STEP 13
To see whether the effect of the animal’s genetic sex on protein abundances is reflective of the underlying genetic factors, we compared the obtained effect sizes directly with the results from Liu et al., 2015, a study on identical twins that addressed to what extent the variation of 342 human plasma proteins can be explained by genetic factors, environment and age. We found that 37% of the environmental effect on the human plasma proteome could be recovered in the DO mice as diet-dependent (Spearman’s rho, two-sided t-test) (Figure S5A). The genetic effect on the human plasma proteome and the impact of the animal’s sex on protein variation correlated positively as well (Spearman’s rho, two-sided t-test).
proteomics data from Chick et al. (2016), Nature (DO Mouse strains)
split_complex_input_files.zip (4.6MB)input files for the machine-learning setup, split complexes
aebersold_liu_twin_data.txt (45.6KB)downloaded from Liu et al.(2015), Molecular Systems Biology
Python code required for calculating effects on protein variation and comparing to Liu et al.(2015), Molecular Systems Biology
output file from machine-learning setup, summarizing variance for all proteins
Supplementary Figure 5