About - iRefWeb - Wodak Lab

You have:

  • discovered a protein or a gene likely to be involved in a disease, and you want to find out what is known about its interactions with other proteins.
  • identified a group of co-expressed genes, and would like to check if the proteins they code for interact physically.
  • found a set of genes associated with a specific phenotype, or a cellular process and would like to prioritize them for further analysis, based on their interaction partners in the cell.

To undertake any of these tasks you would need to overcome several major hurdles. You’ll have to consolidate data on protein interactions across the many public databases that curate them from the scientific literature. This in turn will require that you solve the problem of cross-referencing genes and proteins across biological databases—a tedious and frustrating undertaking. Once you have done all that, you’ll be faced with the huge body of protein interaction data you know very little about, and wondering if you can trust any of it.

iRefWeb overcomes all these hurdles for you. Developed in the Wodak Lab at Toronto's Hospital for Sick Children, with Ian Donaldson, it is a web interface to a broad landscape of data on protein-protein interactions (PPI) consolidated from major public databases:

  • BIND
  • BioGRID
  • DIP
  • IntAct
  • HPRD
  • MINT
  • MPact
  • MPPI

The consolidation process is achieved through a rigorously documented procedure for mapping protein IDs across databases, enabling systematic backtracking of the links used to establish the identity of the interaction partners. This process also includes mapping proteins into their canonical isoforms and protein-coding genes, whenever possible.

Using iRefWeb, researchers can gauge the reliability of an interaction using simple criteria, such as the number of supporting publications, the scale of the corresponding studies (high- or low-throughput) or the detection methods used in the original experiments. They can furthermore compare and contrast the PPI information extracted from the same publication by different databases. This allows to uncover possible inconsistencies, and follow up on them through links to source databases and various supporting evidence.

iRefWeb also presents interactive visualization of the aggregated interactions for a protein of interest, using the Cytoscape Web (Lopez et al, 2010; Cytoscape Web: an interactive web-based network browser), as well as various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins, and cited publications. A number of supporting-evidence filters allow users to automatically crop the PPI dataset to produce a subset of higher-quality interactions, which aids the generation of more meaningful organism-specific interaction networks or 'interactomes'.

All the consolidated data and the custom filtered versions are available for download.

Browse proteins
Browse interactions
iRefWeb 4.1
In collaboration with Ian Donaldson — using iRefIndex Version 9.0
Watch a webinar (or browse the slides) on how to use iRefWeb here.