genomewide characterization of host-pathogen interactions by ...

log2(ratio IFN-γ-treated / control) of C57BL/6 BMM
log2(ratio IFN-γ-treated / control) of C57BL/6 BMM
Maren Depke
Results
Gene Expression Pattern of Bone-Marrow Derived Macrophages after Interferon-gamma Treatment
A
B
10
8
6
4
135 307 89
2
0
-2
genes regulated by IFN-γ
in BALB/c BMM (442)
genes regulated by IFN-γ
in C57BL/6 BMM (396)
-4
-6
-8
-10
-10 -8 -6 -4 -2 0 2 4 6 8 10
log 2 (ratio IFN-γ-treated / control) of BALB/c BMM
C
D
10
8
6
4
16 29 23
2
0
-2
proteins regulated by IFN-γ
in BALB/c BMM (45)
proteins regulated by IFN-γ
in C57BL/6 BMM (52)
-4
-6
-8
-10
-10 -8 -6 -4 -2 0 2 4 6 8 10
log 2 (ratio IFN-γ-treated / control) of BALB/c BMM
Fig. R.3.2: Comparison of IFN-γ effects on gene expression pattern and protein abundance in BALB/c BMM and C57BL/6 BMM.
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 IFN-γ effects in BALB/c BMM and C57BL/6 BMM.
B, D. Log 2-transformed ratio data “IFN-γ treated BALB/c BMM” / “medium control BALB/c BMM” were plotted on the x-axis and log 2-
transformed ratio data “IFN-γ treated C57BL/6 BMM” / “medium control C57BL/6 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 differential
expression/abundance caused by IFN-γ only in BALB/c BMM are shown in dark gray, while that with significant differential
expression/abundance caused by IFN-γ only in C57BL/6 BMM are displayed in light gray. Genes/proteins significantly regulated by
IFN-γ in both BALB/c BMM and C57BL/6 BMM 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.
Strain differences in gene expression [Maren Depke] and protein abundances [Dinh Hoang
Dang Khoa] between BMM of BALB/c and C57BL/6 mice in untreated medium control and in
IFN-γ treated samples
The comparison of C57BL/6 BMM and BALB/c BMM at the non-treated medium control level
and at the IFN-γ treated level resulted in 100 (control level) and 93 (IFN-γ treated level) genes
that featured a higher expression in C57BL/6 BMM and 122 (control level) and 137 (IFN-γ treated
level) genes that exhibited a higher expression in BALB/c BMM.
94