Exploring zebrafish genomic, functional and phenotypic data using ZFIN

Abstract

The zebrafish model organism database (ZFIN) provides a Web resource of zebrafish genomic, genetic, developmental, and phenotypic data. ZFIN curates and integrates data from current literature and from direct data submissions from laboratories. In addition, ZFIN collaborates with other bioinformatics organizations to provide links to other relevant data. These data can be accessed through a variety of Web-based search and display tools. This unit focuses on some of the basic methods to search, visualize, and analyze ZFIN data, including genes, gene expression, mutants, morphants, transgenics, anatomical structures, and antibodies. ZFIN's GBrowse genome viewer, BLAST, and protocol and antibody wikis are also discussed.

Figure 1

The Zebrafish Model Organism Database (ZFIN) home page layout features three navigation tabs at the top of the page (Research, General Information, and ZIRC). The left side of the main section is dedicated to ZFIN resources and advanced search forms, and the right side is primarily external resource links (e.g., Zebrafish International Resource Center, external genome browsers, and genomics resources).

Figure 2

Appearing at the top of every ZFIN page is the Research navigation tab (a), General Information navigation tab (b) and ZIRC navigation tab (c). When a tab is selected by clicking, a list of related links is opened and displayed horizontally below the tab.

Figure 3

Site Search offers a quick search of ZFIN when a term is typed in the search field at the upper right of any ZFIN page. Results are displayed in a table sorted by category, with the number of results in each category listed in parentheses. Clicking the hyperlinked category name provides further filtering of results.

Figure 4

A view of the list of categories from Site Search with the individual results below. Clicking the headings in the individual results below the category list will direct the user to the selected detail page in ZFIN. The heading in bold above the table indicates the search performed. In this example, choosing the Genes/Markers/Clones category narrowed the search result set for cadherin. Note the arrow to the left of the selected category in the table.

Figure 5

A view of the advanced search form for Publications. The form offers several options for searching publications in ZFIN, including the use of author name, publication date, keywords, or search terms from the title or abstract. The pulldown menu expanded on the left provides a mechanism for searching based on unique publication IDs, and the menu expanded on the right allows filtering based on publication type. An option is also provided to select the number of results to display per page.

Figure 6

The Publication Search Results page features a list of records matching the search parameters, each hyperlinked to the publication abstract in ZFIN. Buttons at the top provide formatting and output options, and the pagination bar below the list provides the means to page through the results. The Modify Search hyperlink at the upper right redirects to the bottom of the page where the search form is reproduced, allowing further modification, filtering or initiation of a new search.

Figure 7

Genes/Markers/Clones Search Results page displaying the search results for myosin, with matches to genes, morpholinos, BACs, transgenic constructs and antibodies. Click on hyperlinks to view results for each category.

Figure 8

Gene Search Results page showing matches for myosin in Genes result category.

Figure 9

Gene Detail Page for myh6. This figure shows the various sections of the Gene page in an alternating color scheme. The different types of data can be grouped into the following categories: (a) Gene nomenclature, (b) Gene expression, (c) Mutants and Targeted knockdowns, (d) Gene product information, (e) Antibodies, (f) Clones and Probes, (g) Sequence Information, (h) Links to Gene pages at other resources, (i) Mapping data, (j) Orthology, and (k) Citations. A brief description of each section is provided in the text of the protocol.

Figure 10

Gene Expression Search form showing a search for fgf8a expression data in wild-type fish only. Note that some options are mutually exclusive. Selection of the Show Only WT Expression invalidates the Genotype or Background and MO Knockdown: Gene name options. They are grayed out to indicate they are no longer valid options.

Figure 11

Gene Expression Search Results page showing the Figure Gallery; a collection of all images relevant to the query, depicting 165 images for fgf8a in wild-type fish. This figure depicts the summary list portion of search results page for fgf8a in wild-type fish. Matching entries are summarized by publication, figure (including thumbnail image when available), genotype or background, stage range, and anatomy terms. All items are hyperlinked to data detail pages.

