Supporting online material for:
Protein-protein interactions more conserved within than across species

Sven Mika & Burkhard Rost

Material

Table App_1: Large-scale protein-protein interaction data sets from IntAct [1] ^∆

Dataset	Organism	Method	Number of pair interactions
Ito (2001) [2]	Saccharomyces cerevisiae	Y2H	4524
Uetz (2000) [3]	Saccharomyces cerevisiae	Y2H	1495
Ho (2002) [4]	Saccharomyces cerevisiae	MS	29098
Gavin (2002) [5]	Saccharomyces cerevisiae	TAP	19254
Giot (2003) [6]	Drosophila melanogaster	Y2H	20667
Stanyon (2004) [7]	Drosophila melanogaster	Y2H	1615
Formstecher (2005) [8]	Drosophila melanogaster	Y2H	1674
Li (2004) [9]	Caenorhabditis elegans	Y2H	4037
Bouwmeester (2004) [10]	Homo sapiens	TAP + others	1670

∆ Numbers as taken unfiltered directly from IntAct [1].

Fig App_1: Each curve above shows the accuracy (red) as shown in Figure 3 (manuscript) and the number of true positives counted at a certain HSSP-value cutoff (green).

Fig App_2: Results of varying the parameters of our experimental setup to measure the performance of homology inference of protein-protein interactions. Four experiments (A-D) were performed with differences to the experimental setup of Fig 3 (Methods section in manuscript) described below:

A: Different sampling of intra- vs. inter-species: we allowed transfers of the type A-B to A’-B or A-B to A-B’ (Methods). The performance became significantly better for intra-species PPI-transfers, thus further widening the gap between intra and inter-species transfers.

B: Inclusion of transfers within the same data set: we included homology transfers within the same experimental dataset (Methods). The effect was very similar to those observed for different sampling (#1), i.e. widening the gap between intra- and inter-species inferences.

C: Using TAP-like data (Table App_1, Supplementary Online Material) as a constraint for the negatives. To illustrate this assume that TAP pulled down a complex of six proteins. While we cannot infer that all 15 possible interactions are physical, all could be. Therefore, we ignored a false postive prediction (did not count it) if we could find the interaction in those 15 TAP protein-protein pairs. The accuracy slightly increased for both yeast vs yeast (intra-species) comparisons as well as for non-yeast vs yeast (inter-species) comparisons. Note that yeast is the only organism with available TAP-like data.

D: We used a redundant dataset (instead of a non-redundant, bias-reduced set) from organism o (Fig. 7) to hunt for interologs in organism p (Fig. 7). The main message indicated by the results for this latter experiment (#4) stays the same as in our original procedure (Methods): Intra species comparisons are more accurate than inter-species comparisons. Due to more samples in the dataset for organism o (Fig. 7) and thus higher counts, the errors slightly decreased.

References for 'Supporting online material'

1. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, et al. (2004) IntAct - an open source molecular interaction database. Nucleic Acids Res 32: D452-455.

2. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.

3. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.

4. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.

5. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.

6. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.

7. Stanyon CA, Liu G, Mangiola BA, Patel N, Giot L, et al. (2004) A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol 5: R96.

8. Formstecher E, Aresta S, Collura V, Hamburger A, Meil A, et al. (2005) Protein interaction mapping: a Drosophila case study. Genome Res 15: 376-384.

9. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543.

10. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, et al. (2004) A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6: 97-105.