Model organism database for Xenopus laevis and X. (Silurana) tropicalis serving as the principal centralized resource of genomic, development data and community information for Xenopus research. Xenbase gathers information for frog researchers, including both data about frogs as well as a frog stock center, a list of suppliers, meetings, and people working in the field. Xenbase welcomes data submissions from the Xenopus community. They are able to incorporate sequence data, expression data and images obtained using in situ hybridization or immunohistochemistry, protocols, and development movies. However, if you have other data that you feel would be valuable to the community, they will try to determine, how best to integrate your data.
Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis.
Gene pages are automatically assembled from data piped from the Entrez Gene, Gurdon Institute, JGI, Metazome, MGI, OMIM, PubMed, Unigene, Zfin, commercial suppliers and others. These data are then supplemented with in-house annotation.
Xenbase has implemented the Gbrowse genome browser and also provides a BLAST service that allows users to specifically search either laevis or tropicalis DNA or protein targets. A table of Xenopus gene synonyms has been implemented and allows the genome, genes, publications and high-throughput gene expression data to be seamlessly integrated with other Xenopus data and to external database resources, making the wealth of developmental and functional data from the frog available to the broader research community.
Through the Xenbase interface you may:
* Blast Xenopus ESTs, unigene sets or the tropicalis sequence;
* Search for Xenopus genes;
* Browse the genome using the Xenbase or JGI genome browsers;
* View development stages and cell fate maps;
* Search publications about Xenopus;
* Search for people, labs and organizations in the Xenopus Community. View job postings and events in the Xenopus community; and
* Learn about research methods and protocols (e.g. antisense and morpholinos) and obtain materials.
Xenbase's core feature is the Gene Page, which presents genomic and functional information, sequence links, orthology, and publications, and will soon incorporate expression data.
Resource Type: Resource
Version: Latest Version
molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard
Additional Resource Types
database, atlas, data repository, image repository
xenopus laevis, xenopus tropicalis
Xenbase: Xenopus laevis and tropicalis biology and genomics resource, Xenbase: Xenopus laevis and tropicalis biology and genomics resource
NICHD, NSF, Alberta Network for Proteomics Innovation, R01 HD045776, P41 HD064556, 9630621, 9983061
OMICtools, One Mind Biospecimen Bank Listing, Biobank
No materials may be reproduced without permission, Acknowledgement requested, The community can contribute to this resource
Created 4 years ago by Anonymous
- Bowes JB
- Nucleic Acids Res.
- 2010 22
Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog pages. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expression search interface. The gene catalog has grown to contain over 15,000 genes. Collaboration with the European Xenopus Research Center (EXRC) has resulted in a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and the clearinghouse for Xenopus gene nomenclature.
- James-Zorn C
- Nucleic Acids Res.
- 2013 20
Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus and Xenopus data to workers using other model organisms. As an amphibian Xenopus serves as a useful evolutionary bridge between invertebrates and more complex vertebrates such as birds and mammals. Xenbase content is collated from a variety of external sources using automated and semi-automated pipelines then processed via a combination of automated and manual annotation. A link-matching system allows for the wide variety of synonyms used to describe biological data on unique features, such as a gene or an anatomical entity, to be used by the database in an equivalent manner. Recent updates to the database include the Xenopus laevis genome, a new Xenopus tropicalis genome build, epigenomic data, collections of RNA and protein sequences associated with genes, more powerful gene expression searches, a community and curated wiki, an extensive set of manually annotated gene expression patterns and a new database module that contains data on over 700 antibodies that are useful for exploring Xenopus cell and developmental biology.