ArticleNucleic acids research2023
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- ArtemisiaDB: A comprehensive multi-omics database for Artemisia annua.Plant communications · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- The Plant Sucrose Synthase Gene Family: Multi-Level Regulatory Networks and Functional Diversification in Plants.Biomolecules · 2026Review
- Polyploidy and plant resilience to environmental stresses: Molecular mechanisms and future applications.Plant communications · 2026Review
- Large-scale plant genomic identification and analysis uncoverHorticulture research · 2026Article
- AI-integrated digital breeding for crop improvement.Frontiers in plant science · 2026Review
- Transcriptomics Data Mining to Identify Novel Regulatory Genes of Iron Uptake in Drought-Stressed Wheat.International journal of molecular sciences · 2025Article
- The evolution of the aquaporin gene family and drought tolerance mechanisms in green plants.Horticulture research · 2025Article
- Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity.The plant genome · 2025Article
- Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets.NAR genomics and bioinformatics · 2024Article
- Genome-wide identification of3 Biotech · 2024Article
- Candidate Genes and Favorable Haplotypes Associated with Iron Toxicity Tolerance in Rice.International journal of molecular sciences · 2024Article
- Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae).Protoplasma · 2024Article
- Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity.Plant cell reports · 2024Review
- Integrating omics databases for enhanced crop breeding.Journal of integrative bioinformatics · 2023Review
- CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis.Bioinformatics (Oxford, England) · 2023Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis.bioRxiv : the preprint server for biology · 2023Article
- Comparative analysis of tissue-specific genes in maize based on machine learning models: CNN performs technically best, LightGBM performs biologically soundest.Frontiers in genetics · 2023Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the last decade, RNA-seq has produced a massive amount of plant transcriptomic sequencing data deposited in public databases. Reanalysis of these public datasets can generate additional novel hypotheses not included in original studies. However, the large data volume and the requirement for specialized computational resources and expertise present a barrier for experimental biologists to explore public repositories. Here, we introduce PlantExp (https://biotec.njau.edu.cn/plantExp), a database platform for exploration of plant gene expression and alternative splicing profiles based on 131 423 uniformly processed publicly available RNA-seq samples from 85 species in 24 plant orders. In addition to two common retrieval accesses to gene expression and alternative splicing profiles by functional terms and sequence similarity, PlantExp is equipped with four online analysis tools, including differential expression analysis, specific expression analysis, co-expression network analysis and cross-species expression conservation analysis. With these online analysis tools, users can flexibly customize sample groups to reanalyze public RNA-seq datasets and obtain new insights. Furthermore, it offers a wide range of visualization tools to help users intuitively understand analysis results. In conclusion, PlantExp provides a valuable data resource and analysis platform for plant biologists to utilize public RNA-seq. datasets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.