From: Probabilistic prediction and ranking of human protein-protein interactions
Module abbreviation | Features considered | Data source | Description | Scoring function | Bins |
---|---|---|---|---|---|
E | Expression | GDS596 from the Gene Expression Omnibus [70] | Gene expression profiles from 79 physiologically normal tissues obtained from various sources [71] | Pearson correlation of co-expression over all conditions | 20 of equal size covering the correlation value range (-1 to +1) |
O | Orthology | InParanoid [72], BIND [66], DIP [65] and GRID [69] databases | Interactions of homologous protein pairs from yeast, fly, worm and human | Organism-based using InParanoid score | 13 |
C (Combined) | Localization | PSLT predictions [54] | PSLT is a human subcellular localization predictor that considers nine different compartments (ER, Golgi, cytosol, nucleus, peroxisome, plasma membrane, lysosome, mitochondria and extracellular) | Qualitative score: proximity of compartments | 4 (same, neighboring, different compartments, or not localized) |
Domain co-occurrence | InterPro [73] and Pfam [74] | Protein domains and motifs | Chi-square | 5 covering range of Chi-square scores | |
PTM co-occurrence | HPRD [15] and UniProt [76] | Post-translational modifications |
| 4 covering range of PTM scores | |
D | Disorder | VLS2 predictions [78] | Prediction of protein intrinsic disorder | Sum of the percent disorder for each protein in a pair | 6 covering range of scoring function (0 to 200%) |
T | Transitive | - | Module that considers local topology of underlying network predicted using combinations of above features |
| 5 covering range of scoring function |