Framework
FunCoup is a statistical framework of data integration for finding functional coupling (FC) between proteins. It transfers information from model organisms (M. musculus, D. melanogaster, C. elegans, S. cerevisiae etc.) via orthologs found by InParanoid program (Remm et al., 2001).
Data
Data of different sources and various natures, such as contacts of whole proteins and individual domains, mRNA and protein expression, localization in tissues and cellular compartments, miRNA and TF targeting, similar phylogenetic profiles etc., are collected and probabilistically evaluated in a Bayesian network (BN), trained on sets of known FC cases (e.g. KEGG, IntAct, HPRD, or GRID resources) vs. sets of randomly picked protein pairs as background reference (more details here).
Optimization
To address known drawbacks of Bayesian predictors, FunCoup has optimized several aspects:
Compared to previous framework configurations of this sort (see Suthram et al., 2006), the net gain in performance is tens of percentage points in either sensitivity or specificity. The number of simultaneously used model organisms (5-8) and individual datasets (50-60) has been estimated as maximal for practical purposes. However, novel approaches and high-throughput technologies in genomics and proteomics may deliver new orthogonal datasets that will further boost the performance of FunCoup.
The interactomes
With these features, the FunCoup framework predicted global interactomes for H. sapiens, M. musculus, R. norvegicus, C. intestinalis, D. melanogaster, C. elegans, S. cerevisiae, A. thaliana.
All of them are avalable for both complete download and web querying. See more details here.
Web interface
The query page of the web site is designed to maximally alleviate retrieval of compact sub-networks most relevant to the user's research interest. See help page and "Getting started" for more details.