Using ZFIN: Data Types, Organization, and Retrieval

Slyke, Ceri E. Van; Bradford, Yvonne M.; Howe, Douglas G.; Fashena, David; Ramachandran, Sridhar; Ruzicka, Leyla; Staff, Zfin

doi:10.1007/978-1-4939-7737-6_11

Cited by 13 publications

(9 citation statements)

References 32 publications

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“…ZFIN collects, organizes, and makes available a wide range of data on zebrafish, including genes, gene function, sequences, mutants, transgenic lines, human disease models, expression, phenotype, orthology, sequence targeting reagents and antibodies. Data at ZFIN can be accessed through ZFIN search interfaces, download files, and ZebrafishMine (zebrafishmine.org), a data mining resource (1). Community services include nomenclature support for genes and alleles, ZFIN pages for researchers, laboratories and companies, and a wiki for researchers to share antibody and protocol information.…”

Section: Introductionmentioning

confidence: 99%

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

Ruzicka

Howe

Ramachandran

et al. 2018

Nucleic Acids Research

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132

104

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The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.

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Section: Introductionmentioning

confidence: 99%

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

Ruzicka

Howe

Ramachandran

et al. 2018

Nucleic Acids Research

Self Cite

132

104

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“…OR candidates with at least 40 % sequence identity over at least 100 amino acids to another OR are considered as OR genes. The OR repertoires (Table 1) were compared to relevant publications and public resources including Mouse Genome Informatics (MGI, [55]), Rat Genome Database (RGD, [56]), The Zebrafish Information Network (ZFIN, [57]), as well as Ensembl [58] and NCBI [59]. The sizes of the identified repertoires are in good agreement with those resources, as well as with published studies [24,25,31].…”

Section: Methodsmentioning

confidence: 54%

A unified nomenclature for vertebrate olfactory receptors

Olender

Jones²,

Bruford³

et al. 2020

Preprint

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Background Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results Here we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5 . Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~50% in dog and cow and to ~30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

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“…OR candidates with at least 40% sequence identity over at least 100 amino acids to another OR are considered as OR genes. The OR repertoires (Table 1) were compared to relevant publications and public resources including Mouse Genome Informatics (MGI, [55]), Rat Genome Database (RGD, [56]), The Zebrafish Information Network (ZFIN, [57]), as well as Ensembl [58] and NCBI [59]. The sizes of the identified repertoires are in good agreement with those resources, as well as with published studies [24,25,31].…”

Section: Or Gene Sequencesmentioning

confidence: 54%

A unified nomenclature for vertebrate olfactory receptors

et al. 2020

View full text Add to dashboard Cite

Background: Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors~1000 OR genes and pseudogenes; however, different gene duplication/ deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results: Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to~50% in dog and cow and to~30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions: We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

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Using ZFIN: Data Types, Organization, and Retrieval

Cited by 13 publications

References 32 publications

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

A unified nomenclature for vertebrate olfactory receptors

A unified nomenclature for vertebrate olfactory receptors

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