Table 1 Improvements over the previous integration analysis for human PPI predictions
| Â | Â | Rhodes et al. | This study |
|---|---|---|---|
Gold standard positive (HPRD version) | Â | Aug, 2004 | Sep, 2005 (About 10000 more interactions) |
Number of data types integrated | Â | 4 (PPI, GO, Microarray, DDI) | 7 (PPI, GO, Microarray, DDI, Phenotypic, Genetic, Gene context) |
Number of datasets integrated | Â | 13 | 27 |
Info from model organism | Â | Only the PPI is applied | All the possible large scale data from model organism |
Datasets for each data type | Gene expression | 5 | 3 |
| Â | PPI dataset | 4 yeast, 1 worm and 1 fly | 5 yeast, 1 worm, 2 fly and 2 Human |
| Â | GO dataset | Human | yeast, worm, fly, mouse and human |
| Â | Phenotypic | None | 2 yeast and 1 fly datasets |
| Â | Genetic interaction | None | 2 yeast datasets |
| Â | DDI interactions | Interpro annotation | Domain-domain interaction score dataset |
| Â | Gene context | None | 3 yeast datasets |
Method to validate the results | Â | One simple test using the old HPRD as training set and the updated HPRD as test set | 10-fold cross-validation |
Size of integrated network under TP/FP ratio of 1 | Â | 38,379 interactions among 5,791 proteins | 180,010 interactions among 9,901 proteins |
Data query | Â | One time spread sheet download | Online query options with selectable data types and confidence level; data can be downloaded through spreadsheet or network graphs. |
Network visualization and analysis | Â | Only support one single gene's search and none for download or analysis | Network cluster extraction, visualization, drill-down and download options |