The mouse Gene Expression Database (GXD): 2021 update

Baldarelli, Richard M.; Smith, Cyndi M.; Finger, Jacqueline H.; Hayamizu, Terry F.; McCright, Ingeborg J.; Xu, Jingxia; Shaw, David R.; Beal, Jonathan S; Blodgett, Olin; Campbell, J. A.; Corbani, Lori E.; Frost, Pete J.; Giannatto, Sharon C; Miers, Dave; Kadin, James A.; Richardson, Joel E.; Ringwald, Martin

doi:10.1093/nar/gkaa914

Cited by 91 publications

(81 citation statements)

References 19 publications

(19 reference statements)

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“…Recently, we have reported the expression profile of the human VDAC isoforms (Zinghirino et al, 2020 ) from the RNA-seqGTEx (Ardlie et al, 2015 ) and the RNA-seq CAGE RIKEN FANTOM 5 (FANTOM5) (Noguchi et al, 2017 ) Projects of Expression Atlas repository of EMBL-EBI (Papatheodorou et al, 2019 ). Here, we complement this information with the expression profile of VDAC mouse isoforms from the mouse gene expression database (GXD) (Baldarelli et al, 2021 ) and the FANTOM5 project repository ( Figure 2 and Table 1 ). The aim is to evaluate the expression profiles of VDAC isoforms between the two species.…”

Section: Vdac Gene Expression In Different Tissuesmentioning

confidence: 99%

VDAC Genes Expression and Regulation in Mammals

et al. 2021

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VDACs are pore-forming proteins, coating the mitochondrial outer membrane, and playing the role of main regulators for metabolites exchange between cytosol and mitochondria. In mammals, three isoforms have evolutionary originated, VDAC1, VDAC2, and VDAC3. Despite similarity in sequence and structure, evidence suggests different biological roles in normal and pathological conditions for each isoform. We compared Homo sapiens and Mus musculus VDAC genes and their regulatory elements. RNA-seq transcriptome analysis shows that VDAC isoforms are expressed in human and mouse tissues at different levels with a predominance of VDAC1 and VDAC2 over VDAC3, with the exception of reproductive system. Numerous transcript variants for each isoform suggest specific context-dependent regulatory mechanisms. Analysis of VDAC core promoters has highlighted that, both in a human and a mouse, VDAC genes show features of TATA-less ones. The level of CG methylation of the human VDAC genes revealed that VDAC1 promoter is less methylated than other two isoforms. We found that expression of VDAC genes is mainly regulated by transcription factors involved in controlling cell growth, proliferation and differentiation, apoptosis, and bioenergetic metabolism. A non-canonical initiation site termed “the TCT/TOP motif,” the target for translation regulation by the mTOR pathway, was identified in human VDAC2 and VDAC3 and in every murine VDACs promoter. In addition, specific TFBSs have been identified in each VDAC promoter, supporting the hypothesis that there is a partial functional divergence. These data corroborate our experimental results and reinforce the idea that gene regulation could be the key to understanding the evolutionary specialization of VDAC isoforms.

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Section: Vdac Gene Expression In Different Tissuesmentioning

confidence: 99%

VDAC Genes Expression and Regulation in Mammals

et al. 2021

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“…Cre reporter data represent allele patterns created through the tissue-specific activity of the Cre recombinase rather than gene expression patterns. However, from a strictly technical point of view, Cre reporter data are similar to knock-in reporter in situ data, a data type that GXD has long captured (Smith et al 2019;Baldarelli et al 2021). Therefore, the CrePortal takes advantage of GXD infrastructure to record and search for recombinase activity patterns.…”

Section: Accessing Data At the Creportal Web Interfacementioning

confidence: 99%

Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource

et al. 2021

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Recombinase alleles and transgenes can be used to facilitate spatio-temporal specificity of gene disruption or transgene expression. However, the versatility of this in vivo recombination system relies on having detailed and accurate characterization of recombinase expression and activity to enable selection of the appropriate allele or transgene. The CrePortal (http://www.informatics.jax.org/home/recombinase) leverages the informatics infrastructure of Mouse Genome Informatics to integrate data from the scientific literature, direct data submissions from the scientific community at-large, and from major projects developing new recombinase lines and characterizing recombinase expression and specificity patterns. Searching the CrePortal by recombinase activity or specific recombinase gene driver provides users with a recombinase alleles and transgenes activity tissue summary and matrix comparison of gene expression and recombinase activity with links to generation details, a recombinase activity grid, and associated phenotype annotations. Future improvements will add cell type-based activity annotations. The CrePortal provides a comprehensive presentation of recombinase allele and transgene data to assist researchers in selection of the recombinase allele or transgene based on where and when recombination is desired.

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“…NCIthesaurus cancer terms, rare disease). The newest bespoke DO slims include the ‘DO_RAD_slim’ created for the RadoNorm project ( https://www.radonorm.eu/ ), an EU project focused on reducing the risks of radon and naturally occurring radioactive material (NORM) exposure, and ‘DO_GXD_slim’ created for the Gene eXpression Database ( 33 ).…”

Section: Introductionmentioning

confidence: 99%

The Human Disease Ontology 2022 update

Schriml

Munro

Schor

et al. 2021

Nucleic Acids Research

163

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The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO’s 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and genomic resources around the world. This update reports on the addition of 1,793 new disease terms, a 14% increase of textual definitions and the integration of 22 137 new SubClassOf axioms defining disease to disease connections representing the DO’s complex disease classification. The DO’s updated website provides multifaceted etiology searching, enhanced documentation and educational resources.

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The mouse Gene Expression Database (GXD): 2021 update

Cited by 91 publications

References 19 publications

VDAC Genes Expression and Regulation in Mammals

VDAC Genes Expression and Regulation in Mammals

Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource

The Human Disease Ontology 2022 update

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