The Gene Ontology knowledgebase in 2023

Genetics, Journal Year: 2023, Volume and Issue: 224(1)

Published: March 3, 2023

Abstract The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins noncoding RNAs). GO annotations cover from organisms across tree life as well viruses, though most function knowledge currently derives experiments carried out in relatively small number model organisms. Here, we provide an updated overview knowledgebase, efforts broad, international consortium scientists that develops, maintains, updates knowledgebase. consists three components: (1) GO—a computational structure describing functional characteristics genes; (2) annotations—evidence-supported statements asserting specific product has particular characteristic; (3) Causal Activity Models (GO-CAMs)—mechanistic models molecular “pathways” (GO biological processes) created by linking multiple using defined relations. Each these components continually expanded, revised, response to newly published discoveries receives extensive QA checks, reviews, user feedback. For each components, description current contents, recent developments keep up date with new discoveries, guidance on how users can best make use data provide. We conclude future directions for project.

Language: Английский

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Harmonizing model organism data in the Alliance of Genome Resources

Genetics, Journal Year: 2022, Volume and Issue: 220(4)

Published: Feb. 25, 2022

The Alliance of Genome Resources (the Alliance) is a combined effort 7 knowledgebase projects: Saccharomyces Database, WormBase, FlyBase, Mouse the Zebrafish Information Network, Rat and Gene Ontology Resource. seeks to provide several benefits: better service various communities served by these projects; harmonized view data for all biomedical researchers, bioinformaticians, clinicians, students; more sustainable infrastructure. has cross-organism useful comparative views gene function, expression, human disease relevance. basis shared calls orthology relationships use common ontologies. key types are alleles variants, function based on ontology annotations, phenotypes, association disease, protein-protein genetic interactions, participation in pathways. information presented uniform pages that allow facile summarization about each organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, human). knowledge freely available alliancegenome.org portal, as downloadable files, APIs. We expect other existing emerging bases join union features base currently provides.

Language: Английский

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Xenbase: key features and resources of the Xenopus model organism knowledgebase

Genetics, Journal Year: 2023, Volume and Issue: 224(1)

Published: Feb. 9, 2023

Abstract Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates diverse genomic and biological data from research on laboratory frogs laevis tropicalis. The goal of to accelerate discovery empower research, enhance impact data, facilitate dissemination these data. also enhances value through high-quality curation, integration, providing bioinformatics tools optimized for experiments, linking human other organisms. plays an indispensable role in making interoperable accessible broader biomedical community accordance with FAIR principles. provides annotated updates organizations such as NCBI, UniProtKB, Ensembl, Gene Ontology consortium, most recently, Alliance Genomic Resources, common clearing house humans This article brief overview key recently added features Xenbase. New include processing high-throughput sequencing NCBI Expression Omnibus; curation anatomical, physiological, expression phenotypes newly created Phenotype Ontology; annotations; new anatomical drawings Normal Table development; integration latest v10.1 genome annotations. Finally, we highlight areas future development at continue support community.

Language: Английский

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Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse

Genetics, Journal Year: 2024, Volume and Issue: 227(1)

Published: March 26, 2024

Abstract Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic genomic aspects human biology disease using the laboratory mouse as model system. The Database (MGD) Gene Expression (GXD) are core MGI databases that share data system architecture. serves central community resource integrated about genome features, variation, expression, gene function, phenotype, models acquired from peer-reviewed publications, author submissions, major bioinformatics resources. To facilitate integration standardization data, biocuration scientists annotate terms controlled metadata vocabularies biological ontologies (e.g. Mammalian Phenotype Ontology, Developmental Anatomy, Disease etc.), by applying international standards for gene, allele, strain nomenclature. basic scientists, translational researchers, providing access FAIR-compliant in both human-readable compute-ready formats. accessible at https://informatics.jax.org. Here, we present an overview types represented highlight recent enhancements with focus on new functionality MGD GXD.

