From: Gene expression and metabolism preceding soft scald, a chilling injury of ‘Honeycrisp’ apple fruit
Data type | Timepoints | Objective | Analysis |
---|---|---|---|
Transcriptomic, normalized | 0–8 wk | Latent trends | Principal components analysis (PCA) |
normalized | 0–8 wk | Differential expression in the multivariate case | ANOVA-simultaneous component analysis |
raw counts | 0 wk | Pre-harvest environmental effects | RobiNA edge R differential expression according to soft scald riska |
raw counts | 2 wk | Effects of chilling | RobiNA edge R differential expression according to soft scald riska |
- | Functional characterization of significant transcripts | Gene Ontology overrepresentation analysis | |
Metabolomic, means centered, standard deviation squared | 0–8 wk | Latent trends | Principal components analysis (PCA) |
0–8 wk | Differential expression in the multivariate case | ANOVA-simultaneous component analysis | |
0 wk | Pre-harvest environmental effects | t-test/ Pearson’s correlation + Ward clustering algorithm heatmap visualization | |
2 wk | Effects of chilling | t-test/ Pearson’s correlation + Ward clustering algorithm heatmap visualization | |
Transcriptomic and metabolomic, normalized and set to a common scale by means centering | 0–8 wk | Correlation among expressed genes and metabolites | Pearson’s correlation via Cytoscape Expression Correlation plug-in at r = │0.95│, followed by network subtraction with the Network Analyzer plug-in |