Functional analysis beyond enrichment: Non-redundant reciprocal linkage of genes and biological terms

Abstract

Functional analysis of large sets of genes and proteins is becoming more and more necessary with the increase of experimental biomolecular data at omic-scale. Enrichment analysis is by far the most popular available methodology to derive functional implications of sets of cooperating genes. The problem with these techniques relies in the redundancy of resulting information, that in most cases generate lots of trivial results with high risk to mask the reality of key biological events. We present and describe a computational method, called GeneTerm Linker, that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. The algorithm is tested with a small set of well known interacting proteins from yeast and with a large collection of reference sets from three heterogeneous resources: multiprotein complexes (CORUM), cellular pathways (SGD) and human diseases (OMIM). Statistical Precision, Recall and balanced F-score are calculated showing robust results, even when different levels of random noise are included in the test sets. Although we could not find an equivalent method, we present a comparative analysis with a widely used method that combines enrichment and functional annotation clustering. A web application to use the method here proposed is provided at http://gtlinker.cnb.csic.es. © 2011 Fontanillo et al.