From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes
Abstract Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic co...
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| Veröffentlicht in: | Genetics (Austin) 2023-05, Vol.224 (1) |
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| creator | Bradford, Yvonne M Van Slyke, Ceri E Howe, Douglas G Fashena, David Frazer, Ken Martin, Ryan Paddock, Holly Pich, Christian Ramachandran, Sridhar Ruzicka, Leyla Singer, Amy Taylor, Ryan Tseng, Wei-Chia Westerfield, Monte |
| description | Abstract
Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity. |
| doi_str_mv | 10.1093/genetics/iyad032 |
| format | Article |
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Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.</description><identifier>ISSN: 1943-2631</identifier><identifier>ISSN: 0016-6731</identifier><identifier>EISSN: 1943-2631</identifier><identifier>DOI: 10.1093/genetics/iyad032</identifier><identifier>PMID: 36864549</identifier><language>eng</language><publisher>US: Oxford University Press</publisher><subject>Animals ; Annotations ; Danio rerio ; Gene Expression ; Genetic engineering ; Genome ; Genomics - methods ; Genotype & phenotype ; Humans ; Knowledgebase & Database Resources ; Mutation ; Phenotype ; Phenotypes ; Point mutation ; Vertebrates ; Zebrafish ; Zebrafish - genetics</subject><ispartof>Genetics (Austin), 2023-05, Vol.224 (1)</ispartof><rights>The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. 2023</rights><rights>The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c461t-6e107669fe20c1aae5401cdb1e128851e63a01b6ac371def6dd5a13bfd83c6813</citedby><cites>FETCH-LOGICAL-c461t-6e107669fe20c1aae5401cdb1e128851e63a01b6ac371def6dd5a13bfd83c6813</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,1584,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36864549$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Wood, V</contributor><creatorcontrib>Bradford, Yvonne M</creatorcontrib><creatorcontrib>Van Slyke, Ceri E</creatorcontrib><creatorcontrib>Howe, Douglas G</creatorcontrib><creatorcontrib>Fashena, David</creatorcontrib><creatorcontrib>Frazer, Ken</creatorcontrib><creatorcontrib>Martin, Ryan</creatorcontrib><creatorcontrib>Paddock, Holly</creatorcontrib><creatorcontrib>Pich, Christian</creatorcontrib><creatorcontrib>Ramachandran, Sridhar</creatorcontrib><creatorcontrib>Ruzicka, Leyla</creatorcontrib><creatorcontrib>Singer, Amy</creatorcontrib><creatorcontrib>Taylor, Ryan</creatorcontrib><creatorcontrib>Tseng, Wei-Chia</creatorcontrib><creatorcontrib>Westerfield, Monte</creatorcontrib><title>From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes</title><title>Genetics (Austin)</title><addtitle>Genetics</addtitle><description>Abstract
Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.</description><subject>Animals</subject><subject>Annotations</subject><subject>Danio rerio</subject><subject>Gene Expression</subject><subject>Genetic engineering</subject><subject>Genome</subject><subject>Genomics - methods</subject><subject>Genotype & phenotype</subject><subject>Humans</subject><subject>Knowledgebase & Database Resources</subject><subject>Mutation</subject><subject>Phenotype</subject><subject>Phenotypes</subject><subject>Point mutation</subject><subject>Vertebrates</subject><subject>Zebrafish</subject><subject>Zebrafish - genetics</subject><issn>1943-2631</issn><issn>0016-6731</issn><issn>1943-2631</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqFUU1v1DAQjRCIlsKdE7LEBQmW2nHijU8VqrpQqYILXLhYs_Fk11ViB49T2D_R34zDbqvChZNH8z48T68oXgr-XnAtTzfoMbmWTt0OLJflo-JY6EouSiXF4wfzUfGM6JpzrnTdPC2OpGpUVVf6uLhdxTCwYeqTg77HHlnnaMtSYD54SuAtRMvQ37gY_IA-0Tu2DT_Z99XlZwZEbuOJjVv0Ie1GnMFpAM-sIwRCNgSLfd5mHzYfy_DXGDHLgs-7LIKUR5r_m2F6XjzpoCd8cXhPim-ri6_nnxZXXz5enn-4WrSVEmmhUPClUrrDkrcCAOuKi9auBYqyaWqBSgIXawWtXAqLnbK2BiHXnW1kqxohT4qzve84rQe0bQ4WoTdjdAPEnQngzN-Id1uzCTdGcFE3jayzw5uDQww_JqRkBkct9j14DBOZctnISiv9h_r6H-p1mKLP-Uyp67qUS65nFt-z2hiIInb31whu5rbNXdvm0HaWvHqY4l5wV28mvN0TwjT-3-43-ty8Rg</recordid><startdate>20230504</startdate><enddate>20230504</enddate><creator>Bradford, Yvonne M</creator><creator>Van