Kerfuffle：一个多物种基因共定位分析的网络工具
Kerfuffle: a web tool for multi-species gene colocalization analysis
摘要：
在真核生物中，作为基因组大规模功能组织基础的进化压力还没有得到很好的理解。最近的证据表明，功能相似的基因可能在真核生物基因组中共定位（簇），这表明染色质水平的基因调控在塑造协调基因的物理分布中的作用。然而，目前可用的生物信息学工具很少允许系统地研究几个进化上遥远的物种之间的基因共定位。Kerfuffle是一个网络工具，旨在通过识别现有物种（目前多达47个，从人类到蠕虫）的组装基因组中的重要基因共定位和保守性来帮助发现，可视化和量化基因组的物理组织。Kerfuffle只要求用户指定一个人类基因列表和其他感兴趣物种的名称。在没有用户进一步输入的情况下，软件查询e！Ensembl BioMart服务器获取位置信息，并发现指定的所有基因和物种的同源关系。使用这些信息，Kerfuffle进行多物种聚类分析，提供可下载的聚类基因列表，进行Monte Carlo统计显著性计算，估计跨物种的保守基因簇，绘制直方图和交互式图表，允许用户保存查询，并使用Circos软件生成可下载的聚类可视化。这些分析可用于通过询问与每个簇相关的富集分子通路来进一步探索基因簇的功能作用。
英文摘要：
The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes. However, few of the bioinformatic tools currently available allow for a systematic study of gene colocalization across several, evolutionarily distant species. Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled genomes of available species (currently up to 47, from humans to worms). Kerfuffle only requires the user to specify a list of human genes and the names of other species of interest. Without further input from the user, the software queries the e!Ensembl BioMart server to obtain positional information and discovers homology relations in all genes and species specified. Using this information, Kerfuffle performs a multi-species clustering analysis, presents downloadable lists of clustered genes, performs Monte Carlo statistical significance calculations, estimates how conserved gene clusters are across species, plots histograms and interactive graphs, allows users to save their queries, and generates a downloadable visualization of the clusters using the Circos software. These analyses may be used to further explore the functional roles of gene clusters by interrogating the enriched molecular pathways associated with each cluster.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
