Conduct time-course experiments to account for post-transcriptional regulation delays.
Perform ribosome profiling to assess translation efficiency.
Analyze protein turnover rates using cycloheximide chase assays.
| Condition | mRNA Fold Change | Protein Fold Change | Half-Life (hr) |
|---|---|---|---|
| Control | 1.0 ± 0.2 | 1.0 ± 0.3 | 12.4 ± 1.1 |
| Drought | 3.8 ± 0.5 | 1.2 ± 0.4 | 9.1 ± 0.8 |
Perform phylogenetic epitope analysis to identify conserved regions in related proteins (e.g., At2g24695, At2g24697).
Test antibody binding against recombinant homologs using surface plasmon resonance (SPR).
Use CRISPR-edited lines with mutations in homologous genes to isolate specific signals.
Apply ANOVA with Tukey’s post hoc test for time-series or treatment-group comparisons.
Use network analysis tools (e.g., STRING, Cytoscape) to identify context-dependent protein interaction clusters.
Employ mixed-effects models to account for batch variability in large-scale experiments.
Combine super-resolution microscopy with Förster resonance energy transfer (FRET) to probe protein-protein interactions.
Correlate granule dynamics with oxidative stress markers (e.g., H2O2 levels) using fluorescent reporters.
Validate findings via dominant-negative mutant overexpression to disrupt granule assembly.
Perform weighted gene co-expression network analysis (WGCNA) to identify modules correlated with protein abundance.
Overlay chromatin accessibility data (ATAC-seq) to explore transcriptional regulation mechanisms.
Use machine learning classifiers (e.g., random forests) to predict protein function from phosphorylation patterns.