Table I. Annotation coherence among interacting proteins for selected protein interaction data sets. For each top-level annotation class of “Function,” “Location,” and “Complex” in the Munich Information Center for Protein Sequences, we classified an interaction as intra-annotation if both proteins were annotated and shared at least one common annotation item, or interannotation if both proteins were annotated but no common annotation was shared. The sum of the intra- and inter-annotation can add up to less than the total number of interactions due to cases where at least one protein lacks any annotation. The number in parenthesis gives the percentage of the total number of interactions in Column 3. The Methods Section provides descriptions and characteristics of the separate data sets. Abbreviations: AP/MS, affinity purification/mass spectrometry; PCA, protein-fragment complementation assay; Y2H, yeast two-hybrid.
| Network | Number of Proteins | Number of Interactions | Function |
Location |
Complex |
|||
|---|---|---|---|---|---|---|---|---|
| Intra-annotation | Inter-annotation | Intra-annotation | Inter-annotation | Intra-annotation | Inter-annotation | |||
| Manually curated binary interaction | ||||||||
| BGS | 1061 | 1239 | 1176 (95%) | 41 (3%) | 1092 (88%) | 83 (7%) | 521 (42%) | 102 (8%) |
| High-confidence high-throughput | ||||||||
| AP/MS | 1274 | 7879 | 6722 (85%) | 1007 (13%) | 6914 (88%) | 626 (8%) | 2462 (31%) | 819 (10%) |
| PCA | 1076 | 2530 | 1315 (52%) | 732 (29%) | 1802 (71%) | 530 (21%) | 161 (6%) | 109 (4%) |
| Y2H | 1962 | 2703 | 1161 (43%) | 834 (31%) | 1691 (63%) | 580 (21%) | 148 (6%) | 113 (4%) |
| Raw high-throughput | ||||||||
| AP/MS | 2551 | 18,043 | 9537 (53%) | 7315 (40%) | 12,486 (69%) | 5048 (28%) | 1393 (8%) | 2731 (15%) |