ArticleBioinformatics (Oxford, England)2017
The Tomato Expression Atlas.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor.Nature communications · 2019Pooled it
- The novel function of the bZIP transcription factor VSF-1 in mediating fruit firmness in tomato.Horticulture research · 2026Article
- Far-red perception by vegetative organs and not fruits drives fruit growth responses in tomato plants.Plant physiology · 2026Article
- Splicing regulation by RS2Z36 controls ovary patterning and fruit growth in tomato.Plant molecular biology · 2026Article
- SlERF-RD1 acts as a developmental coordinator integrating plant canopy architecture and the ethylene-mediated ripening cascade in tomato.Plant cell reports · 2026Article
- Multi-Omic Advances in Olive Tree (Biology · 2025Review
- Tomato HAIRY MERISTEM4, expressed in the phloem, is required for proper shoot and fruit development.Horticulture research · 2025Article
- Genome-Wide Identification and Expression Analysis of Hexokinase Gene Family Under Abiotic Stress in Tomato.Plants (Basel, Switzerland) · 2025Article
- Elucidation of the key flavonol biosynthetic pathway in goldenHorticulture research · 2025Article
- A novel NAC transcription factor mediates negative regulation of early ethylene production and ripening in tomato fruits.Frontiers in plant science · 2025Article
- Uncoupling FRUITFULL's functions through modification of a protein motif identified by co-ortholog analysis.Nucleic acids research · 2024Article
- StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes.Plant cell reports · 2024Article
- Article
- Class I TCP in fruit development: much more than growth.Frontiers in plant science · 2024Review
- PEATmoss: A Gene Expression Atlas for Bryophytes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The dissection of tomato flavor: biochemistry, genetics, and omics.Frontiers in plant science · 2023Review
- Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress.Plant physiology · 2022Article
- A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales.EvoDevo · 2022Article
- All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter.Journal of experimental botany · 2022Article
- Perturbations in the Carotenoid Biosynthesis Pathway in Tomato Fruit Reactivate the Leaf-Specific Phytoene Synthase 2.Frontiers in plant science · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWith the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal context of expression data and help elucidate gene function. Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of resolution within an organ, enhancing hypothesis development and testing in addition to candidate gene identification. This atlas can be adapted to different types of expression data from diverse multicellular species. AVAILABILITY AND IMPLEMENTATION: The Tomato Expression Atlas is available at http://tea.solgenomics.net/ . Source code is available at https://github.com/solgenomics/Tea . CONTACT: jr286@cornell.edu or lam87@cornell.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
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.