ArticleThe Plant cell2009
PLAZA: a comparative genomics resource to study gene and genome evolution in plants.
Article in The Plant cell, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
What it found
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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.
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Who cites it
133 citing papers in PubMed.
- Natural variation in tetrapyrrole biosynthetic enzymes and their regulation modifies the maize chlorophyll mutant Oy1-N1989.Plant physiology · 2025Article
- Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions.Functional & integrative genomics · 2025Review
- Comparative analysis, diversification, and functional validation of plant nucleotide-binding site domain genes.Scientific reports · 2024Article
- Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.G3 (Bethesda, Md.) · 2023Article
- DELLA functions evolved by rewiring of associated transcriptional networks.Nature plants · 2023Article
- Conservation of land plant-specific receptor-like cytoplasmic kinase subfamily XI possessing a unique kinase insert domain.Frontiers in plant science · 2023Article
- Structural and functional characteristics and expression profile of the 20S proteasome gene family in Sorghum under abiotic stress.Frontiers in plant science · 2023Article
- De novo transcriptome analysis of Justicia adhatoda reveals candidate genes involved in major biosynthetic pathway.Molecular biology reports · 2022Article
- Chromosome-scale assembly and annotation of the perennial ryegrass genome.BMC genomics · 2022Article
- PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants.Nucleic acids research · 2022Article
- Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.Genome biology and evolution · 2021Article
- Molecular characterization and expression of cyclic nucleotide gated ion channels 19 and 20 inSaudi journal of biological sciences · 2021Article
- Analysis of a gene family for PDF-like peptides from Arabidopsis.Scientific reports · 2021Article
- Copy number analyses of DNA repair genes reveal the role of poly(ADP-ribose) polymerase (PARP) in tree longevity.iScience · 2021Article
- Rootstock effects on scion gene expression in maritime pine.Scientific reports · 2021Article
- Article
- Molecular study of drought response in the Mediterranean coniferEcology and evolution · 2020Article
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- Reconstruction of the Evolutionary Histories of UGT Gene Superfamily in Legumes Clarifies the Functional Divergence of Duplicates in Specialized Metabolism.International journal of molecular sciences · 2020Article
- Article
73 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.
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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.