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%) candidate genes within the top 20%, while ToppNet ranked 12 of 16 (75%) candidate genes among the top 20%.
Keywords for this software
References in zbMATH (referenced in 8 articles )
Showing results 1 to 8 of 8.
- Wang, Y. X. Rachel; Li, Lexin; Li, Jingyi Jessica; Huang, Haiyan: Network modeling in biology: statistical methods for gene and brain networks (2021)
- Zhang, Rong; Ren, Zhao; Celedón, Juan C.; Chen, Wei: Inference of large modified Poisson-type graphical models: application to RNA-seq data in childhood atopic asthma studies (2021)
- Safo, Sandra E.; Long, Qi: Sparse linear discriminant analysis in structured covariates space (2019)
- Schmich, Fabian; Kuipers, Jack; Merdes, Gunter; Beerenwinkel, Niko: netprioR: a probabilistic model for integrative hit prioritisation of genetic screens (2019)
- Safo, Sandra E.; Li, Shuzhao; Long, Qi: Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information (2018)
- Teng, Yanbo; Ding, Yanjun; Zhang, Mingming; Chen, Xinren; Wang, Xizi; Yu, Hang; Liu, Chonghui; Lv, Hongchao; Zhang, Ruijie: Genome-wide haplotype association study identifies risk genes for non-small cell lung cancer (2018)
- Gottlieb, Assaf; Varshavsky, Roy; Linial, Michal; Horn, David: Uffizi: a generic platform for ranking informative features (2010) ioport
- Chen, Jing; Bardes, Eric E.; Aronow, Bruce J.; Jegga, Anil G.: Toppgene suite for gene list enrichment analysis and candidate gene prioritization (2009) ioport
Further publications can be found at: https://toppgene.cchmc.org/help/publications.jsp