What are the differences between the generic PPI databases?

The IMEx Interactome PPI data come from InnateDB, a database aimed at facilitating systems-level analysis of the mammalian innate immune system by annotating the relationships between biological pathways and molecules related to the innate immune system. All interactions are manually curated from the literature according to the International Molecular Exchange Consortium (IMEx) standards.

The STRING Interactome integrate PPI interaction data from many sources, including using direct (physical associations from experimental data) and indirect (functional associations based on computational predictions) evidence, for over 2000 species. The key distinguishing factor of the STRING project is that they assign a confidence score to each interaction, with interactions with more evidence scoring higher. The “Confidence score cut-off” can be adjusted to restrict addition of PPIs below the specified value from being added to your network. Checking the “Require experimental evidence” box will exclude PPIs that are supported by computational predictions only. The data were downloaded from the STRING database (version 10).

The Rolland Interactome PPI data are a collection of human binary PPIs from the literature in 7 public databases. Binary PPIs refer to direct physical interactions between proteins. To produce the Rolland Interactome, 33 000 binary human PPIs were collected from the literature. Of these, the 11 045 with multiple supporting studies were retained.

The HuRI (The Human Reference Interactome) systematically interrogates human binary protein-protein interactions by using high throughput yeast two-hybrid method in addition to high confidence PPIs extracted from the literature (~ 50 000 interactions in total)