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ZFIN

http://zfin.org/

Sprague, J., Douglas, S., Westerfield, M., The ZFIN GROUP (Clements, D., Conlin, T., Edwards, P., Frazer, K., Schaper, K., Segerdell, E.)

The Zebrafish International Resource Center University of Oregon Eugene, OR 97403-5274

Contact   judys@cs.uoregon.edu


Database Description

The Zebrafish Information Network (1), ZFIN, is a web-based community resource that serves as the central location for the curation and integration of zebrafish, genetic, genomic, and developmental data. ZFIN provides an anatomical atlas and dictionary, developmental staging criteria, research methods, pathology information, as well as integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish research community. ZFIN gathers, curates, and integrates data from many sources. ZFIN maintains curated mapping data from the 6 zebrafish mapping panels. Researchers may use ZFIN's map viewer to generate integrated maps by specifying desired panels, desired marker types, a marker or gene name, or a location on a linkage group. Curators update ZFIN daily through annotation of genes, mapping information, homologies, alleles, and publications. ZFIN maintains links to key information sources providing sequence and homology information. Nomenclature is an important aspect of ZFIN data curation. Zebrafish gene names are reviewed to consolidate multiple names for the same gene, to assign uniform names to all members of gene families, and to clarify the relationships between genes in the zebrafish and other vertebrates. ZFIN's on-line locus/allele registration form provides a means for automatic approval for new mutant locus names. ZFIN may be accessed at http://zfin.org .

Recent Developments

A Consolidated Map of the Zebrafish Genome: ZFIN maintains a consolidated map of the zebrafish genome. This map was created by John Postlethwait et al. (unpublished, http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-REFCROSS-010114-1) to facilitate strategies for the molecular cloning of genes that have been identified by mutations. The consolidated map contains all of the coding sequences positioned on all 6 of the zebrafish mapping panels. These sequences have been intercalated into the MGH panel (2), a diploid meiotic map of microsatellites. The MGH macrosatellite map serves as the standard because each of the 6 zebrafish mapping panels is based on a framework map of microsatellites. ZFIN regenerates the consolidated map whenever a panel is updated. This consolidated map may be queried using the ZFIN map viewer. Gene Expression Data: ZFIN now provides for an integrated analysis of genotype, phenotype, and expression data through access to data from RNA in situ hybridization assays, chiefly those of Bernard and Christine Thisse (unpublished, http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-010810-1). These data relate anatomical structures, systems, and developmental stages with the expression of tagged genes and ESTs linked to sequence information deposited in Genbank. Researchers can use a combination of search parameters to identify genes that are expressed in various anatomical structures, systems, and developmental stages or to find the expression patterns for genes or gene families. ZFIN displays images as well as text summaries describing the data. Work is under way to support additional types of expression data. Links to the Zebrafish International Resource Center: ZFIN maintains links to the Zebrafish International Resource Center which allow the researcher to order strains or probes and to submit new mutant strains.

Acknowledgements

We would like to thank our colleagues Dr. John Postlethwait and Allen Day for providing ZFIN with their mapping panel consolidation algorithm and Drs. Bernard and Christine Thisse for their gene expression data. We would also like to thank the mapping laboratories for providing access to their mapping data and to many individual researchers who have submitted data. Funds for the development of the Zebrafish Information Network are provided by the NIH (RR/HD12546).

REFERENCES

  1. Sprague, J., Doerry, E., Douglas, S., Westerfield, M., and ZFIN GRP, (Conlin, T., Clements, D., Edwards, P., Frazer, K., Schaper, K., Segerdell, E.) (2001) The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acids Res. 29,87-90.
  2. Knapik, E.W., Goodman, A., Atkinson, O.S., Roberts, C.T., Shiozawa, M., Sim, C.U., Weksler-Zagen, S., Trolliet, M.R., Futrell, C., Innes, B.A., Koike, G., McLaughlin, M., Pierre, L., Simon, J.S., Vilallonga, E., Roy, M., Chiang, P.W., Fishman, M.C., Driever, W., and Jacob, H.J. (1996) A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms. Development 123:451-460.

Category   Genomic Databases

Go to the abstract in the NAR 2001 Database Issue.

 

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