The Zebrafish Information Network: major gene page and home page updates

Abstract

The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms.

Figure 1.

The new zfin.org home page. The new zfin.org home page showing site-wide menu choices (top), search box (middle) and link buttons to the most used features (bottom left). The lower portion of the home page is not shown, including sections for ‘New Data in ZFIN’, as well as jobs, meetings and news posts.

Figure 2.

The default view of the new expression section on the myl7 gene page. (A) Links to all expression data in ZFIN for the gene, cross species-comparisons for expression of the gene at The Alliance or Bgee, and high throughput expression data sets at GEO or Expression Atlas. (B) The wild type expression summary ribbon. Colored blocks indicate where annotations have been made.

Figure 3.

Expression image gallery and annotation summary table for myl7 in the musculature system. Clicking on colored blocks in summary ribbons opens a new view including an image gallery and annotation summary table. Hovering over one of the colored developmental stage blocks provides a listing of specific stages included in that block.

Figure 4.

The Gene Ontology section for myl7. The default view shows the summary ribbon. Clicking on a colored block in the ribbon opens the data table. Shown here is the display for the myl7 gene including the annotation table after clicking on the ‘cell differentiation’ block in the biological process portion of the GO ribbon.

Figure 5.

The new constructs table for the actb1 gene. The data in the constructs table help researchers decide which construct is of interest to them without having to visit each individual construct page.