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4DXpress: a database for cross-species expression pattern comparisons.

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T - Nucleic Acids Res. (2007)

Bottom Line: Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species.Genes are linked to public microarray data in ArrayExpress.We have mapped developmental stages between the species to be able to compare developmental time phases.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

ABSTRACT
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress.

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The comparative view shows expression patterns of a list of selected genes (medaka Six3 and its Drosophila orthologue Optix). Expression annotation and images can be easily compared between the genes on a single page.
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Figure 3: The comparative view shows expression patterns of a list of selected genes (medaka Six3 and its Drosophila orthologue Optix). Expression annotation and images can be easily compared between the genes on a single page.

Mentions: When picking an individual gene entry the full information on that gene is displayed: external identifiers, gene description, expression pattern annotation using stage and anatomy ontologies, images of stained embryos and orthology relationships (visualized as a network). From the gene view a list of orthologues can be selected and their expression annotation and images can be compared to each other on a single page. A cropped screenshot comparing medaka Six3 and its Drosophila orthologue Optix is shown in Figure 3.Figure 3.


4DXpress: a database for cross-species expression pattern comparisons.

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T - Nucleic Acids Res. (2007)

The comparative view shows expression patterns of a list of selected genes (medaka Six3 and its Drosophila orthologue Optix). Expression annotation and images can be easily compared between the genes on a single page.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238840&req=5

Figure 3: The comparative view shows expression patterns of a list of selected genes (medaka Six3 and its Drosophila orthologue Optix). Expression annotation and images can be easily compared between the genes on a single page.
Mentions: When picking an individual gene entry the full information on that gene is displayed: external identifiers, gene description, expression pattern annotation using stage and anatomy ontologies, images of stained embryos and orthology relationships (visualized as a network). From the gene view a list of orthologues can be selected and their expression annotation and images can be compared to each other on a single page. A cropped screenshot comparing medaka Six3 and its Drosophila orthologue Optix is shown in Figure 3.Figure 3.

Bottom Line: Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species.Genes are linked to public microarray data in ArrayExpress.We have mapped developmental stages between the species to be able to compare developmental time phases.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

ABSTRACT
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress.

Show MeSH