Table 1.
Data sources integrated to predict localization information
| Species | Data set | Proteins | Localizations |
|---|---|---|---|
| Localization | |||
| Saccharomyces cerevisiae (22 localizationsa) | Localization-known proteins | 3914 | 5184 |
| Localization-known and having interactions | 3206 | 4284 | |
| Ambiguous | 237 | 189 335 | |
| Localization-unknown | 1530 | 0 | |
| Drosophila melanogaster (12 localizationsb) | Localization-known | 2187 | 2398 |
| Localization-known and having interactions | 1610 | 1778 | |
| Localization-unknown and having interactions | 5656 | 0 | |
| Homo sapiens (13 localizationsc) | Localization-known | 4570 | 5251 |
| Localization-known and having interactions | 2684 | 3093 | |
| Localization-unknown and having interactions | 3767 | 0 | |
| Species | Data set | Proteins | Interactions |
| Interaction | |||
| Saccharomyces cerevisiae | BioGRID | 5184 | 70 700 |
| DIP | 4931 | 17 471 | |
| SGD | 5395 | 56 035 | |
| Drosophila melanogaster | BioGRID | 7545 | 25 463 |
| DIP | 7038 | 20 719 | |
| Homo sapiens | BioGRID | 7378 | 20 968 |
| Feature | Description | ||
| Protein feature | |||
| Sequences | UniProt (for SC and HS) and FlyBase (for DM) | ||
| Chemical property | Hydrophobicity, hydrophilicity and side-chain mass | ||
| Motifs | InterPro | ||
| Functions | InterPro and GO | ||
Here, we only considered the proteins with sequence information.
a22 SC localizations are actin, bud, bud neck, cell periphery, cytoplasm, early Golgi, endosome, ER, ER to Golgi, Golgi, late Golgi, lipid particle, microtubule, mitochondrion, nuclear periphery, nucleolus, nucleus, peroxisome, punctate composite, spindle pole, vacuolar membrane, vacuole.
b12 DM localizations are actin, cell periphery, centrosome, cytosol, ER, golgi, lysosome, mitochondrion, nucleolus, nucleus, peroxisome, vacuole.
c13 HS localizations are actin, cell cortex, centrosome, cytosol, ER, golgi, lysosome, mitochondrion, nucleolus, nucleus, peroxisome, plasma membrane, vacuole. Further details regarding localizations and interactions of SC, DM and HS are in Supplementary Figure S1 and Tables S1–S4.