genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Pathogen Gene Expression Profiling
Table R.5.5: Fractions of known annotated and newly detected transcripts in the results of group comparisons with statistical testing
of S9 infection experiment staphylococcal array data sets.
group comparison a
total number of
sequences with
absolute fold
change equal to or
greater than 2 AND
significant with
p* < 0.05
number of known
transcribed
sequences with
absolute fold
change equal to or
greater than 2 AND
significant with
p* < 0.05
number of new
transcribed sequences
with absolute fold
change equal to or
greater than 2 AND
significant with
p* < 0.05
exponential growth phase vs. 1 h serum/CO 2 control 76 57 19
2.5 h internalization vs. 1 h serum/CO 2 control 765 565 200
6.5 h internalization vs. 1 h serum/CO 2 control 627 489 138
2.5 h serum/CO 2 control vs. 1 h serum/CO 2 control 905 655 250
2.5 h anaerobic incubation vs. 1 h serum/CO 2 control 680 480 200
a The 080604_SA_JH_Tiling array contains 3882 sequences of which 2825 are known transcripts. The remaining 1057 sequences were
identified as new transcripts in the tiling array analysis. All sequences were included in statistical testing.
Comparison of differentially regulated sequences in 2.5 h and 6.5 h internalized staphylococci
The gene expression signatures of 2.5 h and 6.5 h internalized staphylococci, which resulted
from statistical comparison with the baseline of 1 h serum/CO 2 control including multiple testing
correction and minimal absolute fold change cutoff 2, were compared in a Venn diagram
(Fig. R.5.10 A). For 408 sequences, differential expression was observed in both time points of
internalized samples, while 357 and 219 sequences were specific for the 2.5 h and 6.5 h
internalization signature, respectively. This corresponds to a fraction of 53 % of sequences
regulated after 2.5 h of internalization, which were also differentially expressed after 6.5 h. Vice
versa, 65 % of differentially expressed sequences at the 6.5 h time point were also found to be
regulated after 2.5 h. When examining the induced and repressed sequences separately, it was
first obvious that sequences regulated at both time points always possessed the same regulation
direction in these two time points (Fig. R.5.10 B). Further, induction accounted for a bigger
fraction than reduction in the differentially expressed sequences, although the excess was only
small at the 6.5 h time point.
A
B
357 408 219
2.5 h
repressed
repressed 6.5 h
induced
176 121
induced
181
187
98
sequences differentially
expressed in the comparison
“2.5 h internalization” vs.
“1 h serum/CO 2 control”
sequences differentially
expressed in the comparison
“6.5 h internalization” vs.
“1 h serum/CO 2 control”
221
Fig. R.5.10: Comparison of the 2.5 h and 6.5 h signatures of internalized staphylococci.
Both internalized samples were compared to the baseline of 1 h serum/CO 2 control with statistical testing and multiple testing
correction (p* < 0.05), and a minimal absolute fold change cutoff of 2 was applied. The comparison of differentially expressed
sequences at the 2.5 h and 6.5 h time point was performed for all regulated sequences (A) and for induced and repressed sequences
separately (B).
In the 2.5 h samples 402 sequences were induced (181 specifically for that time point), 363
were repressed (176 specifically for that time point), while in the 6.5 h samples 319 exhibited
induction (98 specifically for that time point) and 308 exhibited repression (121 specifically for
that time point). Therefore, the 408 sequences differentially expressed in both time points
consisted of 221 induced and 187 repressed sequences.
143