Supplementary Materials

Supplementary Materials for:

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

Arunachalam Vinayagam, Ulrich Stelzl,* Raphaele Foulle, Stephanie Plassmann, Martina Zenkner, Jan Timm, Heike E. Assmus, Miguel A. Andrade-Navarro, Erich E. Wanker*

*To whom correspondence should be addressed. E-mail: stelzl{at} (U.S.); erich.w{at} (E.E.W.)

This PDF file includes:

  • Fig. S1. Topological properties of the Y2H PPI network.
  • Fig. S2. Gene Ontology annotation of interacting proteins.
  • Fig. S3. Predicting causal interactions using a naïve Bayesian classifier.
  • Fig. S4. Extracting canonical signaling pathways as shortest path connections (SPCs) from a KEGG PPI network.
  • Fig. S5. Distribution of SPCs in groups of SPCs that connect receptor and transcription factor families (grouped SPCs).
  • Fig. S6. Topological comparison of the undirected HPPI1 and the directed HPPI2.
  • Fig. S7. Enriched motifs identified with Mfinder.
  • Fig. S8. Dynamics of EGF/ERK signal flow from receptor to transcription factors.
  • Legends for Tables S1, S2, and S6
  • Table S3. Human PPI interaction data sets used to construct the HPPI1 network.
  • Table S4. Features used by a naïve Bayesian classifier to predict edge directions.
  • Table S5. Comparison of different classifier performance for edge direction prediction.
  • Table S7. EGF/ERK signal flow mediated by different functional proteins.
  • Table S8. Enrichment of single- and multisite EGF-responsive phosphoproteins.
  • Table S9. Dynamics of EGF/ERK signal flow in HPPI2 network.
  • Table S10. Dynamics of EGF/ERK signal flow from receptor to transcription factors.
  • Table S11. Proteins tested in an ERK phosphorylation ELISA assay.
  • Table S12. Characterization of MAPK6-interacting proteins.
  • References

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Baits selected for Y2H screening.
  • Table S2 (Microsoft Excel format). Y2H interactions in the Y2H PPI network.
  • Table S6 (Microsoft Excel format). Directed interactions in HPPI2 network.

[Download Tables S1, S2, and S6 (Compressed)]

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Format: Microsoft Excel. Files are packaged as a compressed archive, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the instructions below.

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Citation: A. Vinayagam,U. Stelzl, R. Foulle,S. Plassmann, M. Zenkner, J. Timm, H. E. Assmus, M. A. Andrade-Navarro, E. E. Wanker, A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction. Sci. Signal. 4, rs8 (2011).

© 2011 American Association for the Advancement of Science