All three datasets, which are downloadable from the BIND website, are protein-protein interactions obtained by the Two Hybrid Test. The Gene Association files are from the Gene Ontology website. The middle column lists all the proteins where the interactions between them are tested in the experiments.

The Saccharomyces cerevisiae dataset has 7903 interactions and 4141 proteins. 3554 proteins have at least one GO annotation in GO database. After removing redundancy and self-links, the dataset has 7686 interactions and 4141 proteins. 5802 (75.5%) interactions have at least one alternative path, 1884 (24.5%) interactions have no alternative path. The average length of the alternative path is 4.98. Note that the alternative path is not necessarily the shortest path according to its definition. All functional classes (function class level is set to 2) are been found along the paths.

The Drosophila melanogaster dataset has 24477 interactions and 7621 proteins. 6132 proteins have at least one GO annotation in GO database. After removing redundancy and self-links, the dataset has 22437 interactions and 7621 proteins. 19732 (87.9%) interactions have at least one alternative path, 2705 (12.0%) interactions have no alternative path. The average length of the alternative path is 4.64.

The Caenorhabditis elegans dataset has 5123 interactions and 2911 proteins. 2175 proteins have at least one GO annotation in GO database. After removing redundancy and self-links, the dataset has 5025 interactions and 2911 proteins. 3312 (65.9%) interactions have at least one alternative path, 1713 (34.1%) interactions have no alternative path. The average length of the alternative path is 3.93.