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    Welcome to MaizeGDB!

    MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.

    MaizeGDB is a founding member of AgBioData, a consortuim of agriculture-related online resources which is committed to making agriculture-related research data FAIR.

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    Maize Genetics Meeting

    The 68th Annual Maize Genetics Meeting will be held from February 26th - March 1st, 2026 at the Maritim Hotel, Cologne, Germany.

    The 67th Annual Maize Genetics Meeting was held from March 6th - 9th, 2025 at the Union Station, St. Louis, Missouri, USA.


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  • Genomes
    Representative genome - B73
    Zm-B73-REFERENCE-NAM-5.0
    Zm-B73-REFERENCE-GRAMENE-4.0
    B73 RefGen_v3
    B73 RefGen_v2
    B73 RefGen_v1
    BAC-based B73

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    Zm-W22-REFERENCE-NRGENE-2.0
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    Karytypes of Mo17 and B73

    Complete collection of genome assemblies

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    Featured tools at MaizeGDB

    A resource to BLAST your sequence against maize genomes and annotations.
    A data warehouse to access genomic, proteomic, and literature data for maize.
    A platform to compare gene and protein expression data across multiple genomes.
    A set of comprehensive metabolic pathway resources for maize.

    New tools at MaizeGDB


    Fusariuim Protein Toolkit     A set of tools and datasets to explore the functions and structures of the Fusarium proteome.

    Phylostrata     Phylostratigraphy determines the level of evolutionary conservation of a given protein.

    PanEffect     PanEffect: A tool to explore the variant effects across the maize pan-genome.

    SNPversity 2.0     A tool to access large-scale maize genetic variation data.

    Foldseek Search     Fast comparisons of large protein structure sets.

    Other tools at MaizeGDB

    • SNPversity 2.0
      • SNPversity: A tool to access large-scale maize genetic variation data.
    • TYPSimSelector
      • TYPSimSelector: A tool that sorts identity-by-state values derived from SNP datasets for accessions in the Ames Diversity Panel (a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa).
    • PanEffect
      • PanEffect: A tool to explore the variant effects across the maize pan-genome.
    • Bin viewer
      • Bin Viewer: A tool to explore data in regions defined by genetic bins.
    • GenomeQC
      • GenomeQC: A tool to assess the quality of genome assemblies and annotations.
    • Maize Feature Store
      • MFS: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications.
    • Pedigree Viewer
      • Pedigree Viewer: A tool to visualize maize pedigree data and networks.
    • PAST
      • PAST: A tool that assigns your SNPs to genes and your genes to metabolic pathways.
    • Genome Context Viewer
      • GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
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Home> Expression

Expression Data at MaizeGDB

About expression data at MaizeGDB
MaizeGDB provides selected expression data on individual genes and for whole genomes. Below is a list of places to look for expression data. MaizeGDB does not incorporate all available expression data; these can be accessed through NCBI’s SRA and GEO databases. To suggest data for inclusion at MaizeGDB, please contact us.

Tools for expression data

(Are we missing your favorite tool?)
qTeller_logo
qTeller
qTeller (QTL Teller), is a tool that allows users to view gene expression information within a chromosomal interval for QTL or mutant mapping. qTeller, which uses a large collection of expression data from a wide range of published experiments, also facilitates single or two gene scatter plots which are particularly useful for comparing expression patterns of closely related homologs. qTeller also allows visualization of expression information from the maize syntenic orthologs of Sorghum, Rice, Setaria, and Brachypodium. qTeller was developed by James Schnable while he was a graduate student at UC Berkeley.
MaizeMine
MaizeMine
MaizeMine v1.4 integrates the Zea mays Zm-B73-REFERENCE-NAM-5.0 genome assembly with many biological data sets. Homologues are provided for several other monocots and Arabidopsis thaliana. The tabs below show categories for template queries, which provide simple search menus. "Alias and DBxref" template queries are for id conversion between the Z. mays Zm00001eb.1 and RefSeq gene sets and between Zm00001eb.1 and the older MaizeGDB/Gramene gene sets (AGPv4_Zm00001d.2 and AGPv3.21_5b+).

Find Expression for Individual Genes
Expression of Zm-B73-REFERENCE-NAM-5.0 gene models: On the B73 v5 genome browser, select tracks from the RNA-seq tab. Search by gene or region in qTeller. Data in qTeller can also be accessed through Maize Mine. Expression data associated with other versions of this gene model, if any, can be found on the gene model/locus page on the "PAN-GENE" tab in the Overview section.

Expression of Zm-B73-REFERENCE-REFERENCE-GRAMENE-4.0 gene models: On GBrowse, select tracks forRNSseq. Search by gene or region in qTeller. Expression data associated with other versions of this gene model, if any, can be found on the "PAN-GENE" tab of the gene model/locus page.

Expression of gene models from any NAM founder line On JBrowse, select the NAM founder genome from the upper left pull down menu, then select the RNA-seq tracks. Search by gene or region in qTeller.

Expression of B73 RefGen_v3, and B73 RefGen_v2, gene models: Can be found on the individual gene model page. On GBrowse for v3, and v2, go to the "select tracks" tab, and select tracks for Expression and Transcripts. Expression data associated with other versions of this gene model, if any, can be found on the "PAN-GENE" tab of the gene model/locus page.

Expression for other Genomes: If available, this may be found on the genome’s browser. From the Genome Data Center, go to the "All Genomes" section and open the section named "Complete table of 49 genomes". Click on the assembly name of your genome of interest. If a genome browser is available, it will be shown here, and you can check for expression tracks. Expression data associated with other versions of this gene model, if any, can be found on the "PAN-GENE" tab of the gene model/locus page.

Find Expression for Genome Regions
If available, this may be found on the appropriate genome’s browser. From the Genome Data Center, go to the "All Genomes" section and open the "Complete table of 49 genomes". Click on the assembly name of your genome of interest. If a genome browser is available, it will be shown here, and you can check for expression tracks. You can select the region of genome you are interested in, select expression tracks and visualize or download from the browser.

Expression data for Zm-B73-REFERENCE-NAM-5.0 and Zm-B73-REFERENCE-REFERENCE-GRAMENE-4.0 can be searched at qTeller and Maize Mine.

Expression for all NAM founder lines can be searched at qTeller.

Find Expression for Whole Genomes
FPKM (i.e. normalized) data for Zm-B73-REFERENCE-NAM-5.0 and Zm-B73-REFERENCE-REFERENCE-GRAMENE-4.0, and all NAM founder lines that were the inputs for qTeller can be downloaded here.

Bam/bigwig files for Zm-B73-REFERENCE-NAM-5.0 (un-normalized) and be downloaded here.

Bam/bigwig files for all NAM founder lines (un-normalized) can be downloaded here.

B73v5/Mo17 CAU RNA-seq bam/bigwig files (un-normalized) can be downloaded here.

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