ToppGene Suite swMATH ID: 30169 Software Authors: Chen, J., E. E. Bardes, B. J. Aronow, A. G. Jegga Description: ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. 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 Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703978/ Related Software: glasso; DEseq; SILGGM; TestBMN; huge; GlobalMIT; MAST; MrTADFinder; slingshot; SNN-Cliq; CIDR; GenClust; DINGO; SCODE; SCENIC; DNA; Sincera; SC3; ARACNE; KEGG Cited in: 6 Documents Further Publications: https://toppgene.cchmc.org/help/publications.jsp all top 5 Cited by 23 Authors 2 Long, Qi 2 Safo, Sandra E. 1 Beerenwinkel, Niko 1 Celedon, Juan C. 1 Chen, Wei 1 Chen, Xinren 1 Ding, Yanjun 1 Huang, Haiyan 1 Kuipers, Jack B. 1 Li, Jingyi Jessica 1 Li, Lexin 1 Li, Shuzhao 1 Liu, Chonghui 1 Lv, Hongchao 1 Merdes, Gunter 1 Ren, Zhao 1 Schmich, Fabian 1 Teng, Yanbo 1 Wang, Xizi 1 Yu, Hang 1 Zhang, Mingming 1 Zhang, Rong 1 Zhang, Ruijie all top 5 Cited in 6 Serials 1 Biometrics 1 Statistical Science 1 Statistical Applications in Genetics and Molecular Biology 1 Statistical Analysis and Data Mining 1 The Annals of Applied Statistics 1 Journal of Theoretical Biology Cited in 3 Fields 5 Statistics (62-XX) 3 Biology and other natural sciences (92-XX) 1 Computer science (68-XX) Citations by Year