Network analyses for protein function discovery

Project leader

Funding source

Swedish Research Council - Vetenskapsrådet (VR)

Project Details

Start date: 01/01/2009
End date: 31/12/2011
Funding: 1800000 SEK


The project aims to develop computational methods and databases that will be used to discover protein function in networks of functionally coupled genes/proteins. The research includes data collection of relevant genomics, proteomics, and functional genomics data in human and model organisms, and benchmarking these for functional coupling inference using gold standard reference sets. Orthologs are used to transfer interactions between different species. The networks form the basis for identifying new disease genes as genes that are strongly linked to known disease genes. A generalised mathematical framework for combining heterogeneous sources of functional coupling and orthology assignments to reconstruct networks was recently developed by the Sonnhammer lab. The optimised method was applied to eight eukaryotes and produced the to date most comprehensive networks. This was released as the FunCoup database (, and the underlying ortholog resource as InParanoid ( The networks will be extended to more data types and classes of predicted interactions. We will move towards real pathway reconstruction by developing new algorithms for adding directed links and for incorporating gene regulatory links. A focus will be on disease pathways. We will use the reconstructed networks to identify and rank new candidate disease genes, analyse the crosstalk between diseases, and identify parallel paths involving disease genes.

Last updated on 2017-31-03 at 12:58