genomewide characterization of host-pathogen interactions by ...

log2(ratio C57BL/6 / BALB/c) at IFN-γ-activated level
log2(ratio C57BL/6 / BALB/c) at IFN-γ-activated level
Maren Depke
Results
Gene Expression Pattern of Bone-Marrow Derived Macrophages after Interferon-gamma Treatment
The same comparison using the LC-MS/MS proteome data yielded 112 (control level) and 135
(IFN-γ treated level) proteins with a higher abundance in C57BL/6 BMM and 106 (control level)
and 173 (IFN-γ treated level) proteins with a higher abundance in BALB/c BMM (Table R.3.2 B).
A
B
10
8
6
94 128 102
4
2
genes differentially
expressed between
BALB/c BMM and C57BL/6
BMM at the non-activated
control level (222)
genes differentially
expressed between
BALB/c BMM and C57BL/6
BMM at the IFN-γ-treated
level (230)
0
-2
-4
-6
-8
-10
-10 -8 -6 -4 -2 0 2 4 6 8 10
log 2 (ratio C57BL/6 / BALB/c) at control level
C
D
10
8
6
35 183 125
4
2
proteins differentially
regulated between BALB/c
BMM and C57BL/6 BMM
at the non-activated
control level (218)
proteins differentially
regulated between BALB/c
BMM and C57BL/6 BMM
at the IFN-γ-treated level
(308)
0
-2
-4
-6
-8
-10
-10 -8 -6 -4 -2 0 2 4 6 8 10
log 2 (ratio C57BL/6 / BALB/c) at control level
Fig. R.3.3: Comparison of strain differences between BALB/c BMM and C57BL/6 BMM at non-treated control and IFN-γ treated level.
A, C. Overview on numbers of differentially expressed genes in transcriptome analysis (A) and of proteins with significantly different
abundance in LC-MS/MS analyses (C) when comparing strain differences between BALB/c BMM and C57BL/6 BMM at the non-treated
control level and at the IFN-γ treated level.
B, D. Log 2-transformed ratio data “medium control C57BL/6 BMM” / “medium control BALB/c BMM” were plotted on the x-axis and
log 2-transformed ratio data “IFN-γ treated C57BL/6 BMM” / “IFN-γ treated BALB/c BMM” on the y-axis from transcriptome (B) and LC-
MS/MS (D) analyses.
Coloring distinguishes three different groups of regulated genes or proteins: Genes/proteins with significant strain difference only at
non-treated control level are shown in dark gray, while that with significant strain difference only at IFN-γ treated level are displayed
in light gray. Genes/proteins significantly different between BALB/c BMM and C57BL/6 BMM on both treatment levels, i. e. at nontreated
control and IFN-γ treated level, are colored in black. The minimal absolute fold change cutoff of 1.5 has been applied to all
result lists.
All transcriptome ratio data were derived from mean intensities of three biological replicates, and ratio data of LC-MS/MS analyses
were derived from intensities of one biological replicate analyzed in technical triplicates of each group.
In the comparison of the two mouse strains only 20 out of 222 (control level) and 24 out of
230 (IFN-γ treated level) differentially expressed genes were also identified in LC-MS/MS analysis.
Inversely, 203 out of 218 (control level) and 288 out of 308 (IFN-γ treated level) proteins with
significantly differing abundance were also detected on the Affymetrix array. Due to the limiting
95