MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database

Md Shamimuzzaman,Justin J Le Tourneau,Ethalinda K S Cannon,Deborah A Triant,Carson M Andorf,Christine G Elsik,Amy T Walsh,Deepak R Unni,Hung N Nguyen,John L Portwood,Aditi Tayal,Jack M Gardiner

doi:10.3389/fpls.2020.592730

Abstract

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.

Highlights

Maize (Zea mays L. ssp. mays) is one of the most economically important grain crops in the world, serving as a source of food, feed, and fuel
MaizeMine includes gene expression values for over 80 tissues computed for all three gene sets based on publicly available RNA-seq data (NCBI BioProject PRJNA171684) that had previously been generated for the Z. mays Gene Expression Atlas (Sekhon et al, 2013; Stelpflug et al, 2016)
Along with the gene expression data, MaizeMine includes associated metadata from NCBI Sequence Read Archive (SRA) and BioSamples database, as well as Plant Ontology (Cooper et al, 2013) terms curated based on information from the SRA and the Z. mays Gene Expression Atlas publications (Sekhon et al, 2013; Stelpflug et al, 2016)

Summary

Introduction

Maize (Zea mays L. ssp. mays) is one of the most economically important grain crops in the world, serving as a source of food, feed, and fuel. The availability of the maize B73 genome sequence (Schnable et al, 2009) and numerous additional genomic. MaizeMine: A Data Mining Warehouse for MaizeGDB resources has accelerated both maize breeding and genetics research. With the advent of single molecule sequencing technologies, the maize B73 reference genome has been improved with higher contiguity (Jiao et al, 2017). Multiple research groups have put their efforts into developing improved versions of maize gene annotations (Law et al, 2015; Wang et al, 2016; Jiao et al, 2017). Genomics data generated by the maize research community are stored and curated in the USDA-ARS supported Maize Genetics and Genomics Database (MaizeGDB1) (Portwood et al, 2019)

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Results

Conclusion