ToppGene Suite

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

You can access the ToppGene Suite (http://toppgene.cchmc.org) 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 (http://toppgene.cchmc.org/enrichment.jsp) 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 anil.jegga@cchmc.org or bruce.aronow@cchmc.org