Exploring Zebrafish Genomic, Functional and Phenotypic Data Using ZFIN

Sridhar Ramachandran1, Barbara Ruef1, Christian Pich1, Judy Sprague1

1 University of Oregon, Eugene, Oregon
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.18
DOI:  10.1002/0471250953.bi0118s31
Online Posting Date:  September, 2010
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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. Curr. Protoc. Bioinform. 31:1.18.1‐1.18.44. © 2010 by John Wiley & Sons, Inc.

Keywords: zebrafish; database; phenotype; gene expression; bioinformatics; genomics

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Navigating the Home Page and Utilizing Search Functions
  • Basic Protocol 2: Retrieving Information about Zebrafish Genes
  • Basic Protocol 3: Finding and Viewing Comprehensive Gene Expression Data
  • Basic Protocol 4: Finding Antibodies
  • Basic Protocol 5: Finding Phenotype Data
  • Basic Protocol 6: Browsing the Zebrafish Anatomical Ontology
  • Basic Protocol 7: Using ZFIN BLAST to Search for Zebrafish Sequences
  • Basic Protocol 8: Exploring the Zebrafish Genome Using GBrowse
  • Basic Protocol 9: Contributing and Collaborating via the Community Wiki
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

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Internet Resources
  http://zfin.org/zf_info/catch/catch.html
  ZFIN's external links page includes Web resources and stock centers for zebrafish.
  http://zfin.org/zf_info/downloads.html
  ZFIN's site for downloading large data sets.
  http://zfin.org/zf_info/nomen.html
  Zebrafish Nomenclature guidelines.
  http://zfin.org/cgi‐bin/webdriver?MIval=aa‐new_line.apg
  ZFIN's submission form for proposed mutant/transgenic line names. ZFIN login is required.
  http://zfin.org/cgi‐bin/webdriver?MIval=aa‐new_gene.apg
  ZFIN's submission form for proposed gene names. ZFIN login required.
  http://zfin.org/zf_info/anatomy/dict/sum.html
  ZFIN's links to zebrafish atlases and anatomical resources.
  http://wiki.zfin.org
  The ZFIN Community Wiki, where zebrafish researchers can share information with the rest of the community.
  http://zebrafish.org/zirc/
  The Zebrafish International Resource Center (ZIRC) acquires, maintains and redistributes zebrafish resources.
  http://www.openhelix.com/zfin
  OpenHelix provides tutorial and training materials that introduce new users to ZFIN.
  http://www.sanger.ac.uk/Projects/D_rerio/
  The Danio rerio Sequencing Project at the Sanger Institute describes the genome project and its status.
  http://gmod.org/wiki/Gbrowse
  The GMOD wiki page for GBrowse provides a description, and links to further documentation.
  http://www.obofoundry.org/
  The Open Biomedical Ontologies Web site provides science‐based ontologies in the biomedical domain.
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