ToppGene Suite (http://toppgene.cchmc.org; this web site is free and open to all 
users and does not require a login to access) is a one-stop portal for (i) gene 
list functional enrichment, (ii) candidate gene prioritization using either 
functional annotations or network analysis and (iii) identification and 
prioritization of novel disease candidate genes in the interactome. Functional 
annotation-based disease candidate gene prioritization uses a fuzzy-based 
similarity measure to compute the similarity between any two genes based on 
semantic annotations. The similarity scores from individual features are 
combined into an overall score using statistical meta-analysis. A P-value of 
each annotation of a test gene is derived by random sampling of the whole 
genome. The protein-protein interaction network (PPIN)-based disease candidate 
gene prioritization uses social and Web networks analysis algorithms (extended 
versions of the PageRank and HITS algorithms, and the K-Step Markov method). We 
demonstrate the utility of ToppGene Suite using 20 recently reported GWAS-based 
gene-disease associations (including novel disease genes) representing five 
diseases. ToppGene ranked 19 of 20 (95%) candidate genes within the top 20%, 
while ToppNet ranked 12 of 16 (75%) candidate genes among the top 20%.