OGI and The Centre for Applied Genomics (TCAG) partnered to co-host a 1 hour web conference/webinar about iRefWeb - a web-based interface to a large landscape of protein-protein interactions (PPI), consolidated from major public databases.
The presentation was led by Dr. Andrei Turinsky, Molecular Structure and Function Program, The Hospital for Sick Children, Toronto and included:
- an introduction to iRefWeb,
- search function and evidence supporting interactions found,
- how to filter the data,
- visualizing interactions, and
- consistency and consolidation across databases.
Can the entire database be downloaded as a flat file?
Yes, the whole database or any of its pre-filtered subsets (e.g. the whole human interactome, the whole yeast interactome, etc.) can be downloaded as a single file in MITAB format. In all cases please use the "Download Interactome" button at the top of the Search page.
One can also get the whole dataset from the iRefIndex site at http://irefindex.uio.no/wiki/iRefIndex, although without search or filter options.
Is the database being updated as new versions come out?
Yes, we perform frequent data consolidation using the most current versions of the source databases. The current release 7.0 of the consolidated interaction set was built in September 2010. The next release 8.0 is scheduled for January 2011.
Does the tool work with Cytoscape?
You can download the interactions of your choice as a MITAB file and import them into Cytoscape using the "File> Import> Network from Table" Cytoscape menu. You may also wish to selectively pre-process the columns of your choice. For example, you may choose to retain only the first and second MITAB columns (which contain unique identifiers for the interactor pairs or members of multi-protein complexes) and remove the namespace prefixes "uniprotkb", "refseq" to improve the Cytoscape link-out and display options.
For a detailed description of the MITAB format please see: http://irefindex.uio.no/wiki/README_MITAB2.6_for_iRefIndex_7.0
Please also note that several Cytoscape plug-ins developed by our teams use iRefWeb interactions. iRefScape is a cytoscape plug-in developed by Donaldson Group that accesses iRefIndex data (http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.9x). Also, OrthoNets is a plug-in developed at the Wodak Lab that displays iRefWeb interactions, and can accept a simple list of iRefWeb interation IDs as input (http://wodaklab.org/orthonets/). The latter could be created using one of the save options of the "Download Interactome" button of the search page.
Can you link to a protein from other web sites?
You can link from your web site to an iRefWeb page of a specific protein. For example, protein E6 of Human papillomavirus type 16, which was used in the webinar, has the iRefWeb interactor ID 3005274. Its web page is available at http://wodaklab.org/iRefWeb/interactor/show/3005274, its full list of its interactions is at http://wodaklab.org/iRefWeb/search?search.q=act_id:3005274, and its neighborhood graph is at http://wodaklab.org/netility/graph?type=PROTEIN&id=3005274.
The first of these URLs also provides a listing of the various names, aliases and IDs associated with E6, and the links to other genomic and proteomic databases, such as UniProt and NCBI RefSeq.
If you do not know the iRefWeb ID of your protein, you can still link to its list of interactions using a protein name, protein ID or gene ID. E.g. for human P53 with a UniProt accession P04637, the corresponding list is at http://wodaklab.org/iRefWeb/search/index?search.filter[alias].values=P04637.
You can see the iRefWeb interactor ID of the protein in question by finding some of its interactions via the iRefWeb search, then examining the list of the interactors within any of the individual interaction pages.
Is the graphical output adjustable for generating figures for publications?
Yes, the tab "Graph Actions" on the left of the visualization page has a button "Export Graph" and a drop-down list of supported image formats, including PNG and PDF.
Is it possible to import one's own annotations/interactions?
No, there is currently no import option in iRefWeb. You can check whether any of your interactions are already in iRefWeb by doing a search for a list of your genes. But if these interactions are not in iRefWeb, you would need to merge them on your own with any interactions that you choose to download from iRefWeb.