Figure 2.

The Deletion of Each Yeast Kinase Triggers a Unique Reconfiguration of Enzyme Expression in the Cell

(A) Similarity and overlap between enzyme expression proteomes obtained upon kinase deletion in S. cerevisiae. Each cell represents the overlap in the compendium of differentially expressed enzymes (relative to the parental strain BY4741-pHLUM) between any pair of kinase knockouts. An enzyme is considered differentially expressed if the fold change > |log₂(1.4/0.714)|, BH adj. p < 0.01. The matrix distinguishes between upregulated (red, upper right part of the matrix) and downregulated (blue, lower left part) enzymes. For illustration purposes, rows and columns are clustered according to the Jaccard distance between the proteomes, disregarding the directionality of the expression changes. The overlap between each pair of proteomes is shown as Jaccard similarity.

(B) The fraction of differentially expressed metabolic enzymes in comparison to total differential protein expression in all kinase mutants (bar chart). The absolute average similarity of kinase deletion enzyme proteomes, across all kinase mutants, is depicted as a black line. The typical kinase deletion causes a unique enzyme expression signature, with a median dissimilarity between kinase proteome pairs of 88% (average overlap between enzymes differentially expressed = 12%).

(C) The typical overlap of perturbed enzyme proteomes in kinases mutants is not more than ∼25% (dotted median line).

(D) Enzyme expression changes (log₂-fold change) are not better explained by the signaling pathway annotations as obtained from KEGG or Reactome databases compared to randomly assembled pathways. More comparisons are provided in Figures S9 and S10.