Analysis of K. lactis and a potential 30 min compositional bias artifact.

This analysis compares phosphate starvation transcriptional responses in *Saccharomyces cerevisiae* across three independent studies spanning 14 years (Zhou & O'Shea 2011, Gurvich et al. 2017, GRE Lab 2023) and two expression profiling platforms (microarray, RNA-seq). I demonstrate that transcriptional stress responses exhibit hierarchical temporal kinetics: pathway-specific metabolic responses (PHO regulon) achieve strong magnitude correlation by 1h (ρ=0.81-0.83), while systemic cellular adjustments (ribosomal repression, general stress) show near-perfect directional concordance (93-97%) but weak magnitude correlation (ρ=-0.08 to 0.28) at early timepoints. This pattern reflects a fundamental distinction between biological commitment and quantitative maturation. The conservation of this hierarchical temporal structure across three laboratories, 13 years, and two platforms validates that early magnitude variability reflects intrinsic features of transcriptional program maturation compounded by laboratory-specific pre-sequencing sample handling (growth phase, harvest timing, RNA stabilization), rather than measurement error. Core metabolic reprogramming signatures (canonical PHO induction, ribosomal repression) are highly reproducible, while peripheral responses (marginal PHO genes like DUR3/ISC10, stress intensity) exhibit greater context-dependent variability. All datasets converge to concordant response patterns by 2h post-starvation, confirming that transcriptional programs mature predictably beyond the initial commitment phase despite varying baseline conditions across laboratories.