genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
The second group comprised transporter genes with induced gene expression in at least one
analyzed time point of internalized staphylococci. This applied for example to the phosphate ABC
transporter operon SAOUHSC_01384 to SAOUHSC_01389, pho/pst (Fig. R.5.31).
A
fold change in comparison to
baseline 1 h serum/CO 2 control
phnE
SAOUHSC_
00103 phnC SAOUHSC_
00105 metN1 SAOUHSC_
00424
SAOUHSC_
00426 metN2
S. aureus
RN1HG
sample
conditions
and time
points
exponential growth phase -1.4 -1.5 -1.6 -1.2 3.3 2.8 2.0 1.6
2.5 h internalized -1.1 1.2 2.0 4.8 6.6 5.8 3.6 1.6
6.5 h internalized 2.9 3.6 5.2 7.4 16.6 12.8 7.6 2.4
2.5 h serum/CO 2 control -1.0 1.1 1.3 1.5 48.7 39.8 22.7 3.1
6.5 h serum/CO 2 control -1.4 -1.4 -1.1 -1.4 21.6 20.1 10.5 2.4
2.5 h anaerobic incubation -1.5 -1.1 1.1 1.7 3.9 2.8 1.8 1.4
Fig. R.5.32: Phosphonate transporter and methionine
binding protein 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
100.0
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
phnE
SAOUHSC_00103
phnC
SAOUHSC_00105
metN1
SAOUHSC_00424
SAOUHSC_00426
metN2
Induction was detected for phosphonate ABC transporters (operon SAOUHSC_00102 to
SAOUHSC_00104, including phnE and phnC, and the adjacent SAOUHSC_00105), methionine
import ATP-binding protein gene metN1 and transporter/permease SAOUHSC_00424 and
SAOUHSC_00426 from the same operon, and the separately encoded methionine import ATPbinding
protein gene metN2 (Fig. R.5.32).
A
fold change in comparison to
baseline 1 h serum/CO 2 control
oppF
SAOUHSC_
00169
SAOUHSC_
00923
oppC oppD SAOUHSC_
00926
oppA
SAOUHSC_
00928
appD appF SAOUHSC_
00931
appC
S. aureus
RN1HG
sample
conditions
and time
points
exponential growth phase 1.3 1.2 1.4 1.4 1.4 1.3 1.3 1.3 1.3 -1.1 1.5 1.5
2.5 h internalized 1.3 5.2 2.7 2.7 3.0 2.4 2.4 1.2 -1.0 -1.5 -1.2 -1.2
6.5 h internalized 2.2 17.8 4.8 4.9 5.0 4.3 4.4 2.8 1.9 1.2 1.5 1.0
2.5 h serum/CO 2 control 4.9 27.6 8.3 8.2 9.0 7.5 7.6 8.2 3.1 1.7 1.6 1.3
6.5 h serum/CO 2 control 3.4 20.6 4.2 5.2 5.7 5.5 5.6 10.2 4.1 2.4 1.8 1.3
2.5 h anaerobic incubation 1.2 1.8 5.4 5.1 6.0 4.6 4.8 3.4 1.5 -1.0 -1.0 -1.0
Fig. R.5.33: Peptide and oligopeptide 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. 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
100.0 oppF
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_00169
SAOUHSC_00923
oppC
oppD
SAOUHSC_00926
oppA
SAOUHSC_00928
appD
appF
SAOUHSC_00931
appC
164