FIG 5 .

ppGpp upregulates transcription of genes involved in respiration, while cdiAMP exerts a response associated with cell envelope functions. (a) Network of GO categories significantly (P ≤ 0.001) enriched in the groups of genes upregulated (pink line) or downregulated (blue line) with each nucleotide (based on GO analysis results presented in Data Set S5). The line thickness is proportional to the P value, with thicker lines indicating greater significance. (b) Identification of genes highly connected in the S. cerevisiae stringent genetic interaction network that exhibited significant changes in transcription in response to ppGpp, cdiAMP, or cdiGMP based on the log₂ fold change (FC) in transcript abundance, which was plotted against the degree of connectivity in the network. Red points indicate genes that were significantly differentially expressed, while names correspond to those that were differentially transcribed with a degree connectivity of ≥30.