparison see Fig. R.2.3; and Fig. R.2.4, panel ). Only one sequence corresponding to one
gene was significantly different in intensity between both groups (Table R.2.1). For all arrays
except one array from a specific animal the signal intensities of this gene were low and their p-
value for expression was high. i. e. the expression was absent (Fig. R.2.5 A). The array data from
the single outlying animal caused statistical significance, but the result is not biologically relevant
because it is obviously due to an unknown, animal-specific factor and not to treatment.
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