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Sci. Signal., 21 December 2010
[DOI: 10.1126/scisignal.2001182]

Supplementary Materials for:

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: aebersold{at}imsb.biol.ethz.ch

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.
  • References

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Other Supplementary Material for this manuscript includes the following:

Technical Details

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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).

© 2010 American Association for the Advancement of Science


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