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Xenbase: a Xenopus biology and genomics resource.

Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada.

ABSTRACT
Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. 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.

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Xenbase gene page screenshot. A screenshot of the display generated by a search for ‘pax8’. Xenopus tropicalis is arranged on the left when species-specific data is displayed and X. laevis-specific data in the right column. Data common to the both species is not restricted to this format and is presented throughout the corresponding row.
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Figure 1: Xenbase gene page screenshot. A screenshot of the display generated by a search for ‘pax8’. Xenopus tropicalis is arranged on the left when species-specific data is displayed and X. laevis-specific data in the right column. Data common to the both species is not restricted to this format and is presented throughout the corresponding row.

Mentions: Data from the two contributing Xenopus species are arranged in columns, with information in the left column representing tropicalis data and that in the right, laevis data (Figure 1). There are exceptions to this layout, for example data regarding orthologs from mammalian and non-mammalian species and GO terms common to the gene products of both species. At the moment only one of the two paralogs from the tetraploid species, laevis, is displayed and paired with data from the orthologous tropicalis gene. In the future, data on the laevis paralog will also be made available through a tab system. When laevis genomic data becomes available it will also be arranged on the right side of the page, although there has been no firm agreement on when this project will begin.Figure 1.


Xenbase: a Xenopus biology and genomics resource.

Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD - Nucleic Acids Res. (2007)

Xenbase gene page screenshot. A screenshot of the display generated by a search for ‘pax8’. Xenopus tropicalis is arranged on the left when species-specific data is displayed and X. laevis-specific data in the right column. Data common to the both species is not restricted to this format and is presented throughout the corresponding row.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238855&req=5

Figure 1: Xenbase gene page screenshot. A screenshot of the display generated by a search for ‘pax8’. Xenopus tropicalis is arranged on the left when species-specific data is displayed and X. laevis-specific data in the right column. Data common to the both species is not restricted to this format and is presented throughout the corresponding row.
Mentions: Data from the two contributing Xenopus species are arranged in columns, with information in the left column representing tropicalis data and that in the right, laevis data (Figure 1). There are exceptions to this layout, for example data regarding orthologs from mammalian and non-mammalian species and GO terms common to the gene products of both species. At the moment only one of the two paralogs from the tetraploid species, laevis, is displayed and paired with data from the orthologous tropicalis gene. In the future, data on the laevis paralog will also be made available through a tab system. When laevis genomic data becomes available it will also be arranged on the right side of the page, although there has been no firm agreement on when this project will begin.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada.

ABSTRACT
Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. 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.

Show MeSH