Slyke, Ceri E</creator><creator>Howe, Douglas G</creator><creator>Fashena, David</creator><creator>Frazer, Ken</creator><creator>Martin, Ryan</creator><creator>Paddock, Holly</creator><creator>Pich, Christian</creator><creator>Ramachandran, Sridhar</creator><creator>Ruzicka, Leyla</creator><creator>Singer, Amy</creator><creator>Taylor, Ryan</creator><creator>Tseng, Wei-Chia</creator><creator>Westerfield, Monte</creator><general>Oxford University Press</general><general>Genetics Society of America</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>4T-</scope><scope>4U-</scope><scope>7QP</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20230504</creationdate><title>From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes</title><author>Bradford, Yvonne M ; Van Slyke, Ceri E ; Howe, Douglas G ; Fashena, David ; Frazer, Ken ; Martin, Ryan ; Paddock, Holly ; Pich, Christian ; Ramachandran, Sridhar ; Ruzicka, Leyla ; Singer, Amy ; Taylor, Ryan ; Tseng, Wei-Chia ; Westerfield, Monte</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c461t-6e107669fe20c1aae5401cdb1e128851e63a01b6ac371def6dd5a13bfd83c6813</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Animals</topic><topic>Annotations</topic><topic>Danio rerio</topic><topic>Gene Expression</topic><topic>Genetic engineering</topic><topic>Genome</topic><topic>Genomics - methods</topic><topic>Genotype & phenotype</topic><topic>Humans</topic><topic>Knowledgebase & Database Resources</topic><topic>Mutation</topic><topic>Phenotype</topic><topic>Phenotypes</topic><topic>Point mutation</topic><topic>Vertebrates</topic><topic>Zebrafish</topic><topic>Zebrafish - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bradford, Yvonne M</creatorcontrib><creatorcontrib>Van Slyke, Ceri E</creatorcontrib><creatorcontrib>Howe, Douglas G</creatorcontrib><creatorcontrib>Fashena, David</creatorcontrib><creatorcontrib>Frazer, Ken</creatorcontrib><creatorcontrib>Martin, Ryan</creatorcontrib><creatorcontrib>Paddock, Holly</creatorcontrib><creatorcontrib>Pich, Christian</creatorcontrib><creatorcontrib>Ramachandran, Sridhar</creatorcontrib><creatorcontrib>Ruzicka, Leyla</creatorcontrib><creatorcontrib>Singer, Amy</creatorcontrib><creatorcontrib>Taylor, Ryan</creatorcontrib><creatorcontrib>Tseng, Wei-Chia</creatorcontrib><creatorcontrib>Westerfield, Monte</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Docstoc</collection><collection>University Readers</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genetics (Austin)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bradford, Yvonne M</au><au>Van Slyke, Ceri E</au><au>Howe, Douglas G</au><au>Fashena, David</au><au>Frazer, Ken</au><au>Martin, Ryan</au><au>Paddock, Holly</au><au>Pich, Christian</au><au>Ramachandran, Sridhar</au><au>Ruzicka, Leyla</au><au>Singer, Amy</au><au>Taylor, Ryan</au><au>Tseng, Wei-Chia</au><au>Westerfield, Monte</au><au>Wood, V</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes</atitle><jtitle>Genetics (Austin)</jtitle><addtitle>Genetics</addtitle><date>2023-05-04</date><risdate>2023</risdate><volume>224</volume><issue>1</issue><issn>1943-2631</issn><issn>0016-6731</issn><eissn>1943-2631</eissn><abstract>Abstract
Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.</abstract><cop>US</cop><pub>Oxford University Press</pub><pmid>36864549</pmid><doi>10.1093/genetics/iyad032</doi><oa>free_for_read</oa></addata></record> |
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| ispartof | Genetics (Austin), 2023-05, Vol.224 (1) |
| issn | 1943-2631 0016-6731 1943-2631 |
| language | eng |
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| source | MEDLINE; Oxford University Press Journals All Titles (1996-Current); EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | Animals Annotations Danio rerio Gene Expression Genetic engineering Genome Genomics - methods Genotype & phenotype Humans Knowledgebase & Database Resources Mutation Phenotype Phenotypes Point mutation Vertebrates Zebrafish Zebrafish - genetics |
| title | From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes |
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