Mouse Genome Database: From sequence to phenotypes and disease models

Eppig, Janan T.; Richardson, Joel E.; Kadin, James A.; Smith, Cynthia L.; Blake, Judith A.; Bult, Carol J.

doi:10.1002/dvg.22874

Cited by 15 publications

(11 citation statements)

References 47 publications

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“…MGD also integrates these murine data into the context of human disease data based on orthology and gene expression 32,24 . This integrated resource allowed us to exploit the associations of mouse genes and their phenotypes for enrichment purposes using VLAD, and gives us an entry into identification of potential mouse models for future study 33 .…”

Section: Mammalian Phenotype Enrichment Analysismentioning

confidence: 99%

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

Dolan

Hill

Mukherjee

et al. 2020

Preprint

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The emergence of the SARS-CoV-2 virus and subsequent COVID-19 pandemic initiated intense research into the mechanisms of action for this virus. It was quickly noted that COVID-19 presents more seriously in conjunction with other human disease conditions such as hypertension, diabetes, and lung diseases. We conducted a bioinformatics analysis of COVID-19 comorbidity-associated gene sets, identifying genes and pathways shared among the comorbidities, and evaluated current knowledge about these genes and pathways as related to current information about SARS-CoV-2 infection. We performed our analysis using GeneWeaver (GW), Reactome, and several biomedical ontologies to represent and compare common COVID-19 comorbidities. Phenotypic analysis of shared genes revealed significant enrichment for immune system phenotypes and for cardiovascular-related phenotypes, which might point to alleles and phenotypes in mouse models that could be evaluated for clues to COVID-19 severity. Through pathway analysis, we identified enriched pathways shared by comorbidity datasets and datasets associated with SARS-CoV-2 infection.

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Section: Mammalian Phenotype Enrichment Analysismentioning

confidence: 99%

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

Dolan

Hill

Mukherjee

et al. 2020

Preprint

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“…The next section, the ‘Disease Summary’, provides disease-specific information from resources outside of FlyBase, primarily from OMIM phenotype and genotype reports, organized as so to be useful to geneticists and molecular biologists. This section also includes links to informational resources such as GeneReviews ® (26) and the MGI (Mouse Genome Informatics) Human-Mouse Disease Connection (27). …”

Section: Introductionmentioning

confidence: 99%

FlyBase at 25: looking to the future

et al. 2016

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Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.

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“…To test whether isoDMBs truly reflect regional changes in chromatin properties, we proceeded to study the overlap of isoDMBs with annotated mouse genes and with isochores (Supplementary Table 11). GRCm38/mm10 mouse gene coordinates were obtained using the Mouse Genome Database (MGB; 62 ). Isochores represent regions with a tendency for base composition uniformity 40 , and their coordinates for GRCm38/mm10 mouse genome annotation were obtained using IsoFinder 63 .…”

Section: Methodsmentioning

confidence: 99%

Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice

Chamorro-García

Díaz-Castillo

Shoucri

et al. 2017

Preprint

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Ancestral environmental exposures to non-mutagenic agents can exert effects in unexposed descendants. This transgenerational inheritance has significant implications for understanding disease etiology. The obesogen hypothesis proposes that exposure to obesogenic chemicals can lead to increased adiposity, in vivo. Here we show that exposure of F0 mice to the obesogen tributyltin (TBT) throughout pregnancy and lactation predisposes unexposed F4 male descendants to obesity when dietary fat is increased. Analyses of body fat, plasma hormone levels, and visceral white adipose tissue DNA methylome and transcriptome collectively indicate that the F4 obesity is consistent with a leptin resistant, "thrifty phenotype". Ancestral TBT exposure induces global changes in DNA methylation together with altered expression of metabolism-relevant genes when the F4 animals were exposed to dietary challenges. Analysis of chromatin accessibility in F3 and F4 sperm reveal significant differences between control and TBT groups and significant similarities between F3 and F4 TBT groups that overlap with areas of differential methylation in F4 adipose tissue. Taken together, our data suggest that ancestral TBT exposure induces changes in higher order chromatin organization transmissible through meiosis and mitosis.Non-technical summaryAncestral obesogen exposure in mice causes obesity in untreated F4 male descendants by inducing heritable changes in genome architecture that predispose these animals to become obese when dietary fat is increased modestly. This result is consistent with these animals having a leptin-resistant, "thrifty" phenotype

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Mouse Genome Database: From sequence to phenotypes and disease models

Cited by 15 publications

References 47 publications

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

FlyBase at 25: looking to the future

Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice

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