genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
Besides the beforementioned two-component system SaeRS, whose gene expression was
increased, further regulators were differentially expressed in the internalization experiment. The
transcription factors SarT, SarU, and Rot belong to the virulence associated Sar family. SarT and
sarU were repressed in internalized staphylococci at the 6.5 h time point, whereas rot was
repressed at the 2.5 h time point (Fig. R.5.20 A, B). Expression intensity of sarU gene was very
low.
A
B
10.00
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
saeR saeS sarT sarU rot
exponential growth phase -1.8 -1.8 2.1 -1.0 -1.6
2.5 h internalized -1.2 -1.2 -1.6 -1.7 -2.4
6.5 h internalized 2.1 1.7 -4.6 -2.2 -1.7
2.5 h serum/CO 2 control 1.7 1.5 -4.5 2.6 1.6
6.5 h serum/CO 2 control 2.5 1.9 -13.3 1.2 -1.2
2.5 h anaerobic incubation 1.9 1.5 -1.0 1.1 1.1
Fig. R.5.20: Expression of regulator genes.
A. Overview on fold change values relative to the baseline sample “1 h serum/CO 2 control” and on significance in statistical group
comparisons. Differentially expressed genes are marked by gray filling for the corresponding sample condition/time point.
Genes which were significant in statistical testing (p* < 0.05) but did not pass the absolute fold change cutoff 2 are indicated in bold
without filling. The sample “6.5 h serum/CO 2 control” could not be included in statistical testing because of small group size (n = 2).
B. Overview on mean normalized gene expression intensity. After the global normalization by inter-chip scaling and detrending, each
individual gene has been normalized to the expression level of the baseline sample “1 h serum/CO 2 control”. Although not being
continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection.
(exp. − exponential growth phase; 1 h co. – 1 h serum/CO 2 control; 2.5 h int. − 2.5 h internalization; 6.5 h int. − 6.5 h internalization;
2.5 h co. − 2.5 h serum/CO 2 control; 6.5 h co. − 6.5 h serum/CO 2 control; 2.5 h anae. − 2.5 h anaerobic incubation)
1.00
0.10
0.01
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
S. aureus RN1HG sample conditions and time points
saeR
saeS
sarT
sarU
rot
A
B
10.0
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
prsA vraR vraS
exponential growth phase 1.1 -1.1 -1.1
2.5 h internalized 2.0 1.8 1.6
6.5 h internalized 1.6 1.4 1.3
2.5 h serum/CO 2 control -1.2 -1.2 -1.1
6.5 h serum/CO 2 control -1.9 -1.1 -1.0
2.5 h anaerobic incubation 1.9 1.4 1.6
1.0
0.1
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
S. aureus RN1HG sample conditions and time points
prsA
vraR
vraS
Fig. R.5.21: Gene expression of prsA and its regulatory two-component system’s genes vraR and vraS.
A. Overview on fold change values relative to the baseline sample “1 h serum/CO 2 control” and on significance in statistical group
comparisons. Differentially expressed genes are marked by gray filling for the corresponding sample condition/time point.
Genes which were significant in statistical testing (p* < 0.05) but did not pass the absolute fold change cutoff 2 are indicated in bold
without filling. The sample “6.5 h serum/CO 2 control” could not be included in statistical testing because of small group size (n = 2).
B. Overview on mean normalized gene expression intensity. After the global normalization by inter-chip scaling and detrending, each
individual gene has been normalized to the expression level of the baseline sample “1 h serum/CO 2 control”. Although not being
continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection.
(exp. − exponential growth phase; 1 h co. – 1 h serum/CO 2 control; 2.5 h int. − 2.5 h internalization; 6.5 h int. − 6.5 h internalization;
2.5 h co. − 2.5 h serum/CO 2 control; 6.5 h co. − 6.5 h serum/CO 2 control; 2.5 h anae. − 2.5 h anaerobic incubation)
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