MaizeMine facilitates meta-analysis of diverse data sets through genomic data integration

Authors: GARDINER, JACK - University Of Missouri; TRIANT, DEBORAH - University Of Missouri; WALSH, AMY - University Of Missouri; Andorf, Carson; ELSIK, CHRISTINE - University Of Missouri

Submitted to: Maize Annual Meetings
Publication Type: Abstract Only
Publication Acceptance Date: 3/6/2021
Publication Date: 3/8/2021
Citation: Gardiner, J.M., Triant, D.A., Walsh, A., Andorf, C.M., Elsik, C.G. 2021. MaizeMine facilitates meta-analysis of diverse data sets through genomic data integration. In: Maize Annual Meeting, March 8-12, 2021, Virtual Meeting. p.69.

Interpretive Summary:

Technical Abstract: High-throughput genomic technologies have facilitated the generation of numerous high-quality genomic datasets. Maize researchers frequently need to conduct comparative analysis between their own datasets and published or publicly available data. MaizeMine (http://maizemine.maizegdb.org), MaizeGDB’s data mining warehouse, allows researchers without scripting skills to integrate their data with publicly available data and perform meta-analysis. The MaizeMine List tool allows users to upload identifiers to create custom lists, perform sets of operations such as unions and intersections, and execute template queries with lists. Users can easily compare their results with published results by uploading genomic coordinates or identifiers. Currently, MaizeMine utilizes the InterMine data warehousing system to integrate genomic sequences from the B73_RefGen_v3 and B73_RefGen_v4 genome assemblies, three sets of gene annotations (AGPv3, AGPv4, NCBI RefSeq), Gene Ontology (GO), protein annotations (UniProt), protein families and domains (InterPro), homologs (Ensembl Compara), and pathways (CornCyc, KEGG, Plant Reactome). In our most recent update of MaizeMine (v1.3), we have added data sets for a SNP array (Illumina SNP50), whole genome EMS mutagenesis sites, three insertional mutagenesis collections (Vollbrecht AcDs, Barken_Mu Illumina, and McCarty Uniform Mu), maize-Gamer annotations, and root and shoot transcriptional start sites. MaizeMine also provides pre-computed variant effects and expression levels based on RNA-seq data from the Zea mays Gene Expression Atlas (NCBI BioProject PRJNA171684). Database cross-references facilitate easy gene identifier conversion between AGPv3, AGPv4 and RefSeq. MaizeMine also provides simple and sophisticated search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. With the release of the significantly improved Zm-B73-Reference-NAM-5.0 assembly (aka B73_RefGen_v5) and Official Gene Model annotations on January, 2021, we will move forward in the coming year to update MaizeMine with B73-RefGen_v5 data sets as they become available. In addition to older, v5 updated data sets, new data sets (GWAS, Chromatin characterization, TF-binding sites, DNA methylation, Bonn-Mu insertions, etc.) will be incorporated and will contribute towards making MaizeMine an even more robust resource for the maize research community.