Genome‐scale studies using high‐throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user‐defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new computational approach, GenFam, which allows annotation, classification, and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three hundred and eighty‐four unique gene families and supports gene family analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web‐based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web‐based application, source code, and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.

中文翻译：

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GenFam：用于基于基因家族的分类和功能富集分析的Web应用程序和数据库。

使用高通量测序（HTS）技术的基因组规模研究在不同实验条件下产生了大量差异表达基因。需要进一步挖掘这些基因清单以缩小生物学相关基因和相关功能的范围，以指导下游的功能遗传分析。一种流行的方法是通过富集分析工具在用户定义的列表中确定统计上代表过多的基因，这些工具依赖于基于基因本体论（GO）术语的基因功能注释。在这里，我们提出了一种新的计算方法GenFam，它允许基于基因家族的基因进行注释，分类和富集，从而简化了可能与查询相关的候选基因家族和相关基因的识别。GenFam及其集成数据库包含384个独特的基因家族，并支持60个植物基因组的基因家族分析。使用GenFam对属于不同进化枝和科的植物物种进行了四次比较案例研究，证明了其相对于现有功能丰富工具的鲁棒性和全面性。为了使植物生物学家易于使用，GenFam可作为基于Web的应用程序使用，用户可以在其中以表格和图形格式输入基因ID并导出富集结果。用户还可以通过从各种统计富集测试和多种测试校正方法中进行选择来定制分析参数。此外，可免费使用和下载基于Web的应用程序，源代码和数据库。网站：http：// mandadilab。webfactional.com/home/。源代码和数据库：http://mandadilab.webfactional.com/home/dload/。