PUBLICATION
From Multi-Allele Fish to Non-Standard Environments, How ZFIN Assigns Phenotypes, Human Disease Models, and Gene Expression Annotations to Genes
- Authors
- Bradford, Y.M., Van Slyke, C.E., Howe, D.G., Fashena, D., Frazer, K., Martin, R., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Singer, A., Taylor, R., Tseng, W.C., Westerfield, M.
- ID
- ZDB-PUB-230303-47
- Date
- 2023
- Source
- Genetics 224(1): (Journal)
- Registered Authors
- Bradford, Yvonne, Fashena, David, Howe, Doug, Martin, Ryan, Paddock, Holly, Pich, Christian, Ramachandran, Sridhar, Ruzicka, Leyla, Singer, Amy, Taylor, Ryan, Tseng, Wei-Chia, Van Slyke, Ceri E., Westerfield, Monte
- Keywords
- Danio rerio, ZFIN, expression, human disease model, model organism database, phenotype, zebrafish
- MeSH Terms
-
- Animals
- Gene Expression
- Genome*
- Genomics/methods
- Humans
- Phenotype
- Zebrafish*/genetics
- PubMed
- 36864549 Full text @ Genetics
Citation
Bradford, Y.M., Van Slyke, C.E., Howe, D.G., Fashena, D., Frazer, K., Martin, R., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Singer, A., Taylor, R., Tseng, W.C., Westerfield, M. (2023) From Multi-Allele Fish to Non-Standard Environments, How ZFIN Assigns Phenotypes, Human Disease Models, and Gene Expression Annotations to Genes. Genetics. 224(1):.
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 Danio 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping