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Cite this (Arabidopsis Hormone Database, RRID:SCR_001792)

URL: http://ahd.cbi.pku.edu.cn

Resource Type: Resource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resource

Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.

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Cite this (Plant Metabolic Network, RRID:SCR_003778)

URL: http://www.plantcyc.org/

Resource Type: Resource, topical portal, ontology, training resource, database, analysis service resource, production service resource, data analysis service, image collection, service resource, portal, storage service resource, data repository, controlled vocabulary, data or information resource

Broad network of plant metabolic pathway databases with two types of databases: a reference database called PlantCyc and single species/taxon databases, such as AraCyc. Additional external metabolic pathway databases are affiliated with the PMN. These databases remain under the autonomous control of the PMN collaborators who provide them. PMN draws upon the work of many individuals with expertise in annotating genomes, generating metabolic pathway databases, curating biochemical information from the literature, and forming extensive network of collaborations with biological databases and biochemistry researchers. In addition to providing biochemical reaction diagrams, organism-specific metabolic maps, detailed descriptions of enzymes and pathways, and links to other resources, the PMN website houses tutorials to help guide teachers and students as they learn more about the valuable bioinformatic data and analysis tools that are crucial elements of modern biological research. Please help expand the content of the PMN databases, including AraCyc and PlantCyc! Any and all new data submissions related to plant biochemical pathways are welcomed. You can also correct an existing pathway. The PMN has several tools available for analyzing the data presented in PlantCyc and the other species-specific metabolic databases. You may browse the pathway ontology, compound ontology, and enzyme commission ontology. *PlantCyc: a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. It provides access to manually curated or reviewed information about shared and unique metabolic pathways present in over 350 plant species. * AraCyc: provides access to manually curated or reviewed information about metabolic pathways for the model plant Arabidopsis thaliana. The pathways may be unique to Arabidopsis or shared with other organisms. Data from gene expression, proteomic, and metabolomic experiments in Arabidopsis can be overlaid on a metabolic pathway map using the OMICS Viewer. * PoplarCyc: provides access to manually curated or reviewed information about metabolic pathways for the model tree Populus trichocarpa and a few other related Populus species and hybrids. The pathways may be unique to poplar or shared with other organisms. Data from gene expression, proteomic, and metabolomic experiments in poplar can be overlaid on a metabolic pathway map using the OMICS Viewer.

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