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

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.

Genome-wide association analysis of hyperspectral reflectance data to dissect growth-related traits genetic architecture in maize under inoculation with plant growth-promoting bacteria

“…Model convergence was assessed using trace plots of the posterior means of the parameters. For each selected SNP associated with hyperspectral patterns, genes within an interval of 50 kilobase pair (kbp) upstream and downstream of the SNP were explored using the MaizeMine V1.3 server (Shamimuzzaman et al, 2020). One challenge was the many Manhattan plots that potentially needed to be generated owing to the three manually measured phenotypes, 150 hyperspectral wavelengths, and 131 hyperspectral indices.…”

Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping

“…Maize B73 RefGen_v4 was the data mining resource of the Maize Genetics and Genome Database (MaizeGDB). 1 We compared these clean data to the reference genome, Maize B73 RefGen_v4 ( Shamimuzzaman et al, 2020 ), using the Burrows-Wheeler Aligner (BWA) software ( Jia et al, 2013 ), and SAMtools software ( Zhou et al, 2015 ) was used to remove duplicates (command: rmdup). Then, we used a Bayesian model to detect polymorphic sites in the population, and filtered and screened high-quality SNPs using a minor allele frequency (MAF) > 0.05 and call rate >80%.…”

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

“…Among these, qTeller is a comparative RNA-seq expression platform that helps to compare expression between two genes visually. Maizemine is a data mining respiratory for the MaizeGDB [ 102 ]. It enables researchers to create and export customized annotated datasets that can be combined with their research data for use in downstream analyses.…”