Table 1.

Improvements over the previous integration analysis for human PPI predictions

		Rhodes et al.	This study
Gold standard positive (HPRD version)		Aug, 2004	Sep, 2005 (About 10000 more interactions)
Number of data types integrated		4 (PPI, GO, Microarray, DDI)	7 (PPI, GO, Microarray, DDI, Phenotypic, Genetic, Gene context)
Number of datasets integrated		13	27
Info from model organism		Only the PPI is applied	All the possible large scale data from model organism
Datasets for each data type	Gene expression	5	3
	PPI dataset	4 yeast, 1 worm and 1 fly	5 yeast, 1 worm, 2 fly and 2 Human
	GO dataset	Human	yeast, worm, fly, mouse and human
	Phenotypic	None	2 yeast and 1 fly datasets
	Genetic interaction	None	2 yeast datasets
	DDI interactions	Interpro annotation	Domain-domain interaction score dataset
	Gene context	None	3 yeast datasets
Method to validate the results		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		38,379 interactions among 5,791 proteins	180,010 interactions among 9,901 proteins
Data query		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		Only support one single gene's search and none for download or analysis	Network cluster extraction, visualization, drill-down and download options