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Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects

  • Christine G. Elsik
  • Aditi Tayal
  • Deepak R. Unni
  • Gregory W. Burns
  • Darren E. Hagen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1757)

Abstract

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.

Key words

Hymenoptera Apis mellifera Genome Database Data mining Orthology Pathway Gene expression Single nucleotide polymorphism InterMine 

Notes

Acknowledgments

The authors would like to thank Colin M. Diesh for his contributions to the development of HymenopteraMine, HGD BLAST, and HGD JBrowse/Apollo. This work was supported by USDA National Institute of Food and Agriculture Hatch Project 1009273 and Agriculture and Food Research Initiative Competitive grant no. 2010-65205-20407.

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Christine G. Elsik
    • 1
    • 2
    • 3
  • Aditi Tayal
    • 1
  • Deepak R. Unni
    • 1
  • Gregory W. Burns
    • 1
  • Darren E. Hagen
    • 1
  1. 1.Division of Animal SciencesUniversity of MissouriColumbiaUSA
  2. 2.Division of Plant SciencesUniversity of MissouriColumbiaUSA
  3. 3.MU Informatics InstituteUniversity of MissouriColumbiaUSA

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