Of characterized resistance-related transcripts, those of the NBS-LRR-type and in some cases, sub-families such as NB-ARC and RPM1, were found to be both up-regulated and down-regulated in the R vs S comparison (down-regulation means up-regulation in the S vs R comparison), though actual transcripts associated with each group were not shared.
Comparison of regulation profiles between tissues at a certain time of day indicated tissue-specificity of responses to 131I administration.
The first two comparisons highlight regulation in the infected plants by the rust fungi, while the third comparison highlights gene expression differences between the two types of infection, resistant and susceptible.
In comparison, up-regulation was comparatively weak in all instances, i.e., below 20-fold.
Interestingly, several of these enriched clusters were shared between the different pairwise comparisons including regulation of neurogenesis, transcription and kinase activity.
In comparison, down-regulation of emerin caused nuclear morphological deformation in approximately 20% of cells (not shown), which is consistent with our previous report [25].
Though we focused largely on differential transcript expression, we performed these differential expression analyses on both the genes and the transcripts to allow comparisons between regulation at the gene and isoform levels.
Comparison of GC regulation in ribosome-bound fractions versus GC regulation in the full data set revealed no significant differences suggesting that GCs do not directly regulate mRNA translation.
The comparison of transcript regulation with differences in de novo synthesized protein demonstrates the flexible coupling between transcript regulation and translation.
Of the two positively regulated signal cascades found in the 1 h to 3 h comparison, only "positive regulation of I-kappaB kinase/NF-kappaB cascade" was significantly changed between 3 h and 6 h.
