genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Pathogen Gene Expression Profiling
stationary phase t 2
stationary phase t 4
exponential growth
exponential growth
Fig. R.5.2: Scatter plots comparing mean signal intensities of treatment groups.
The signals of the three groups of “stationary phase t 2”, “stationary phase t 4”, and “exponential growth phase” were plotted after
combining the three biological replicates. All sequences available on the array are shown.
Table R.5.1: Results of group comparisons with statistical testing of stationary phase and exponential growth staphylococcal array
data sets.
number of sequences
group comparison a
significant with p* < 0.05 in textbook oneway
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
stationary phase t 2 vs. exponential growth phase 2243 1423
stationary phase t 4 vs. exponential growth phase 1399 1086
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 genes in t 2 and t 4 of stationary phase in pMEM
The gene expression signatures of t 2 and t 4 stationary phase S. aureus RN1HG, which resulted
from statistical comparison with the baseline of exponential growth including multiple testing
correction and minimal absolute fold change cutoff 2, were compared in a Venn diagram
(Fig. R.5.3 A). For 940 sequences, differential expression was observed in both time points of
stationary phase, while 483 and 146 sequences were specific for the t 2 and t 4 stationary phase
signature, respectively.
This corresponds to a fraction of 66 % of sequences regulated at t 2 , which were also
differentially expressed at t 4 . Vice versa, 87 % of differentially expressed sequences at the t 4 time
point were also found to be regulated at t 2 . 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.5.3 B). Further, a slightly
higher number of repressed sequences was visible in the differentially expressed sequences, but
induction accounted for almost the same number of sequences as repression.
In the t 2 samples, 696 sequences were induced (225 specifically for that time point), 727 were
repressed (258 specifically for that time point), while in the t 4 samples 540 exhibited induction
(69 specifically for that time point) and 546 exhibited repression (77 specifically for that time
point). Therefore, the 940 sequences differentially expressed in both time points consisted of 471
induced and 469 repressed sequences.
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