Quiescence (G0) regulation and prediction of candidate TFs. Figure 4A: G0 in S. cerevisiae occurs when a saturated culture is depleted of nutrients. As exponential growth stops with the exhaustion of glucose, cells pass diauxic shift and switch to slower respiratory growth. Growth is halted in post-diauxic phase, cells differentiate into quiescent and non-quiescent populations and enter G0. Culture viability starts decreasing rapidly as G0 progresses. Two sets of process-specific genes were used in independent m:Explorer runs: genes expressed during diauxic shift (yellow box), and genes expressed in G0 cultures (blue box, G0 maintenance). Figure 4B: Venn diagram for cell cycle genes, diauxic shift genes, and G0 maintenance genes. Statistically significant enrichment is observed between diauxic shift and quiescence genes (Fisher's exact test, p = 0.0005, 62 genes). Figure 4C: Log-scaled TF scores from diauxic shift and G0 maintenance predictions (top - TFs 1-50, bottom - TFs 51-97). Bar color represents fraction of final score attributed to G0 profile (diauxic shift - yellow; G0 maintenance - blue). First 12 TFs highlighted with asterisks were selected for experimental testing. TF, transcription factor.
Reimand et al. Genome Biology 2012 13:R55 doi:10.1186/gb-2012-13-6-r55