When can transcript abundance and protein activity move in opposite directions?

Why

Imagine a kinase transcript rises after drug exposure, but the drug also blocks its active site. RNA-seq reports more mRNA, immunoblotting might show unchanged or higher protein, yet a substrate-phosphorylation assay could show lower kinase activity. Post-translational modification, competing binding partners, proteolysis and localization can create the same mismatch even without direct inhibition.

Use a short time course with RNA, total protein and a pathway-proximal functional readout. Where possible, assess turnover or translation and measure a relevant negative control. A single endpoint can conceal lag between transcription and protein synthesis.

Conversely, enzyme activity might increase immediately after phosphorylation without any change in mRNA. State which quantity was measured, what its timescale is and which intervention affects it. Do not equate a high fold change in sequencing with evidence that the biological process accelerated.