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}molgen.mpg.de (U.S.); erich.w{at}mdc-berlin.de (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

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 2.26 MB

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)]

Technical Details

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.

Size: 1.29 MB (compressed); 3.73 MB (decompressed)

Instructions for downloading and decompressing files:

1. Create a temporary folder on your machine's hard drive.
2. Save the compressed archive to the temporary folder you created, using the links above.
3. Decompress the compressed file in the temporary folder using decompression software such as WinZip (Windows; www.winzip.com) or StuffIt Expander (Windows and Mac; www.stuffit.com).

© 2011 American Association for the Advancement of Science