genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
A
B
100.0
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
lukD lukE hlgB hlgC hla
exponential growth phase -1.1 -1.9 -2.9 -5.6 -5.2
2.5 h internalized -1.3 -1.3 3.4 5.3 1.9
6.5 h internalized 6.5 9.0 13.4 17.9 3.2
2.5 h serum/CO 2 control 1.1 1.0 3.1 3.5 1.3
6.5 h serum/CO 2 control 1.4 1.1 8.0 8.9 1.7
2.5 h anaerobic incubation -1.5 -2.0 3.4 5.0 2.4
Fig. R.5.15: Staphylococcal toxin gene expression.
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)
10.0
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
lukD
lukE
hlgB
hlgC
hla
A
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
splF splE splD splC splB splA lip hysA htrA nuc sspA sspB sspC
exponential growth phase -1.3 -1.7 -1.1 -3.3 -5.4 -4.7 -1.4 -1.5 -1.2 -2.6 -1.4 -1.3 1.0
2.5 h internalized 1.6 3.1 3.2 4.8 3.3 3.2 34.2 -2.5 -2.3 -4.4 -2.5 -1.4 -1.1
6.5 h internalized 14.9 25.9 32.0 43.1 35.5 30.4 10.7 -3.0 -2.0 1.2 -1.2 -1.1 1.3
2.5 h serum/CO 2 control 1.9 3.1 3.1 3.8 2.7 2.9 1.3 -2.6 -2.0 4.0 -1.3 -1.0 1.5
6.5 h serum/CO 2 control 9.6 15.8 17.1 22.2 15.4 10.8 27.7 -3.4 -3.1 -1.0 -1.0 1.4 1.7
2.5 h anaerobic incubation -1.0 1.5 1.5 2.2 1.5 1.7 1.9 -1.7 -1.5 1.0 1.1 -1.0 1.3
B
100.0
C
10.0
splF
hysA
10.0
1.0
splE
splD
splC
splB
splA
1.0
htrA
nuc
sspA
sspB
sspC
lip
0.1
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
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
Fig. R.5.16: Extracellular and membrane bound enzyme gene expression.
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, C. Overview on mean normalized gene expression intensity for induced extracellular enzyme (B) and repressed extracellular and
membrane bound enzyme (C) genes. 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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