Elsik Christine G, Tayal Aditi, Unni Deepak R, Burns Gregory W, Hagen Darren E
Division of Animal Sciences, University of Missouri, Columbia, MO, USA.
Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
Methods Mol Biol. 2018;1757:513-556. doi: 10.1007/978-1-4939-7737-6_17.
The Hymenoptera Genome Database (HGD; http://hymenopteragenome.org ) is a genome informatics resource for insects of the order Hymenoptera, which includes bees, ants and wasps. HGD provides genome browsers with manual annotation tools (JBrowse/Apollo), BLAST, bulk data download, and a data mining warehouse (HymenopteraMine). This chapter focuses on the use of HymenopteraMine to create annotation data sets that can be exported for use in downstream analyses. HymenopteraMine leverages the InterMine platform to combine genome assemblies and official gene sets with data from OrthoDB, RefSeq, FlyBase, Gene Ontology, UniProt, InterPro, KEGG, Reactome, dbSNP, PubMed, and BioGrid, as well as precomputed gene expression information based on publicly available RNAseq. Built-in template queries provide starting points for data exploration, while the QueryBuilder tool supports construction of complex custom queries. The List Analysis and Genomic Regions search tools execute queries based on uploaded lists of identifiers and genome coordinates, respectively. HymenopteraMine facilitates cross-species data mining based on orthology and supports meta-analyses by tracking identifiers across gene sets and genome assemblies.
膜翅目基因组数据库（HGD；http://hymenopteragenome.org ）是一个针对膜翅目昆虫的基因组信息资源库，膜翅目昆虫包括蜜蜂、蚂蚁和黄蜂。HGD提供了带有手动注释工具（JBrowse/Apollo）的基因组浏览器、BLAST、批量数据下载以及一个数据挖掘仓库（HymenopteraMine）。本章重点介绍如何使用HymenopteraMine创建可导出以供下游分析使用的注释数据集。HymenopteraMine利用InterMine平台，将基因组组装和官方基因集与来自OrthoDB、RefSeq、FlyBase、基因本体论、UniProt、InterPro、KEGG、Reactome、dbSNP、PubMed和BioGrid的数据，以及基于公开可用RNAseq的预先计算的基因表达信息相结合。内置的模板查询为数据探索提供了起点，而查询构建工具则支持构建复杂的自定义查询。列表分析和基因组区域搜索工具分别根据上传的标识符列表和基因组坐标执行查询。HymenopteraMine有助于基于直系同源关系进行跨物种数据挖掘，并通过跨基因集和基因组组装跟踪标识符来支持元分析。
