ToppGene Suite

Bruce Aronow, Ph.D., is sharing a one-stop, online computational software tool, “ToppGene.”

You can access the ToppGene Suite ( for (a) gene list functional enrichment, (b) candidate gene prioritization using either functional annotations or network analysis or both, and (c) identification and prioritization of novel disease candidate genes.

Toppfun ( is a human genome-centered geneset enrichment and analysis tool that allows for comparisons of user input genes or genelists to a myriad of genetic, genomic, and epigenomic datasets, including PCBC genomic atlas data.

Toppfun  can be used to explore both known and unknown but potentially interesting connections to either a single gene of interest or to a group of genes in a list.  A tutorial and short video how this resource can be used to specifically mine PCBC data will be available soon.

Functional annotation based disease candidate gene prioritization uses fuzzy-based similarity measures 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 from the whole genome. The protein-protein interaction network (PPIN) based disease candidate gene prioritization uses social and Web network analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method).

For further information and help you can contact or



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