Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering

Abstract

Functional Gene Networks (FGNet) is an R/Bioconductor package that generates gene networks derived from the results of functional enrichment analysis (FEA) and annotation clustering. The sets of genes enriched with specific biological terms (obtained from a FEA platform) are transformed into a network by establishing links between genes based on common functional annotations and common clusters. The network provides a new view of FEA results revealing gene modules with similar functions and genes that are related to multiple functions. In addition to building the functional network, FGNet analyses the similarity between the groups of genes and provides a distance heatmap and a bipartite network of functionally overlapping genes. The application includes an interface to directly perform FEA queries using different external tools: DAVID, GeneTerm Linker, TopGO or GAGE; and a graphical interface to facilitate the use.

Fig. 1.

Schematic workflow. A query gene list is analysed through a FEA tool and the generated gene-term sets are used to build: (A) gene’s adjacency matrices; (B) a functional network (general view); (C) a distance heatmap and (D) an intersection network (to highlight multifunctional genes)