Interactions from the LC dataset dominate the composition of predicted protein complexes. (a) Contribution of HTP-PI and LC-PI data to predicted protein complexes. Each of the 420 predicted complexes are binned according to the percentage of LC (blue) or HTP (red) interactions it contains. The two distributions are not exact complements because some interactions are members of both LC-PI and HTP-PI. (b) The overlap of predicted protein complexes with actual protein complexes as defined by co-purification. For a predicted complex and a gold-standard complex, a hit is scored when the two sets of proteins produce a Jaccard similarity of ≥ 0.13. Top panel, green bars indicate the percentage of gold-standard complexes hit by some predicted complex. The sum of the green and yellow bars is the percentage of predicted complexes hit by some gold-standard complex. Bottom panel, the percentage of proteins in gold-standard complexes represented in all predicted complexes. This gives a rough upper bound on the percentage of gold-standard complexes that can be hit. (c) Complexes conserved between yeast and Drosophila are enriched in LC-PI interactions. This histogram is analogous to that shown for yeast-only complexes in Figure 10a. (d) Example of orthology between yeast and fly protein complexes in a cytoskeletal control network. The high degree of LC-PI interconnections between yeast proteins (orange) validates fly HTP interactions (blue) and suggests new potential connections to test between fly proteins. Thick lines indicate direct interactions, thin lines indicate interactions bridged by a common neighbor. Complex layouts were rendered in Cytoscape . (e) Prediction of GO process annotations using conserved versus yeast-only complexes. Green bars indicate the number of correct predictions and yellow bars indicate the number of incorrect predictions, the sum of which is the total number of predictions. Complex and pathway prediction was carried out according to  and results were averaged over five rounds of full tenfold cross-validation.
Reguly et al. Journal of Biology 2006 5:11 doi:10.1186/jbiol36