ArticleNucleic acids research2022
PlantGSAD: a comprehensive gene set annotation database for plant species.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- SPOROCYTELESS/NOZZLE cooperates with MADS-domain transcription factors to regulate an auxin-dependent network controlling Megaspore-Mother-Cell differentiation.Nature communications · 2025Article
- Comparative transcriptomic profiling of field-grown cassava genotypes across season transitions.Scientific data · 2025Article
- Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions.Functional & integrative genomics · 2025Review
- Physiological and Transcriptional Responses to Phosphorus Deficiency and Glucose-6-Phosphate Supplementation inInternational journal of molecular sciences · 2024Article
- Identifying hub genes and key functional modules in leaf tissue of Populus species based on WGCNA.Genetica · 2024Article
- Constitutive expression of cucumber CsACS2 in Arabidopsis Thaliana disrupts anther dehiscence through ethylene signaling and DNA methylation pathways.Plant cell reports · 2024Article
- FungiFun3: systemic gene set enrichment analysis for fungal species.Bioinformatics (Oxford, England) · 2024Article
- Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces.Plants (Basel, Switzerland) · 2024Article
- Nuclear lamina component KAKU4 regulates chromatin states and transcriptional regulation in the Arabidopsis genome.BMC biology · 2024Article
- KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome.BMC plant biology · 2024Article
- Crop-GPA: an integrated platform of crop gene-phenotype associations.NPJ systems biology and applications · 2024Article
- Plant growth regulator extracts from seaweeds promote plant growth and confer drought tolerance in canola (Plant signaling & behavior · 2023Article
- Temporal transcriptomic profiling elucidates sorghum defense mechanisms against sugarcane aphids.BMC genomics · 2023Article
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.Genomics, proteomics & bioinformatics · 2023Article
- RoseAP: an analytical platform for gene function ofFrontiers in plant science · 2023Article
- Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments.Frontiers in plant science · 2023Article
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Authors and funding
11 authors.
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Abstract
With the accumulation of massive data sets from high-throughput experiments and the rapid emergence of new types of omics data, gene sets have become more diverse and essential for the refinement of gene annotation at multidimensional levels. Accordingly, we collected and defined 236 007 gene sets across different categories for 44 plant species in the Plant Gene Set Annotation Database (PlantGSAD). These gene sets were divided into nine main categories covering many functional subcategories, such as trait ontology, co-expression modules, chromatin states, and liquid-liquid phase separation. The annotations from the collected gene sets covered all of the genes in the Brassicaceae species Arabidopsis and Poaceae species Oryza sativa. Several GSEA tools are implemented in PlantGSAD to improve the efficiency of the analysis, including custom SEA for a flexible strategy based on customized annotations, SEACOMPARE for the cross-comparison of SEA results, and integrated visualization features for ontological analysis that intuitively reflects their parent-child relationships. In summary, PlantGSAD provides numerous gene sets for multiple plant species and highly efficient analysis tools. We believe that PlantGSAD will become a multifunctional analysis platform that can be used to predict and elucidate the functions and mechanisms of genes of interest. PlantGSAD is publicly available at http://systemsbiology.cau.edu.cn/PlantGSEAv2/.
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