Language: Английский

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Evidence for widespread cytoplasmic structuring into mesoscale condensates

Nature Cell Biology, Journal Year: 2024, Volume and Issue: 26(3), P. 346 - 352

Published: Feb. 29, 2024

Language: Английский

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The mouse Gene Expression Database (GXD): 2021 update

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D924 - D931

Published: Oct. 3, 2020

Abstract The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, western blot experiments through curation the scientific literature by collaborations with large-scale projects. Since our last report 2019, we have continued to acquire these classical types data; developed a searchable index RNA-Seq microarray that allows users quickly reliably find specific studies ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) GEO (https://www.ncbi.nlm.nih.gov/geo/); expanded include data. Uniformly processed are imported EBI Atlas then other GXD, genetic, functional, phenotypic disease-related information Mouse Genome Informatics (MGI). This integration made accessible via GXD’s enhanced searching filtering capabilities. Further, embedded Morpheus heat map utility into user interface provide additional tools for display analysis data, including visualization, sorting, filtering, hierarchical clustering, nearest neighbors visual enrichment.

Language: Английский

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Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D970 - D979

Published: Oct. 13, 2021

Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying user interface to adapt multispecies echinoderm content. This approach leveraged over 15 years of previous database application development generate fully featured informatics in single year. In addition software stack, uses private cloud physical hosts that support Xenbase. currently supports six species, focused those used for genomics, developmental biology gene regulatory network analyses. Over 38 000 pages, 18 publications, improved genome assemblies, JBrowse browser BLAST + services are available supported anatomical ontology, uniformly applied formal nomenclature, consistent orthology predictions. A novel feature integrating multiple, disparate species. New genomes from diverse phylum will be added as becomes available. common code design integrated knowledgebases ensures parallel improvements each evolves. widely applicable developing resources.

Language: Английский

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Fourth Report on Chicken Genes and Chromosomes 2022

Cytogenetic and Genome Research, Journal Year: 2022, Volume and Issue: 162(8-9), P. 405 - 528

Published: Jan. 1, 2022

none

Language: Английский

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Differential nuclear import sets the timing of protein access to the embryonic genome

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Oct. 6, 2022

Abstract The development of a fertilized egg to an embryo requires the proper temporal control gene expression. During cell differentiation, timing is often controlled via cascades transcription factors (TFs). However, in early development, inactive, and many TF levels stay constant, suggesting that alternative mechanisms govern observed rapid ordered onset Here, we find embryonic access maternally deposited nuclear proteins genome temporally importin affinities, thereby expression downstream targets. We quantify changes proteome during proteins, such as TFs RNA polymerases, enter nucleus sequentially. Moreover, proteins’ corresponds activation. show affinity major determinant protein entry into nuclei. Thus, propose mechanism by which embryos encode biochemical affinities. This process could be critical for organize themselves before deploying regulatory identities.

Language: Английский

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A single-cell, time-resolved profiling of Xenopus mucociliary epithelium reveals nonhierarchical model of development

Science Advances, Journal Year: 2023, Volume and Issue: 9(14)

Published: April 7, 2023

The specialized cell types of the mucociliary epithelium (MCE) lining respiratory tract enable continuous airway clearing, with its defects leading to chronic diseases. molecular mechanisms driving fate acquisition and temporal specialization during epithelial development remain largely unknown. Here, we profile developing Xenopus MCE from pluripotent mature stages by single-cell transcriptomics, identifying multipotent early progenitors that execute multilineage cues before specializing into late-stage ionocytes goblet basal cells. Combining in silico lineage inference, situ hybridization, multiplexed RNA imaging, capture initial bifurcation multiciliated chart type emergence progression types. Comparative analysis nine atlases reveals an evolutionary conserved transcriptional module ciliated cells, whereas secretory distinct function-specific programs across vertebrates. We uncover a nonhierarchical model alongside data resource for understanding biology.

Language: Английский

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