<scp>ZFIN</scp>, The zebrafish model organism database: Updates and new directions

Ruzicka, Leyla; Bradford, Yvonne M.; Frazer, Ken; Howe, Douglas G.; Paddock, Holly; Ramachandran, Sridhar; Singer, Amy; Toro, Sabrina; Slyke, Ceri E. Van; Eagle, Anne; Fashena, David; Kalita, Patrick; Knight, Jonathan; Mani, Prita; Martin, R. D.; Moxon, Sierra; Pich, Christian; Schaper, Kevin; Shao, Xiang; Westerfield, Monte

doi:10.1002/dvg.22868

Cited by 70 publications

(62 citation statements)

References 45 publications

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“…In 2016, MGD joined FlyBase (15), Saccharomyces Genome Database (SGD) (16), WormBase (17), Zebrafish Information Network (ZFIN) (18), Rat Genome Database (RGD) (19) and the Gene Ontology Consortium (GOC) to form the Alliance of Genome Resources (AGR). The Alliance was forged in response to changes in the funding model for biomedical resources at NIH which have been covered in several recent articles Nature (http://www.nature.com/news/funding-for-model-organism-databases-in-trouble-1.20134) and Science(http://science.sciencemag.org/content/351/6268/14.full).…”

Section: New Features and Improvementsmentioning

confidence: 99%

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

et al. 2016

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The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and efficient use of MGD in the advancement of scientific knowledge. Here, we report on recent enhancements made to the resource and new features.

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Section: New Features and Improvementsmentioning

confidence: 99%

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

et al. 2016

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“…While zebrafish are a well-established model laboratory organism (Norton & Bally-Cuif, 2010; Ribas & Piferrer, 2014; Ruzicka et al, 2015), less is known about their ecology in the wild. Zebrafish tend to inhabit shallow, slow-moving freshwater where they use the entire water column and occupy both vegetated margins and open areas (Spence et al, 2006).…”

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confidence: 99%

Correlated evolution of personality, morphology and performance

et al. 2016

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Evolutionary change in one trait can elicit evolutionary changes in other traits due to genetic correlations. This constrains the independent evolution of traits and can lead to unpredicted ecological and evolutionary outcomes. Animals might frequently exhibit genetic associations among behavioural and morphological-physiological traits, because the physiological mechanisms behind animal personality can have broad multitrait effects and because many selective agents influence the evolution of multiple types of traits. However, we currently know little about genetic correlations between animal personalities and nonbehavioural traits. We tested for associations between personality, morphology and locomotor performance by comparing zebrafish (Danio rerio) collected from the wild and then selectively bred for either a proactive or reactive stress coping style (‘bold’ or ‘shy’ phenotypes). Based on adaptive hypotheses of correlational selection in the wild, we predicted that artificial selection for boldness would produce correlated evolutionary responses of larger caudal regions and higher fast-start escape performance (and the opposite for shyness). After four to seven generations, morphology and locomotor performance differed between personality lines: bold zebrafish exhibited a larger caudal region and higher fast-start performance than fish in the shy line, matching predictions. Individual-level phenotypic correlations suggested that pleiotropy or physical gene linkage likely explained the correlated response of locomotor performance, while the correlated response of body shape may have reflected linkage disequilibrium, which is breaking down each generation in the laboratory. Our results indicate that evolution of personality can result in concomitant changes in morphology and whole-organism performance, and vice versa.

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“…Many model organism databases, such as FlyBase, 8 WormBase, 21 and ZFIN, 10 are comprehensive and contain a monumental amount of data accumulated over numerous decades. 45 However, the extremely valuable information in these databases is not easily accessible by those outside the field.…”

Section: Discussionmentioning

confidence: 99%

“…9 Zebrafish data are from ZFIN downloadable files. 10 Fly expression data and GO terms are pulled from the FlyBase website. 8 S. cerevisiae data and S. pombe data are from SGD 19 and PomBase.…”

Section: Server and Data Storingmentioning

confidence: 99%

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

Wang¹,

Al‐Ouran²,

Hu³

et al. 2017

The American Journal of Human Genetics

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194

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One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research.

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ZFIN, The zebrafish model organism database: Updates and new directions

Cited by 70 publications

References 45 publications

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

Correlated evolution of personality, morphology and performance

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

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