Extended Data Fig. 6: Mapping pairwise protein co-regulation onto known protein modules identifies cooperative protein associations across gastruloid development.
From: The proteomic landscape and temporal dynamics of human and mouse gastruloid development
(a) Heatmap displaying pairwise Pearson correlation coefficients among glycolysis (purple) and TCA cycle (green) genes. The upper triangle represents protein-level correlations and the lower triangle represents RNA-level correlations. Black cells denote self-comparisons along the diagonal. (b) Number of observed edges (y-axis) in the correlation network as a function of absolute rPearson (x-axis). (c) Summary of correlated and anticorrelated edges in the network. (d) Fraction of correlated and anticorrelated edges stratified by GOBP, GOCC, Localization, Pathway, GOMF, BioPlex PPI, and Complex databases. Dashed line indicates the fraction of positively correlated edges in the trimmed network. (e) Fraction of correlated edges in the trimmed network explained by at least one database (y-axis) as a function of rPearson (x-axis). Horizontal and vertical dashed lines respectively indicate the fraction of edges explained in annotated network and rPearson at 0.95. (f) Summary of correlated edges in the trimmed network explained by shared membership in a Gene Ontology biological process (GOBP), cellular component (GOCC), molecular function (GOMF), localization, pathway, protein-protein interaction (BioPlex) or protein complex. Dotted line indicates the cumulative number of edges explained within the observed (circles) and annotated (triangle) networks. (g) Distribution of rPearson for protein pairs in CORUM and ComplexPortal complexes. (h) Fraction of complexes detected in correlation network (x-axis) versus size of protein complex (y-axis). Dots colored by database used to curate the protein complexes. (i) Workflow to map cooperative proteins associated with detected modules. (j) Number of cooperative proteins detected (y-axis) as a function of complex size (x-axis). (k) The number of annotated ComplexPortal complexes that were found to be cooperative with each individual protein in the correlation analysis (x-axis), for example ZZZ3 was assigned as a cooperative protein to 32 ComplexPortal protein complexes. (l) Venn diagram indicating the number of cooperative proteins with physical protein-protein interaction evidence to at least one subunit of their associated complex.
