Literature DB >> 20836073

Exploring zebrafish genomic, functional and phenotypic data using ZFIN.

Sridhar Ramachandran1, Barbara Ruef, Christian Pich, Judy Sprague.   

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.

Entities:  

Mesh：

Year:  2010        PMID： 20836073      PMCID： PMC4562798          DOI： 10.1002/0471250953.bi0118s31

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  22 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  The zebrafish genome project: sequence analysis and annotation.

Authors:  Kerstin Jekosch
Journal:  Methods Cell Biol       Date:  2004       Impact factor: 1.441

4.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Authors:  Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Christopher J Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
Journal:  Nat Biotechnol       Date:  2007-11       Impact factor: 54.908

5.  Stages of embryonic development of the zebrafish.

Authors:  C B Kimmel; W W Ballard; S R Kimmel; B Ullmann; T F Schilling
Journal:  Dev Dyn       Date:  1995-07       Impact factor: 3.780

6.  NCBI GEO: archive for high-throughput functional genomic data.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Dmitry Rudnev; Carlos Evangelista; Irene F Kim; Alexandra Soboleva; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Rolf N Muertter; Ron Edgar
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

7.  Linking human diseases to animal models using ontology-based phenotype annotation.

Authors:  Nicole L Washington; Melissa A Haendel; Christopher J Mungall; Michael Ashburner; Monte Westerfield; Suzanna E Lewis
Journal:  PLoS Biol       Date:  2009-11-24       Impact factor: 8.029

8.  The National Institutes of Health and the growth of the zebrafish as an experimental model organism.

Authors:  Deborah B Henken; Rebekah S Rasooly; Lorette Javois; A Tyl Hewitt
Journal:  Zebrafish       Date:  2004       Impact factor: 1.985

9.  An ontology for cell types.

Authors:  Jonathan Bard; Seung Y Rhee; Michael Ashburner
Journal:  Genome Biol       Date:  2005-01-14       Impact factor: 13.583

10.  The vertebrate genome annotation (Vega) database.

Authors:  L G Wilming; J G R Gilbert; K Howe; S Trevanion; T Hubbard; J L Harrow
Journal:  Nucleic Acids Res       Date:  2007-11-14       Impact factor: 16.971
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  3 in total

1.  Homozygous splice mutation in CWF19L1 in a Turkish family with recessive ataxia syndrome.

Authors:  Randi Burns; Karen Majczenko; Jishu Xu; Weiping Peng; Zuhal Yapici; James J Dowling; Jun Z Li; Margit Burmeister
Journal:  Neurology       Date:  2014-10-31       Impact factor: 9.910

2.  The mouse Gene Expression Database (GXD): 2011 update.

Authors:  Jacqueline H Finger; Constance M Smith; Terry F Hayamizu; Ingeborg J McCright; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

Review 3.  Animals devoid of pulmonary system as infection models in the study of lung bacterial pathogens.

Authors:  Yamilé López Hernández; Daniel Yero; Juan M Pinos-Rodríguez; Isidre Gibert
Journal:  Front Microbiol       Date:  2015-02-04       Impact factor: 5.640
  3 in total

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