Relative peptide amount in healthy versus disease sample is proportional to peak AUC or summed intensities.
Study details on disease, sample, techniques and findings are listed in Additional file 1: Table S1.
We find a highly significant enrichment for PVL positive isolates (80.4%) within the disease sample.
For comparison, Figure 3 also shows the proportion of STs within the disease sample.
Firstly, DEGs indentified in each disease sample were mapped to PPI and TRI data.
We identified up-regulated DEGs and down-regulated DEGs for each disease sample.
To check for bias caused by the small number of HA isolates in the disease sample, and the slightly larger size of the disease sample, we also included a dataset consisting of only the 40 community-acquired disease isolates.
We draw comparisons between the individual carriage samples, and between the pooled carriage sample and the disease sample.
An individual deregulated biological network is a network constructed by deregulated PPIs and TRIs identified in one disease sample.
As for the carriage sample, the most frequent clonal complex in the disease sample was CC121 (17.6%; ST121, n = 8, ST947, n = 1).
We are confident that the inclusion of a small number of hospital-acquired isolates does not account for the differences in the disease sample.