Figure 12

Gene Expression Search Results page. A larger image is shown when mousing over a thumbnail image. The text displayed on the image hyperlinks to detail pages. Plaster et al., 2007 links to the Publication Abstract page. Fig. 6 hyperlinks to the Figure Detail page for figure 6 from this publication. Expression patterns for dlx2a, fgf8a, and pax2a are depicted in this figure. Click on the gene symbols to view their respective Gene Detail pages.

Figure 13

An example of a Figure Detail page, including figure 6 from Plaster et al., 2007 and the corresponding gene expression annotations. Follow hyperlinked text to corresponding data detail pages. Click the image to open a larger image. Click on the down arrows associated with gene symbols to advance to the Gene Expression Details summary of data annotated from this image. Note that the Not Detected qualifier indicates the author stated pax2a was not expressed in the midbrain hindbrain boundary at Prim-5. The Fish column data for the same annotation indicates that the wild-type fish were treated with a chemical.

Figure 14

The Antibody Search results page. Shown here is a search for antibodies that label the head of the zebrafish and match the antigen gene alcam. The Antibody Search page with the specified search criteria can be viewed below the Search results.

Figure 15

The Antibody Detail Page for the antibody zn-8. Click on Show all to view all labeled structures. The link next to the antibody name links to the antibody page at the Antibody Community Wiki.

Figure 16

Site map that displays how to find genotype and phenotype details in ZFIN.

Figure 17

The Mutant Search form provides a variety of parameters that can be used to search for specific mutant phenotypes. This figure depicts a search for mutants containing a point mutation in the gene bmp2b.

Figure 18

A portion of the Mutant/Morphant/Transgenics Search Results page for bmp2b point mutations.

Figure 19

The Phenotype Summary page lists all individual figures grouped by publication for the genotype bmp2b^{tc300a/tc300a}(TU). To see the complete list of morpholinos associated with for Fig. 1 for Ramel et al., click on the all 4 link.

Figure 20

Phenotype Data on the Figure View page for Figure 1 from Ramel et al., 2005.

Figure 21

Genotype Detail page for bmp2b^{tc300a/tc300a}(TU).

Figure 22

Anatomical Ontology Browser includes an Anatomical Term search field and a Developmental Stage pulldown menu. These two options can be used individually, or combined to narrow the search results. The Request New Anatomical Term hyperlink allows users to request new anatomical terms for addition to the ontology.

Figure 23

A view of the Affected Anatomy search interface before (a) and after entry of terms (b). One or several terms can be entered in the Enter Search Terms field (a). The Include Substructures check box is selected by default but can be deselected if an exact match is preferred. Selected terms are displayed above the search term field (b). Each term has an X at the left, which can be clicked to remove the term from the list. The search term field has an autocomplete feature, which provides a popup menu with a list of matching terms once three or more letters have been entered. The radio button selections on the lower right (b) allow a choice between finding phenotypes observed in all selected structures or any of the structures.

Figure 24

The Anatomy Detail Page for the structure brain.

Figure 25

The Expression section of the Anatomy Detail page expanded for the structure brain.

Figure 26

The Phenotype section of the Anatomy Detail page expanded for the structure brain.

Figure 27

ZFIN BLAST Query page displaying programs and available datasets at the top, sequence entry choices, and BLAST search options at the bottom. The database menu is expanded in this view. Accession ID BC050482 is entered in the Sequence ID field.

Figure 28

ZFIN BLAST Result page displays the search results for BC050482, an mRNA sequence accession ID. The Results page displays a graphical view of the sequence alignments, a tabulated view of the matches and relevant marker associations in ZFIN and the alignment of the query sequence with each hit.

