ArticleNucleic acids research2008
GreenPhylDB: a database for plant comparative genomics.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed, 86 citations in OpenAlex.
- Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.BMC plant biology · 2023Article
- Mining genes regulating root system architecture in maize based on data integration analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- GreenPhylDB v5: a comparative pangenomic database for plant genomes.Nucleic acids research · 2021Article
- Identification and Characterization of PLATZ Transcription Factors in Wheat.International journal of molecular sciences · 2020Article
- Review
- Transcriptome-based mining and expression profiling of Pythium responsive transcription factors in Zingiber sp.Functional & integrative genomics · 2019Article
- A web-based tool for the prediction of rice transcription factor function.Database : the journal of biological databases and curation · 2019Article
- Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.PloS one · 2018Article
- New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms.Frontiers in plant science · 2017Article
- Evolutionary Analyses of GRAS Transcription Factors in Angiosperms.Frontiers in plant science · 2017Article
- Members of BTB Gene Family of Scaffold Proteins Suppress Nitrate Uptake and Nitrogen Use Efficiency.Plant physiology · 2016Article
- Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread.The New phytologist · 2016Article
- Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice.Planta · 2015Article
- Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula.PloS one · 2014Article
- Three infectious viral species lying in wait in the banana genome.Journal of virology · 2013Article
- The banana genome hub.Database : the journal of biological databases and curation · 2013Article
- Phytozome: a comparative platform for green plant genomics.Nucleic acids research · 2012Article
- The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage.The Journal of biological chemistry · 2011Article
- MicroSyn: a user friendly tool for detection of microsynteny in a gene family.BMC bioinformatics · 2011Article
- GreenPhylDB v2.0: comparative and functional genomics in plants.Nucleic acids research · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GreenPhylDB (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes. The main functions of GreenPhylDB are to assign O. sativa and A. thaliana sequences to gene families using a semi-automatic clustering procedure and to create 'orthologous' groups using a phylogenomic approach. To date, GreenPhylDB comprises the most complete list of plant gene families, which have been manually curated (6421 families). GreenPhylDB also contains all of the phylogenomic relationships computed for 4375 families. A total of 492 TAIR, 1903 InterPro and 981 KEGG families and subfamilies were manually curated using the clusters created with the TribeMCL software. GreenPhylDB integrates information from several other databases including UniProt, KEGG, InterPro, TAIR and TIGR. Several entry points can be used to display phylogenomic relationships for A. thaliana or O. sativa sequences, using TAIR, TIGR gene ID, family name, InterPro, gene alias, UniProt or protein/nucleic sequence. Finally, a powerful phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. sativa/A. thaliana protein(s) and sequences from other plant species.
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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.