ArticleJournal of biomedical semantics2016
Extending gene ontology in the context of extracellular RNA and vesicle communication.
Article in Journal of biomedical semantics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Connecting the Dots: Milestones in the History of Extracellular Vesicle Research.International journal of molecular sciences · 2026Review
- Extracellular RNA communication: A decade of NIH common fund support illuminates exRNA biology.Journal of extracellular vesicles · 2025Review
- Research advances of tissue-derived extracellular vesicles in cancers.Journal of cancer research and clinical oncology · 2024Review
- International Society for Extracellular Vesicles Workshop. QuantitatEVs: multiscale analyses, from bulk to single extracellular vesicle.Journal of extracellular biology · 2024Article
- Extracellular vesicle-mediated delivery of anti-miR-106b inhibits morphine-induced primary ciliogenesis in the brain.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
- Exosome Carrier Effects; Resistance to Digestion in Phagolysosomes May Assist Transfers to Targeted Cells; II Transfers of miRNAs Are Better Analyzed via Systems Approach as They Do Not Fit Conventional Reductionist Stoichiometric Concepts.International journal of molecular sciences · 2022Review
- Challenges and opportunities in the study of extracellular vesicles: Global institutional context and national state of the artBiomedica : revista del Instituto Nacional de Salud · 2021Article
- Selective exosome exclusion of miR-375 by glioma cells promotes glioma progression by activating the CTGF-EGFR pathway.Journal of experimental & clinical cancer research : CR · 2021Article
- Article
- Systems biology approaches to investigating the roles of extracellular vesicles in human diseases.Experimental & molecular medicine · 2019Review
- Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles.Nucleic acids research · 2019Article
- The decade of exosomal long RNA species: an emerging cancer antagonist.Molecular cancer · 2018Review
- Stage-specific follicular extracellular vesicle uptake and regulation of bovine granulosa cell proliferation.Biology of reproduction · 2017Article
- The role of pancreatic cancer-derived exosomes in cancer progress and their potential application as biomarkers.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2017Review
- Urinary extracellular vesicles. A promising shortcut to novel biomarker discoveries.Cell and tissue research · 2017Review
- Exosomes maintain cellular homeostasis by excreting harmful DNA from cells.Nature communications · 2017Article
- Extracellular vesicles in liver diseases.American journal of physiology. Gastrointestinal and liver physiology · 2017Review
- Expansion of the Gene Ontology knowledgebase and resources.Nucleic acids research · 2017Article
- A rigorous method to enrich for exosomes from brain tissue.Journal of extracellular vesicles · 2017Article
- Oncosomes - large and small: what are they, where they came from?Journal of extracellular vesicles · 2016Article
Corrections and comments
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Authors and funding
28 authors.
Funding
Abstract
backgroundTo address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research.
methodsBy following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO. In addition, we have initiated an ongoing process of extractions of gene product annotations associated with these terms from Vesiclepedia and ExoCarta, conversion of the extracted annotations to Gene Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium. As a use case, we have incorporated some of the GO terms into annotations of samples from the exRNA Atlas and implemented a faceted search interface based on such annotations.
resultsWe have added 7 new terms and modified 9 existing terms (along with their synonyms and relationships) to GO. Additionally, 18,695 unique coding gene products (mRNAs and proteins) and 963 unique non-coding gene products (ncRNAs) which are associated with the terms: "extracellular vesicle", "extracellular exosome", "apoptotic body", and "microvesicle" were extracted from ExoCarta and Vesiclepedia. These annotations are currently being processed for submission to GO.
conclusionsAs an inter-community effort, we have made a substantial update to GO in the exRNA context. We have also demonstrated the utility of some of the new GO terms for sample annotation and metadata search.
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