Figure 29

An expanded view of a selected region of the zebrafish genome as displayed in GBrowse. The search performed is shown in the Landmark or Region text field. The GBrowse page is divided into several main sections, including Instructions, Search, Overview, Details, Tracks, and Display Settings. The view is customizable by modifying the size of the region displayed and selecting and moving the tracks within the Details section. The data in the tracks show genome annotation, including the position of genes on the linkage groups, alternatively spliced transcripts, BACs used for assembly, and genes that have expression and/or phenotype data.

Figure 30

Navigating the genome in the Details section. Using the pulldown menu on the lower right side of the Search section (red boxed area), a region spanning 100 bp has been selected and displayed. The nucleotide sequence can be seen at this magnification in the blue schematic representation of the BAC component in the Genome Assembly track. The orientation of the rab23 gene in this view has been flipped. The Flip check box has been selected and the reversed coordinates can be confirmed in the Details section. Note that the region in the Landmark or Region search field is still displayed in the default orientation.

Figure 31

Capturing and analyzing sequence in GBrowse. A 4 kbp region has been selected in the Details section by clicking on the ruler and dragging the mouse. The selection is highlighted as the mouse is dragged across the ruler and the region size is displayed. When the selection is complete, a popup window appears offering hyperlinked choices for changing the magnification and location of the Details display, as well as tools for capturing the sequence as FASTA or performing BLAST analysis.

Figure 32

GBrowse tracks available for the zebrafish genome. The Assembly tracks show the components used in the Vega assembly. The Gene and Transcript tracks show schematic representations of the gene and the exon structure of the transcripts, with arrows indicating their orientation in the genome. The Expression and Phenotype tracks are ZFIN-specific tracks indicating the presence of associated data in the ZFIN database. Selecting and de-selecting the check boxes and updating the image allow customization of the Details view.

Figure 33

The ZFIN Community Wiki home uses Confluence software from Atlassian (http://www.atlassian.com/software/confluence/). The welcome page for the Community Wiki has links to the Protocol Wiki and the Antibody Wiki on the left side. Links to Additional Resources and Help documentation are available on the right. The search field at the upper right can be used to perform a search of all wiki content. The Log In and Sign Up links at the upper right are for registered users to log in or for new members to sign up as registered users, respectively.

Figure 34

A view of a wiki search results page using the word breeding shows the term in the search field at the top followed by a list of results down the left side of the page. The search term is shown in bold within the individual titles and page excerpts in the list. On the right side of the page are several pulldown menus and a text field that provide filtering of the result set.

Figure 35

A view of the ZFIN Protocol Wiki home page. The protocols are organized into Sections corresponding to the chapters in The Zebrafish Book, 5^th edition, which is the source material used to seed the Protocol Wiki. The headings under Sections can be expanded or collapsed by clicking on the + and – buttons. Section headers and protocol titles are hyperlinked to their respective pages on the wiki. The right side of the page provides links to recent wiki content, including added comments and updated pages.

Figure 36

A view of a protocol page in the Protocol Wiki. Below the protocol title is a status line, indicating the registered user who added the protocol, as well as information about the most recent instance of editing. Each protocol can include figures and links to other wiki pages, as in this example where a recipe is hyperlinked to another section of the wiki. Registered users can use the Add Comment hyperlink to comment on the protocol and share their experience and tips. The Tools menu on the right provides links for tracking the edit history of the page and for exporting the protocol.

Figure 37

A view of the ZFIN Antibody Wiki home page. To find an antibody, users can browse a list of antibodies by clicking the appropriate hyperlink on the lower left side of the page. Alternatively, a search can be performed using the text field at the upper left, a method that does not require knowledge of the official name on the antibody record. The lower right side of the Antibody Wiki home page provides hyperlinks to recently added or updated antibody pages and comments.

Figure 38

The individual antibody pages in the Antibody Wiki contain a table view of information, including the name and other aliases and IDs, host organism, isotype, structures labeled, genes and molecules targeted, and suppliers. Information on whether the antibody works on zebrafish and the assays tested are also included on the record. This zn-5 antibody (Fashena and Westerfield, 1999) record shows what a registered user would see, including the Edit button and Add menu on the upper right.