genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
A
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
SAOUHSC_
02557 ureA ureB ureC ureE ureF ureG ureD
exponential growth phase 1.6 3.0 2.2 1.9 1.5 1.4 1.2 1.2
2.5 h internalized -2.6 -2.9 -3.2 -3.0 -1.9 -2.2 -1.9 -2.0
6.5 h internalized -1.1 -1.7 -1.6 -1.4 -1.3 -1.6 -1.4 -1.3
2.5 h serum/CO 2 control -1.8 -3.3 -3.1 -2.1 -1.2 -1.3 -1.3 -1.4
6.5 h serum/CO 2 control -1.5 -2.3 -2.0 -1.1 -1.1 -1.2 -1.4 -1.2
2.5 h anaerobic incubation -1.3 5.0 4.8 3.1 1.7 1.3 1.1 -1.1
Fig. R.5.28: Urea transporter and urease operon 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. 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”
(1 h co.). 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)
B
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
SAOUHSC_02557
ureA
ureB
ureC
ureE
ureF
ureG
ureD
A
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
potA potB potC potD gltS arcD opuD opuCd opuCc opuCb opuCa
exponential growth phase -1.4 -1.4 -1.6 -1.4 -1.1 -1.5 1.0 -1.0 -1.1 -1.1 -1.0
2.5 h internalized -7.1 -8.4 -9.2 -4.9 -2.2 -2.4 -2.1 -3.3 -3.3 -4.6 -4.2
6.5 h internalized -3.9 -4.4 -4.9 -3.7 -3.0 -2.3 -1.7 -1.6 -2.1 -2.7 -3.0
2.5 h serum/CO 2 control -3.3 -3.5 -4.1 -3.1 -4.4 1.4 -4.7 2.1 2.0 1.9 2.1
6.5 h serum/CO 2 control -4.8 -4.3 -5.5 -2.7 -6.0 2.0 -7.0 1.2 1.0 -1.1 -1.0
2.5 h anaerobic incubation -2.9 -3.5 -4.5 -3.7 -4.0 2.1 -3.9 3.2 3.7 3.7 4.6
B
C
10.0
10.0
potA
opuD1
potB
opuCd
1.0
potC
potD
1.0
opuCc
opuCb
gltS
opuCa
arcD
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
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
Fig. R.5.29: Spermidine/putrescine, sodium/glutamate, arginine/ornithine, glycine betaine and amino acid transporter 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. 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. 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” (1 h co.). Although
not being continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection.
Spermidine/putrescine ABC transporter potABCD, sodium/glutamate symporter gltS, arginine/ornithine antiporter arcD (B) and
glycine betaine transporter opuD1 and amino acid ABC transporter opuCdCcCbCa (C).
(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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