Proteomic and phosphoproteomic changes upon CK2 inhibition. (A and B) Volcano plots of log₂ ratio (protein abundance) versus −log₁₀ P value for individual proteins in meiosis in the presence of CK2 inhibitor (CK2i) compared to meiosis in the absence of CK2i (A) and mitosis in the presence of CK2i compared to mitosis in the absence of CK2i (B), respectively. Red points indicate significantly enriched (log₂ ratio >1 and P value <0.05) proteins (total number indicated in red). Blue points indicate significantly depleted (log₂ ratio less than −1 and P value <0.05) proteins (total number indicated in blue). n = 16,105 proteins. (C) Venn diagram indicating the number of unique proteins in the categories enriched in meiosis relative to mitosis and enriched in meiosis in the absence of CK2i relative to meiosis in the presence of CK2i and in the overlap between these two categories. (D) Venn diagram indicating the number of unique proteins in the categories enriched in mitosis relative to meiosis and enriched in meiosis in the presence of CK2i relative to meiosis in the absence of CK2i and in the overlap between these two categories. (E and F) Volcano plots of log₂ ratio (phosphopeptide abundance) versus −log₁₀ P value for individual phosphopeptides in meiosis in the presence of CK2i compared to meiosis in the absence of CK2i (n = 28,583 phosphopeptides) (E) and mitosis in the presence of CK2i compared to mitosis in the absence of CK2i (n = 28,597 phosphopeptides) (F), respectively. Red points indicate significantly enriched (log₂ ratio >1 and P value <0.05) phosphopeptides (total number indicated in red). Blue points indicate significantly depleted (log₂ ratio less than −1 and P value <0.05) phosphopeptides (total number indicated in blue). (G) Venn diagram indicating the number of unique phosphopeptides and proteins containing phosphopeptides in the categories enriched in meiosis relative to mitosis and enriched in meiosis in the absence of CK2i relative to meiosis in the presence of CK2i and in the overlap between these two categories that do not exhibit protein-level changes in the same directions. (H) Venn diagram indicating the number of unique phosphopepetides and proteins containing phosphopeptides in the categories enriched in mitosis relative to meiosis and enriched in meiosis in the presence of CK2i relative to meiosis in the absence of CK2i and in the overlap between these two categories that do not exhibit protein-level changes in the same directions. (I) STRING network analysis of candidate proteins carried out using full STRING network annotations with high confidence (interaction score ≥0.7). Edge color indicates data source with known interactions shown in cyan (from curated databases) and magenta (experimentally determined), predicted interactions shown in emerald green (gene neighborhood), red (gene fusions), royal blue (gene co-occurrence), lime green (text mining), black (co-expression), and lilac (protein homology). K-means clustering with default parameters was used to define functional clusters. The dashed lines represent edges between clusters. CK2i was added at a concentration of 25 µM in meiotic extract and 10 µM in mitotic extract. Datasets 1 and 2 were combined and visualized together in this figure. Individual datasets are visualized separately in Fig. S4 (proteome) and Fig. S5 (phosphoproteome).