Figure 6.
Comparative analyses of phosphoproteomics during hyperammonemia and exercise
(A) UpSet plots of unique and shared differentially expressed phosphoproteins (DEpP) present in at least one of the 6h or the 24h ammonium acetate (AmAc)-treated myotube datasets (Any ammonia) and those DEpP present in at least one of the mouse or human exercise datasets (Any exercise) compared to genes in a verified mitochondrial-localized protein database (MitoCarta3.0), and genes in senescence databases (CSgene and CellAge).
(B) UpSet plot of unique and shared DEpP present in at least one of the 6hAmAc or the 24hAmAc-treated myotube datasets (Any ammonia) and those DEpP present in at least one of the mouse or human exercise datasets (Any exercise) compared to transcription factor and kinase databases.
(C) Heatmap of canonical pathways enriched in the DEpP from the 6hAmAc and 24hAmAc datasets, mouse exercise datasets, and the human exercise dataset.
(D) Scatterplots of expression levels for DPPS in the mouse exercise and hyperammonemic myotube datasets. All myotube experiments were done in n = 3 biological replicates (one 24hAmAc replicate was removed from downstream analyses because of outlier status). Statistical significance cutoff for UpSet plot and scatterplot DEpP/DPPS was padj<0.05 for ammonia and mouse data and padj<0.05 and expression fold change >|1.5| for human data. Functional enrichment analyses were performed with two cutoffs: 1)log2ratio cutoffs were used to identify a similar proportion of foreground molecules in each dataset (500-800), 2) q<0.05 (as defined by each dataset) was used uniformly. The foregrounds were analyzed against each respective dataset as the background. Significance for canonical pathway enrichment was-log(p value) ≥1.3 using a right-sided Fisher exact test. ∗p<0.05, ∗∗p<0.01, Daytime exercise = mice that underwent high-intensity treadmill running during the zeitgeber time (ZT)0 period of “lights on”; MIC = maximal intensity contraction; Mito. = verified mitochondrial-localized molecules; Nighttime exercise = mice that underwent high-intensity treadmill running during the ZT12 period of “lights off”; NS = non-significant; Treadmill (65% max.) exercise = mice exercised at 65% of their maximal running speed on a treadmill.