genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Pathogen Gene Expression Profiling
The different experimental groups were compared with statistical testing to obtain lists of
differentially expressed sequences (Table R.5.4). It has been already described that the three
groups exponential growth phase as inoculation condition, 1 h serum/CO 2 control, and 1 h nonadherent
staphylococci were similar to each other. Non-surprisingly, when comparing 1 h nonadherent
staphylococci to the 1 h serum/CO 2 control samples, no statistically significant
differential expression was detected. Between exponential growth phase and 1 h serum/CO 2
control, 156 sequences were differentially expressed of which 76 exceeded a minimal absolute
fold change of 2. In the comparison of 2.5 h and 6.5 h internalization vs. 1 h serum/CO 2 control,
1392 and 1205 sequences were regarded as differentially expressed, of which 765 and 627
possessed a minimal absolute fold change of 2, respectively. Additionally, 1749 sequences were
differentially expressed between 2.5 h serum/CO 2 control and 1 h serum/CO 2 control, and 905 of
these passed the minimal absolute fold change cutoff 2. The 2.5 h anaerobic signature in
comparison with the baseline of 1 h serum/CO 2 control included 1339 sequences, and still 680
exhibited a minimal absolute fold change of 2.
Table R.5.4: Results of group comparisons with statistical testing of S9 infection experiment staphylococcal array data sets.
group comparison a
number of sequences
significant with p* < 0.05 in
textbook one-way ANOVA with
Benjamini-Hochberg False Discovery
Rate multiple testing correction
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 156 76
1 h non-adherent staphylococci vs. 1 h serum/CO 2 control 0 -
2.5 h internalization vs. 1 h serum/CO 2 control 1392 765
6.5 h internalization vs. 1 h serum/CO 2 control 1205 627
2.5 h serum/CO 2 control vs. 1 h serum/CO 2 control 1749 905
2.5 h anaerobic incubation vs. 1 h serum/CO 2 control 1339 680
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.
Fractions of known genes and newly identified transcribed sequences included on the tiling
array and in the lists of differentially expressed sequences derived from the comparisons of
infection experiment samples
The 080604_SA_JH_Tiling array contains 3882 sequences of which 2825, corresponding to
73 %, are known transcripts and associated with a LocusTag number (SAOUHSC_*). The remaining
1057 sequences were identified as new transcripts in the tiling array analysis. These new
transcripts are expected to belong to all types of RNAs like mRNA and regulatory RNA, but also
formerly unknown transcribed fragments 5’ and 3’ to known genes might be included.
Furthermore, some artifacts might still be included. All sequences, known and new, were
included in statistical testing.
For the internalization-specific signature, 200 and 138 differentially expressed transcripts
belonged to the group of new transcripts at the 2.5 h and 6.5 h time point, respectively
(Table R.5.5). Furthermore, 19 new transcripts were included in the set of differentially expressed
sequences between the inoculation condition of exponential growth and the baseline of 1 h
serum/CO 2 control. In comparison to that baseline, 2.5 h serum/CO 2 control and 2.5 h
anaerobically incubated samples inclosed 250 and 200 differentially expressed new transcripts,
respectively (Table R.5.5).
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