Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Sci. Signal., 26 February 2013
[DOI: 10.1126/scisignal.2003629]

Supplementary Materials for:

Protein Complex–Based Analysis Framework for High-Throughput Data Sets

Arunachalam Vinayagam,* Yanhui Hu, Meghana Kulkarni, Charles Roesel, Richelle Sopko, Stephanie E. Mohr, Norbert Perrimon*

*To whom correspondence should be addressed. E-mail: vinu{at}genetics.med.harvard.edu (A.V.); perrimon{at}receptor.med.harvard.edu (N.P.)

This PDF file includes:

  • Fig. S1. Schematic representation of protein complex scoring.
  • Fig. S2. Snapshots of the COMPLEAT Web interface.
  • Fig. S3. Complex enrichment results of baseline and EGF stimulus.
  • Fig. S4. Baseline compared with EGF stimulus common complexes.
  • Fig. S5. Baseline compared with EGF stimulus dynamic complexes: opposing effects.
  • Fig. S6. Baseline compared with EGF stimulus: baseline-specific dynamic complexes.
  • Fig. S7. Baseline compared with EGF stimulus: stimulus-specific dynamic complexes.
  • Fig. S8. Complex enrichment results of baseline and insulin stimulus.
  • Fig. S9. Baseline compared with insulin stimulus: common complexes.
  • Fig. S10. Baseline compared with insulin stimulus: baseline-specific dynamic complexes.
  • Fig. S11. Baseline compared with insulin stimulus: stimulus-specific dynamic complexes.
  • Table S1. Compilation of literature protein complexes for humans, Drosophila, and yeast.
  • Table S2. PPI data sets used to construct integrated PPI networks for humans, Drosophila, and yeast.
  • Table S3. Predicted protein complexes for humans, Drosophila, and yeast.
  • Table S4. Redundancy in the protein complex resource.
  • Table S5. Overlap of the literature and predicted complexes at the protein level.
  • Table S6. Proteome covered by the protein complex resources.
  • Table S7. Comparison of protein complexes with GO and KEGG with respect to co-citation.
  • Table S8. Comparison of protein complexes with GO and KEGG with respect to protein colocalization.
  • Table S9. Comparison of protein complexes with GO and KEGG with respect to gene coexpression.
  • Table S10. Annotation of the protein complex resource.
  • Table S11. Gene or protein input identifiers supported by the COMPLEAT.
  • Table S20. Dynamic phosphosites changing in response to insulin treatment.

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 2.27 MB

Other Supplementary Material for this manuscript includes the following:

  • Table S12 (Microsoft Excel format). Enriched protein complexes at baseline (mtDER-S2R+ cell line).
  • Table S13 (Microsoft Excel format). Enriched protein complexes at EGF stimulus (mtDER-S2R+ cell line).
  • Table S14 (Microsoft Excel format). Enriched protein complexes at baseline (S2R+ cell line).
  • Table S15 (Microsoft Excel format). Enriched protein complexes at insulin stimulus (S2R+ cell line).
  • Table S16 (Microsoft Excel format). Consistent protein complexes with respect to baseline versus EGF stimulus.
  • Table S17 (Microsoft Excel format). Dynamic protein complexes with respect to baseline versus EGF stimulus.
  • Table S18 (Microsoft Excel format). Consistent protein complexes with respect to baseline versus insulin stimulus.
  • Table S19 (Microsoft Excel format). Dynamic protein complexes with respect to baseline versus insulin stimulus.

[Download Tables S12-S19]

Technical Details

Format: Zip Archive

Size: 314 KB

 


Citation: A. Vinayagam, Y. Hu, M. Kulkarni, C. Roesel, R. Sopko, S. E. Mohr, N. Perrimon, Protein Complex–Based Analysis Framework for High-Throughput Data Sets. Sci. Signal. 6, rs5 (2013).

© 2013 American Association for the Advancement of Science


To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882