EVpedia: a community web portal for extracellular vesicles research

Dae-Kyum Kim¹, Jaewook Lee¹, Sae Rom Kim¹, Dong-Sic Choi¹, Yae Jin Yoon¹, Ji Hyun Kim¹, Gyeongyun Go¹, Dinh Nhung¹, Kahye Hong¹, Su Chul Jang¹, Si-Hyun Kim¹, Kyong-Su Park¹, Oh Youn Kim¹, Hyun Taek Park¹, Ji Hye Seo¹, Elena Aikawa¹, Monika Baj-Krzyworzeka¹, Bas W M van Balkom¹, Mattias Belting¹, Lionel Blanc¹, Vincent Bond¹, Antonella Bongiovanni¹, Francesc E Borràs¹, Luc Buée¹, Edit I Buzás¹, Lesley Cheng¹, Aled Clayton¹, Emanuele Cocucci¹, Charles S Dela Cruz¹, Dominic M Desiderio¹, Dolores Di Vizio¹, Karin Ekström¹, Juan M Falcon-Perez¹, Chris Gardiner¹, Bernd Giebel¹, David W Greening¹, Julia Christina Gross¹, Dwijendra Gupta¹, An Hendrix¹, Andrew F Hill¹, Michelle M Hill¹, Esther Nolte-'t Hoen¹, Do Won Hwang¹, Jameel Inal¹, Medicharla V Jagannadham¹, Muthuvel Jayachandran¹, Young-Koo Jee¹, Malene Jørgensen¹, Kwang Pyo Kim¹, Yoon-Keun Kim¹, Thomas Kislinger¹, Cecilia Lässer¹, Dong Soo Lee¹, Hakmo Lee¹, Johannes van Leeuwen¹, Thomas Lener¹, Ming-Lin Liu¹, Jan Lötvall¹, Antonio Marcilla¹, Suresh Mathivanan¹, Andreas Möller¹, Jess Morhayim¹, François Mullier¹, Irina Nazarenko¹, Rienk Nieuwland¹, Diana N Nunes¹, Ken Pang¹, Jaesung Park¹, Tushar Patel¹, Gabriella Pocsfalvi¹, Hernando Del Portillo¹, Ulrich Putz¹, Marcel I Ramirez¹, Marcio L Rodrigues¹, Tae-Young Roh¹, Felix Royo¹, Susmita Sahoo¹, Raymond Schiffelers¹, Shivani Sharma¹, Pia Siljander¹, Richard J Simpson¹, Carolina Soekmadji¹, Philip Stahl¹, Allan Stensballe¹, Ewa Stępień¹, Hidetoshi Tahara¹, Arne Trummer¹, Hadi Valadi¹, Laura J Vella¹, Sun Nyunt Wai¹, Kenneth Witwer¹, María Yáñez-Mó¹, Hyewon Youn¹, Reinhard Zeidler¹, Yong Song Gho¹

Affiliations

Affiliation

¹ Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M

PMID: 25388151
PMCID: PMC4375401
DOI: 10.1093/bioinformatics/btu741

EVpedia: a community web portal for extracellular vesicles research

Dae-Kyum Kim et al. Bioinformatics. 2015.

. 2015 Mar 15;31(6):933-9.

doi: 10.1093/bioinformatics/btu741. Epub 2014 Nov 10.

Authors

Affiliation

¹ Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea, Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, Department of Clinical Immunology, Polish-American Institute of Paediatrics, Jagiellonian University Medical College, Cracow, Poland, Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands, Section of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden, The Feinstein Institute for Medical Research, Manhasset, NY, USA, Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA, Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR), Palermo, Italy, Innovation in Vesicles and Cells for Application in Therapy, Germans Trias i Pujol Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain, INSERM, UMR837 JEAN-PIERRE Aubert Research Centre, Lille, France, Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary, Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia, Institute of Cancer & Genetics, School of Medicine, Velindre Cancer Centre, Cardiff University, Cardiff, UK, Program in Cellular and Molecular Medicine at Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA, USA, Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA, Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai M

PMID: 25388151
PMCID: PMC4375401
DOI: 10.1093/bioinformatics/btu741

Abstract

Motivation: Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging.

Results: We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research.

Availability and implementation: The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info.

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Figures

**Fig. 1.**
Publication trend of EV studies. This graph shows the number of publications on EVs per year, indicating that the field of EVs is expanding rapidly

**Fig. 2.**
Overall structure of EVpedia. EVpedia provides a comprehensive database for (i) publications and principal investigators, (ii) vesicular proteins, mRNAs, miRNAs, lipids and metabolites and (iii) identification of orthologous vesicular components. For systematic analyses of vesicular components, there is an array of tools for sequence search, set analysis, Gene Ontology enrichment analysis and network analysis. ‘My EVpedia’ is a personalized function of EVpedia to deposit the user’s own datasets, analysis results and publications of interest. Note that red texts indicate newly included functions in the updated version of EVpedia

See this image and copyright information in PMC

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EVpedia: a community web portal for extracellular vesicles research

Affiliation

EVpedia: a community web portal for extracellular vesicles research

Authors

Affiliation

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources