FuncNet is a web-based tool for predicting when human proteins of unknown or poorly-understood function (a query set) are involved in the same processes or phenomena as proteins of a distinct and well-characterized function (a reference set). It is designed to help experimentalists narrow down large lists of proteins from high-throughput experiments to more tractable shortlists of candidates for individual assays.
FuncNet brings together an ensemble of algorithms developed and hosted at various sites throughout Europe, statistically combining their output for broader coverage and greater predictive power. FuncNet was funded by the European Union’s EMBRACE and ENFIN networks.
It is intended to help answer questions like:
- Flow diagram. Click for full size.
Given one set of proteins which are known to share a particular biological function…
… which of these other proteins also share that function?
Or:
Given a particular biological system or phenomenon of interest…
… which of my candidate proteins are most likely to be relevant?
You can submit queries to FuncNet via a web interface. For larger queries (over 100 proteins), we recommend using the FuncNet web services.
FuncNet is a free service for the computational biology community, provided by a consortium of bioinformatics groups, and using industry-standard web-service protocols throughout. You are welcome to use results from FuncNet in your own research. A full paper on FuncNet is on its way; in the meantime, please cite this paper. If you have a protein function comparison algorithm which you would like to plug into FuncNet, please get in touch.
Contact: mailbox ‘info‘ at domain ‘funcnet.eu‘, or leave a comment on any page in this site.
This site is hosted by the Orengo Group at UCL, home of the CATH and Gene3D resources which power many of the FuncNet prediction services.
Technical architecture
FuncNet is an open architecture on which multiple prediction algorithms can be queried in parallel in order to provide higher-quality results.
- FuncNet schematic overview (click for full size)
Each predictor is made available via a SOAP web service using a standardized WSDL interface. This means that every FuncNet prediction service is functionally interchangeable – they can all be invoked via the same message format, and you only need to change the endpoint URL and the service and port names.
However, a better way to submit queries is via a front-end service which is responsible for forwarding the request to each of the predictors in parallel. These scores are then aggregated on the server for the user to retrieve in one operation. The front-end service also performs statistical score integration to turn a set of pairwise predictions into a relevance score for each protein, and is responsible for driving the web interface.
Of course, users can submit queries directly to the individual predictors, although the strength of FuncNet comes from its ability to combine the predictions of multiple algorithms which use distinct methods and sources of evidence.
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