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.

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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.

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© 2013 American Association for the Advancement of Science