Fig. 6

Mitonuclear genotype differentially alters expression of genes associated with distinct functional pathways and transcription factors. KEGG pathway enrichment was performed using the R package GOseq [36] on the gene set from the cluster 1 (top) and cluster 5 (bottom) expression profiles. Expression levels for genes in cluster 1 (a) or cluster 5 (d) that are associated with the significantly enriched KEGG categories for that cluster were standardized to have zero mean and standard deviation of 1 across all samples. The mean of the standardized expression levels for all genes at each time point were plotted in blue for OreR;OreR samples and red for sm21;OreR samples with control time points plotted on the left and rapamycin treated samples on the right. Error bars are standard deviation among replicate libraries. b, e Significantly over-represented KEGG categories in the cluster 1 (b) and cluster 5 (e) gene sets are displayed in the Tables. c, f Network diagrams generated using the R package visNetwork [42] showing the relationship between enriched transcription factors and KEGG categories for cluster 1 (c) and cluster 5 (f). c Genes from cluster 1 enriched KEGG categories that are associated with the transcription factor Abd-B (red) or not (yellow). f Genes from cluster 5 enriched KEGG categories that are associated with the transcription factor Dref (blue), giant (red) or neither (yellow)