Fig. 3

All OXPHOS complexes co-express with complex I, but assembly factors follow divergent transcriptional programs. Histograms (a) and boxplots (b) of co-expression scores with known complex I genes. Genes are grouped as OXPHOS, mitochondrial (nuclear genes encoding proteins with a function in the mitochondria), or other genes in the genome (a). OXPHOS genes are further sub-classified into individual complexes and assembly factors (b). The shaded grey area represents the top 5 % of nuclear genes co-expressing with complex I, which are included in the TF binding site enrichment analysis. The dashed line marks the cutoff score (0.54). Groups are mutually exclusive, i.e. genes occur only in one group; complex I-V genes together with assembly factors make up the OXPHOS group. Histogram counts (a) were normalized to a maximum of 1 for each gene set. Colored boxes in boxplots (b) represent the 50 % of data points above (×0.75) and below (×0.25) the median (×0.50; the black line within the box). Vertical lines (whiskers) connected to the boxes by the horizontal dashed lines represent the largest and the smallest non-outlier data points (which are plotted as individual dots). P values comparing two groups are from Mann–Whitney U tests and those comparing multiple groups are from Kruskal-Wallis tests