FunRich: An open access standalone functional enrichment and interaction network analysis tool
FunRich: An open access standalone functional enrichment and interaction network analysis tool
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DOI：
10.1002/pmic.201400515
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发表时间：
2015-08-01
期刊：
影响因子：
3.4
通讯作者：
Mathivanan, Suresh
中科院分区：
文献类型：
--
作者：
Pathan, Mohashin;Keerthikumar, Shivakumar;Mathivanan, Suresh
随着包括蛋白质组学在内的高通量技术越来越多地被各个实验室获得，迫切需要一种用户友好的生物信息学分析系统。在这里，我们描述FunRich，一个开放访问、独立的功能丰富和网络分析工具。FunRich被设计成供生物学家使用，而计算和数据库专家的支持很少，甚至没有支持。使用FunRich，用户可以对来自不同基因组和蛋白质组资源(>；150万条注释)的背景数据库进行功能丰富分析。除了默认的人类特有的FunRich数据库，用户还可以从UniProt数据库下载数据，UniProt数据库目前支持20个不同的分类，可以对其执行丰富分析。此外，用户可以建立他们自己的定制数据库，并执行不同生物体的浓缩分析。除了蛋白质组学数据集，定制数据库还允许该工具用于基因组学、脂质组学和代谢组学数据集。因此，FunRich允许完全的数据库定制，从而允许将该工具用作浓缩分析的骨架，而不考虑所使用的数据类型或有机体。FunRich()是用户友好的，并提供数据的图形表示(维恩图、饼图、条形图、柱状图、热图和甜甜圈)，具有可定制的字体、比例和颜色(出版质量)。
As high-throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user-friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich () is user-friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).