Figure 3.

Overview of transcriptomic changes in genes encoding proteins targeted to mitochondria during DLS. A, Differential expression analysis of transcripts encoding proteins targeted to mitochondria (Ai), chloroplast (Aii), and whole genome (total present set; Aiii) during DLS (false discovery rate by PPDE threshold was not applied). Transcript data from Breeze et al. (2011) were utilized as a foundation for the analysis of transcripts during DLS. Differential expression analysis was carried out on consecutive time points, with P value cutoffs of 0.05 and 0.01 as indicated at bottom. Four distinct phases of transcriptomic activity were identified and are marked with gray boxes. B, Hierarchical cluster of transcripts encoding proteins targeted to the mitochondrion during DLS. Bi, Transcript data from Breeze et al. (2011) were filtered with a manually curated list of mitochondrial transcripts. These values were normalized to the highest level of expression over the time course and hierarchically clustered using average linkage based on Euclidean distance. Bii, Expression profiles for each distinct cluster were plotted, with mean expression profiles represented by solid red lines. Biii, Each cluster was interrogated individually to assess the presence of significant (P < 0.05) overrepresentation of specific Gene Ontology (GO) categories in the gene lists.