ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.
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DOI：
10.1093/nar/gkp427
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Jegga AG
中科院分区：
文献类型：
--
作者：
Chen J;Bardes EE;Aronow BJ;Jegga AG
ToppGene Suite（http：toppgene.cchmc.org;该网站是免费的，对所有用户开放，不需要登录访问）是一个一站式门户网站，用于（i）基因列表功能富集，（ii）使用功能注释或网络分析的候选基因优先级排序，和（iii）相互作用组中新疾病候选基因的鉴定和优先级排序。基于功能注释的疾病候选基因优先级排序使用基于模糊的相似性度量来计算基于语义注释的任何两个基因之间的相似性。使用统计元分析将来自个体特征的相似性分数组合成总体分数。测试基因的每个注释的P值通过全基因组的随机取样来导出。基于蛋白质-蛋白质相互作用网络（PPIN）的疾病候选基因优先级排序使用社交和Web网络分析算法（PageRank和HITS算法的扩展版本，以及K-Step Markov方法）。我们使用20个最近报道的基于GWAS的基因-疾病关联（包括新的疾病基因）代表5种疾病，证明了ToppGene Suite的实用性。ToppGene将20个候选基因中的19个（95%）排在前20%内，而ToppNet将16个候选基因中的12个（75%）排在前20%内。
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%.
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影响因子：
30.8
作者：
Fisher, Sheila A.;Tremelling, Mark;Anderson, Carl A.;Gwilliam, Rhian;Bumpstead, Suzannah;Prescott, Natalie J.;Nimmo, Elaine R.;Massey, Dunecan;Berzuini, Carlo;Johnson, Christopher;Barrett, Jeffrey C.;Cummings, Fraser R.;Drummond, Hazel;Lees, Charlie W.;Onnie, Clive M.;Hanson, Catherine E.;Blaszczyk, Katarzyna;Inouye, Mike;Ewels, Philip;Ravindrarajah, Radhi;Keniry, Andrew;Hunt, Sarah;Carter, Martyn;Watkins, Nick;Ouwehand, Willem;Lewis, Cathryn M.;Cardon, Lon;Lobo, Alan;Forbes, Alastair;Sanderson, Jeremy;Jewell, Derek P.;Mansfield, John C.;Deloukas, Panos;Mathew, Christopher G.;Parkes, Miles;Satsangi, Jack
通讯作者：
Satsangi, Jack
影响因子：
3
作者：
Berger SI;Posner JM;Ma'ayan A
通讯作者：
Ma'ayan A
影响因子：
3
作者：
Chen J;Xu H;Aronow BJ;Jegga AG
通讯作者：
Jegga AG
影响因子：
3.5
作者：
Gorgels, TGMF;Hu, XF;Bergen, AAB
通讯作者：
Bergen, AAB
影响因子：
14.9
作者：
Peri, S;Navarro, JD;Pandey, A
通讯作者：
Pandey, A