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Cited by 1,367Extracellular vesicles in diseaseCellular transport and secretionCaveolin-1 and cellular processes

Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation

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Kalra, Hina, Simpson, Richard J., Ji, Hong, Aikawa, Elena, Altevogt, Peter, Askenase, Philip, Bond, Vincent C., Borràs, Francesc E. +48 more·2012·PLoS Biology
DOI 10.1371/journal.pbio.1001450PMC PMC3525526
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Abstract

Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.

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  • GAPDH is one of the top five most common proteins associated with EVs.

    “GAPDH is one of the top five most common proteins associated with EVs61.”

    From GAPDH controls extracellular vesicle biogenesis and enhances the therapeutic potential of EV mediated siRNA delivery to the brain (2021) · cites this paper as [61]

    The Vesiclepedia section describes a compendium of proteins identified in EVs, but does not name GAPDH or rank proteins by frequency. Searches for GAPDH, glyceraldehyde-3-phosphate dehydrogenase, and top-five EV proteins found no passage establishing the claimed ranking; page numbers were not available in our copy. (LLM, conf=0.76)

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Authors
Kalra, H., Simpson, R. J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V. C., Borràs, F. E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J. M., Gabrielsson, S., Gho, Y. S., Gupta, D., Harsha, H. C., Hendrix, A., Hill, A. F., Inal, J. M., Jenster, G., Krämer-Albers, E.-M., Lim, S. K., Llorente, A., Lötvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E. N. M., Pandey, A., Patel, T., Piper, M. G., Pluchino, S., Prasad, T. S. K., Rajendran, L., Raposo, G., Record, M., Reid, G. E., Sánchez-Madrid, F., Schiffelers, R. M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B. W. M., Vázquez, J., Vidal, M., Wauben, M. H. M., Yáñez-Mó, M., Zoeller, M., & Mathivanan, S.
Affiliations
  • La Trobe University (AU)
  • Brigham and Women's Hospital (US)
  • German Cancer Research Center (DE)
  • Yale University (US)
  • Morehouse School of Medicine (US)
  • Universitat Autònoma de Barcelona (ES)
  • Harvard University (US)
  • University of Massachusetts Chan Medical School (US)
  • University of Turin (IT)
  • Velindre Cancer Centre (GB)
  • Boston Children's Hospital (US)
  • Karolinska Institutet (SE)
  • Pohang University of Science and Technology (KR)
  • University of Allahabad (IN)
  • Ghent University Hospital (BE)
  • The University of Melbourne (AU)
  • London Metropolitan University (GB)
  • Erasmus MC (NL)
  • Agency for Science, Technology and Research (SG)
  • Oslo University Hospital (NO)
  • University of Gothenburg (SE)
  • Universitat de València (ES)
  • University Medical Center Freiburg (DE)
  • Amsterdam UMC Location University of Amsterdam (NL)
  • Johns Hopkins University (US)
  • Mayo Clinic (US)
  • The Ohio State University (US)
  • Wellcome/MRC Cambridge Stem Cell Institute (GB)
  • Institute of Bioinformatics (IN)
  • University of Zurich (CH)
  • Michigan State University (US)
  • University Medical Center Utrecht (NL)
  • University of Helsinki (FI)
  • Aalborg University (DK)
  • Utrecht University (NL)
  • University of Louisville (US)
  • Spanish National Centre for Cardiovascular Research (ES)
  • Centre National de la Recherche Scientifique (FR)
  • University Hospital Heidelberg (DE)
Corresponding author
Mathivanan, Suresh
ORCID
Venue
PLoS Biology
Publisher
Public Library of Science (PLoS)
Published
2012-12-18
Volume
10
Issue
12
Pages
e1001450
ISSN
  • 1544-9173 (ISSN-L)
  • 1545-7885
DOI
10.1371/journal.pbio.1001450
PMC
PMC3525526
OpenAlex
W2128891846
Cited by
1,367
References
2
Citations by year
2026: 47 · 2025: 46 · 2024: 115 · 2023: 105 · 2022: 111 · 2021: 137 · 2020: 131 · 2019: 120 · 2018: 121 · 2017: 114 · 2016: 114 · 2015: 83 · 2014: 74 · 2013: 43 · 2012: 2
FWCI
25.99
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (acceptedVersion, other-oa)
  • University of Hertfordshire Research Archive (University of Hertfordshire) (acceptedVersion, other-oa)
  • Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by)
  • LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (acceptedVersion)
  • Tesis Doctorals en Xarxa (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion, other-oa)
  • Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
  • Biblos-e Archivo (Universidad Autónoma de Madrid) (submittedVersion, public-domain)
  • University of Hertfordshire Research Archive (University of Hertfordshire) (submittedVersion, other-oa)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • Victoria University Research Repository (Victoria University) (submittedVersion, cc-by)
  • The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion, cc-by)
  • National University of Singapore (submittedVersion)
  • Data Archiving and Networked Services (DANS) (submittedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
  • RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
  • KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
  • Hispana (submittedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • Open Access System for Information Sharing (Pohang University of Science and Technology) (submittedVersion, cc-by-nc-nd)
  • Pure Amsterdam UMC (submittedVersion)
  • VBN Forskningsportal (Aalborg Universitet) (submittedVersion)
  • Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
  • Zurich Open Repository and Archive (University of Zurich)
Funders
  • Wellcome Trust (079249)
  • La Trobe University
  • Medical Research Council
  • National Heart, Lung, and Blood Institute (R01HL114805)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R01DK069370)
  • National Institute on Minority Health and Health Disparities (S21MD000101)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Extracellular vesicles in disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Caveolin-1 and cellular processes
Keywords
extracellular vesicles, manual curation, community annotation, vesicle lipid composition, intercellular communication, biomarkers, drug delivery, vaccine delivery, gene delivery
MeSH terms
Extracellular Space, Research, Apoptosis, Databases as Topic, Exosomes

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