Published July 19, 2019
| Version v1
Journal article
Open
A novel community driven software for functional enrichment analysis of extracellular vesicles data
Authors/Creators
- Mohashin Pathan1
- Shivakumar Keerthikumar1
- David Chisanga2
- Riccardo Alessandro3
- Ching-Seng Ang4
- Philip Askenase5
- Arsen O. Batagov6
- Alberto Benito-Martin7
- Giovanni Camussi8
- Aled Clayton9
- Federica Collino10
- Dolores Di Vizio11
- Juan Manuel Falcon-Perez12
- Pedro Fonseca13
- Pamali Fonseka1
- Simona Fontana3
- Yong Song Gho14
- An Hendrix15
- Esther Nolte-'t Hoen16
- Nunzio Iraci17
- Kenneth Kastaniegaard18
- Thomas Kislinger19
- Joanna Kowal20
- Igor V. Kurochkin6
- Tommaso Leonardi21
- Yaxuan Liang22
- Alicia Llorente23
- Taral R. Lunavat24
- Sayantan Maji25
- Francesca Monteleone3
- Anders Øverbye26
- Theocharis Panaretakis13
- Tushar Patel25
- Héctor Peinado27
- Stefano Pluchino28
- Simona Principe19
- Goran Ronquist29
- Felix Royo12
- Susmita Sahoo22
- Cristiana Spinelli11
- Allan Stensballe18
- Clotilde Théry20
- Martijn J.C. van Herwijnen16
- Marca Wauben16
- Joanne L. Welton30
- Kening Zhao1
- Suresh Mathivanan1
- 1. Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
- 2. Department of Computer Science and Information Technology, La Trobe University, Melbourne, Australia
- 3. Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy
- 4. The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
- 5. Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- 6. Bioinformatics Institute, A*STAR, Singapore, Singapore
- 7. Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
- 8. Department of Medical Science, University of Torino, Medical School, Torino, Italy
- 9. Division of Cancer and Genetics, School of Medicine, Cardiff University, Velindre Cancer Centre, Cardiff, UK
- 10. Department of Medical Science, University of Torino, Medical School, Torino, Italy; Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- 11. Division of Cancer Biology and Therapeutics, Departments of Surgery, Biomedical Sciences and Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- 12. Exosomes Lab, Metabolomics Unit, CIC bioGUNE, CIBERehd. Bizkaia Technological Park, Derio 48160, Bikaia and IKERBASQUE Research Foundation, Bilbao, SPAIN
- 13. Department of Oncology-Pathology, Cancer Centrum Karolinska, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
- 14. Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- 15. Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- 16. Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- 17. Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy; Department of Clinical Neurosciences, Wellcome Trust-Medical Research Council Stem Cell Institute and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK
- 18. Laboratory for Medical Mass Spectrometry, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- 19. Princess Margaret Cancer Centre, Toronto, Canada
- 20. Institut Curie, PSL Research University, INSERM U932, Paris, France
- 21. Department of Clinical Neurosciences, Wellcome Trust-Medical Research Council Stem Cell Institute and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- 22. Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 23. Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- 24. Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- 25. