Table 1. Data types used in this study.
| Data type | Kernel | Type | Number |
| Protein sequence | Pfam | Protein | 6700 |
| Protein sequence | motif | Protein | 6622 |
| Protein sequence | spectrum | Protein | 6700 |
| Yeast two-hybrid | diffusion | Protein | 4155 |
| Genetic interaction | diffusion | Protein | 3344 |
| Affinity capture-MS | diffusion | Protein | 3627 |
| Interologs | RBF | Pair | 1615 |
| Co-expression | RBF | Pair | 6320 |
| Gene ontology | RBF | Pair | 5306 |
| Co-regulation | RBF | Pair | 6270 |
| Co-localization | RBF | Pair | 4156 |
Some types of data described individual proteins and are transformed to pairs by using the TPPK. The remaining data types naturally describe pairs of proteins and can be used directly. The last column indicates the number of proteins with information available for a particular type of data.