ArticlePlant direct2018
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER).
Article in Plant direct, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
- A comparative approach for selecting orthologous candidate genes in genome-wide association studies across multiple species.Plant physiology · 2026Article
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- Go Big or go home: a new gene ontology subset that improves plant gene function prediction.Plant methods · 2026Article
- GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize.Plant communications · 2025Article
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants.Nature plants · 2025Article
- Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions.G3 (Bethesda, Md.) · 2025Article
- Gene family rearrangements and transcriptional priming drive the evolution of vegetative desiccation tolerance in Selaginella.The Plant journal : for cell and molecular biology · 2025Article
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Cuticle development and the underlying transcriptome-metabolome associations during early seedling establishment.Journal of experimental botany · 2024Article
- Genome-wide association studies from spoken phenotypic descriptions: a proof of concept from maize field studies.G3 (Bethesda, Md.) · 2024Article
- Gene ontology functional annotation datasets for the ITAG3.2 and ITAG4.0 tomato (Data in brief · 2024Article
- Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions.BMC genomics · 2024Article
- NAKED ENDOSPERM1, NAKED ENDOSPERM2, and OPAQUE2 interact to regulate gene networks in maize endosperm development.The Plant cell · 2023Article
- Article
- Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism.Communications biology · 2023Article
- A large deletion conferring pale green leaves of maize.BMC plant biology · 2023Article
- Status of genome function annotation in model organisms and crops.Plant direct · 2023Article
- A role for heritable transcriptomic variation in maize adaptation to temperate environments.Genome biology · 2023Article
- Genome-Wide Identification of Expansin Gene Family and Their Response under Hormone Exposure inInternational journal of molecular sciences · 2023Article
6 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
We created a new high-coverage, robust, and reproducible functional annotation of maize protein-coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome and Gramene maize GO annotation sets only cover 41% and 56% of maize protein-coding genes, respectively, this study provides annotations for 100% of the genes. We also compared the quality of our newly derived annotations with the existing Gramene and Phytozome functional annotation sets by comparing all three to a manually annotated gold standard set of 1,619 genes where annotations were primarily inferred from direct assay or mutant phenotype. Evaluations based on the gold standard indicate that our new annotation set is measurably more accurate than those from Phytozome and Gramene. To derive this new high-coverage, high-confidence annotation set, we used sequence similarity and protein domain presence methods as well as mixed-method pipelines that were developed for the Critical Assessment of Function Annotation (CAFA) challenge. Our project to improve maize annotations is called maize-GAMER (GO Annotation Method, Evaluation, and Review), and the newly derived annotations are accessible via MaizeGDB (http://download.maizegdb.org/maize-GAMER) and CyVerse (B73 RefGen_v3 5b+ at doi.org/10.7946/P2S62P and B73 RefGen_v4 Zm00001d.2 at doi.org/10.7946/P2M925).
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