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 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).
- To address known drawbacks of Bayesian predictors, FunCoup has optimized several aspects:
Ways to choose among alternative values from multiple pairs of homologs;
Metrics for comparing mRNA expression profiles,
sub-cellular co-localization, phylogenetic profiles across eukaryotic organisms;
Optimized partitioning to render continuous metrics discrete;
Differential BN training on different types of functional coupling (e.g. physical interactions, metabolic pathway links, signaling links) and then focusing on prediction of respective links from the input data.
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.