The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion

Abstract

ZInC (Zebrafish Insertional Collection, http://research.nhgri.nih.gov/ZInC/) is a web-searchable interface of insertional mutants in zebrafish. Over the last two decades, the zebrafish has become a popular model organism for studying vertebrate development as well as for modeling human diseases. To facilitate such studies, we are generating a genome-wide knockout resource that targets every zebrafish protein-coding gene. All mutant fish are freely available to the scientific community through the Zebrafish International Resource Center (ZIRC). To assist researchers in finding mutant and insertion information, we developed a comprehensive database with a web front-end, the ZInC. It can be queried using multiple types of input such as ZFIN (Zebrafish Information Network) IDs, UniGene accession numbers and gene symbols from zebrafish, human and mouse. In the future, ZInC may include data from other insertional mutation projects as well. ZInC cross-references all integration data with the ZFIN (http://zfin.org/).

Figure 1.

ZInC search interface. Insertion sites within genes have been mapped to a variety of common identifiers. Users can query ZInC with accession numbers from a number of sources, including Ensembl, GenBank, RefSeq and ZFIN. Users can also query by human, mouse or zebrafish gene symbols and names, either individual entries or longer lists. Queries can also be performed on KEGG biological pathways. All searches allow for an exact match (is) or a query with wildcards (contains). In this instance, we searched for a mutant in the gene smoothened using the zebrafish symbol ‘smo’ and by choosing the ‘contains’ radio button, the search will return any gene symbol that has the text string ‘smo’ in it.

Figure 2.

ZInC search results. In Figure 1, the zebrafish gene symbol ‘smo’ was entered in the Search by Single Gene box. Since the ‘contains’ radio button was selected, all zebrafish gene symbols in ZFIN containing the text string ‘smo’ are returned, regardless of whether an integration in the gene is available. IDs in the ZFIN ID column link to ZFIN entries for specific genes. For those genes with an integration, more detailed information is available through the ‘View Integration’ link (Figure 3).

Figure 3.

ZInC integration site details. Clicking on the ‘View Integration’ link on a search results page (Figure 2) results in a detailed view of the integration site. The ‘Integration Position’ column links to the UCSC Genome Browser zoomed in to a 2 Kb window around the integration site, the ‘Ensembl Gene ID’ column links to the Ensembl gene page, and the ‘ORDER FISH’ column links directly to the ZIRC to purchase the desired mutant fish (if available).