genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Host Cell Gene Expression Pattern in an in vitro Infection Model
expression after 2.5 h, infected GFP-positive sorted cells after 2.5 h were statistically compared
to their time matched medium control cells.
Altogether, 86 genes were defined as differentially expressed in infection compared to control
2.5 h after infection. Of these genes, 40 possessed a minimal absolute fold change of 1.5, and 11
genes held a minimal absolute fold change of 2 (Table R.4.1 A). In comparison, for the 6.5 h time
point differential expression in infection compared to control was made up of 2296 genes, of
which 1196 passed an absolute fold change cutoff of 1.5 and still 495 passed a cutoff of 2
(Table R.4.1 B).
Comparison of infection-dependent differentially expressed genes after 2.5 h and 6.5 h
When comparing the infection-dependent changes in gene expression with a minimal
absolute fold change of 1.5 after 2.5 h and after 6.5 h, an overlap of 26 genes was recorded. This
corresponds to 65 % of the genes differentially expressed 2.5 h after infection (Fig. R.4.5 A). If
genes that did not exhibit differential expression relative to the baseline of 2.5 h medium control
had not been excluded from the list of infection-dependent regulated genes after 6.5 h, the
overlap would have even increased by 6 genes to 80 %.
A
B
2.5 h
repressed
repressed 6.5 h
14 26 1170
induced
5
333
induced
9
2
837
genes differentially expressed
in S9 cells between infection
with RN1HG GFP and medium
control 2.5 h after infection
genes differentially expressed
in S9 cells between infection
with RN1HG GFP and medium
control 6.5 h after infection
1
23
Fig. R.4.5: Comparison of infection-dependent regulated genes in S9 cells 2.5 h and 6.5 h after start of infection.
After applying a minimal absolute fold change cutoff of 1.5, 40 genes were differentially expressed in infection compared to control
2.5 h after start of infection, while the number of differentially expressed genes 6.5 h after start of infection increased to 1196. The
overlap between both lists contained 26 genes (A). This group of 26 genes in the overlap could be subdivided into 23 genes which
were induced 2.5 h as well as 6.5 h after start of infection, 2 genes which were repressed in both time points and 1 genes which was
induced 2.5 h after start of infection and repressed after 6.5 h. In general, a bigger fraction of differentially regulated genes was
induced than repressed in each time point. This summed up to 33 or 860 induced genes 2.5 h or 6.5 h after start of infection,
respectively. Repression occurred for 7 genes at the 2.5 h time point and 336 genes at the 6.5 h time point (B).
In a finer resolution, also the direction of regulation was comparable between the two
analyzed time points. Of the 26 genes, which were differentially expressed after 2.5 h as well as
after 6.5 h, 23 were induced and 2 were repressed in both time points. Only for one gene
induction was observed after 2.5 h while the expression was repressed after 6.5 h (Fig. R.4.5 B).
Concluding from this high degree of conformance in the two time points, the RNA expression
profiling 2.5 h after start of infection seemed to catch the very early beginning of the host cell’s
reaction, which was very strongly aggravated during the following 4 hours until the measurement
6.5 h after start of infection.
In each time point, induction of gene expression was more pronounced than repression.
Induction summed up to 33 or 860 genes 2.5 h or 6.5 h after start of infection, respectively.
Repression covered 7 genes at the 2.5 h time point and 336 genes at the 6.5 h time point
(Fig. R.4.5 B).
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