Table 1.
Summary of main relationships in the knowledge base
| Type of network | Type of interaction (source) | Nodes | Relationships |
|---|---|---|---|
| Phenotypic relationships | |||
| OMIM-OMIM | Inferred by Genes (OMIM) | 1843 | 2885 |
| OMIM-OMIM | Phenotypic Similarity (HPO) | 4627 | 149689a |
| Orphan Disease-Orphan Disease | Inferred by Genes (Orphanet) | 1655 | 3568 |
| Orphan Disease-Orphan Disease | Phenotypic Similarity (HPO) | 3068 | 75924a |
| Gene-Gene | Inferred by OMIM (OMIM) | 784 | 3217 |
| Gene-Gene | Inferred by Orphan Disease (Orphanet) | 1641 | 8292 |
| Gene-Gene | Phenotypic Similarity (HPO) | 1681 | 24902a |
| Functional relationships | |||
| Gene-Gene | Functional Similarity (GO Biological Process) | 9123 | 486982a |
| Gene-Gene | Functional Similarity (GO Cellular Component) | 6046 | 565739a |
| Gene-Gene | Functional Similarity (GO Molecular Function) | 8087 | 397683a |
| Gene-Gene | Protein-protein interactions (STRING) | 10316 | 96856 |
| Gene-Gene | Metabolic interactions [Veeramani and Bader[15]] | 535 | 9812 |
aResulting relationships to apply the respective cutoff for low confidence level.