Phosphoproteomic Analysis Reveals Interconnected System-Wide
Responses to Perturbations of Kinases and Phosphatases in Yeast
Bernd Bodenmiller, Stefanie Wanka, Claudine Kraft, Jörg Urban, David Campbell, Patrick G. Pedrioli, Bertran Gerrits, Paola Picotti, Henry Lam, Olga Vitek, Mi-Youn Brusniak, Bernd Roschitzki, Chao Zhang, Kevan M. Shokat, Ralph Schlapbach, Alejandro Colman-Lerner, Garry P. Nolan, Alexey I. Nesvizhskii, Matthias Peter, Robbie Loewith, Christian von Mering, Ruedi Aebersold*
*To whom correspondence should be addressed. E-mail:
This PDF file includes:
- Materials and Methods
- Fig. S1. Power of the analysis approach.
- Fig. S2. Topological properties of the protein phosphorylation network.
- Fig. S3. Abundance distribution of responder phosphoproteins (proteins that contain "regulated" phosphopeptides).
- Fig. S4. Ratio of phosphopeptides that are reduced or increased in abundance.
- Fig. S5. Regulation of phosphopeptides versus regulation of protein abundance.
- Fig. S6. Regulation of phosphopeptides versus regulation of protein abundance.
- Fig. S7. Regulation of phosphopeptides that map to the same protein.
- Table S2. False discovery rate of peptide identification and specificity of phosphopeptide enrichment for each analyzed phosphorylation pattern.
- Table S4. Significant coregulation of kinases and phosphatases.
- Table S5. Overlap of data from this study with other data sets.
- Table S7. Overlap of possible direct targets with other data sets.
- Table S8. Effects of each kinase and phosphatase on the phosphoproteome.
- Table S9. Enrichment of biological processes among the low-impact kinases (bottom half).
- Table S10. Enrichment of biological processes among the high-impact kinases (top half).
- Table S12. Overview of the entire data set.
Format: Adobe Acrobat PDF
Size: 741 KB
Other Supplementary Material for this manuscript includes the following:
- Table S1. List of enzymes.
- Table S3. Information on phosphopeptides and phosphoproteins.
- Table S6. Confirmed STRING interactions.
- Table S11. GO terms.
- Table S13. Information on yeast strains.
Format: Microsoft Excel
Size: 68 KB, 1861 KB, 69 KB, 111 KB, 555 KB
Citation: B. Bodenmiller, S. Wanka, C. Kraft, J. Urban, D. Campbell, P. G. Pedrioli, B. Gerrits, P. Picotti, H. Lam, O. Vitek, M.-Y. Brusniak, B. Roschitzki, C. Zhang, K. M. Shokat, R. Schlapbach, A. Colman-Lerner, G. P. Nolan, A. I. Nesvizhskii, M. Peter, R. Loewith, C. von Mering, R. Aebersold, Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast. Sci. Signal. 3, rs4 (2010).