Fig. 5

S. pneumoniae transcriptional adaptation in response to co-incubation with epithelial cells. We clustered pneumococcal genes based on centered normalized expression and recovered clusters of genes with shared function. a A subset of 20 genes encoding carbohydrate transporters displayed early activation at 30 mpi and returned to basal expression levels at later time points. The unencapsulated strain (∆cps2E, orange box) exhibited a more sustained expression up to 60 mpi than the wild type (wt). b Similarly, 13 genes encoding adherence factors showed the same profile of early activation at 30 mpi and a more sustained expression at 60 mpi in the unencapsulated strain. c Seventeen genes encoding non-carbohydrate transporters were repressed at 30 mpi. d And 45 genes that are part of the competence regulon were activated beginning at 60 mpi until the end of the experiment. e Interestingly, subsets of genes of unknown function showed mixed profiles, including early activation and repression followed by de-repression and late activation