Functional enrichment analyses were performed using ToppFun, a functional enrichment application available at toppgene.cchmc.org as part of the ToppGene suite of web applications [36]. Each paraclique was considered on an individual basis. Entrez ID's for all members of a paraclique were submitted and analyzed for over-representation of genes that belong to a Gene Ontology (GO) category (cellular component, molecular function and biological process), biological pathway, gene family or, similarly, encode a particular protein domain. In order to enhance the specificity and informativeness of these results, we considered only those categories that comprise greater than 3 and fewer than 300 genes, inclusive. Multiple testing was accounted for using a 1% FDR threshold. Results were curated by excluding categories with gene lists more than 80% redundant with other, less enriched, categories.
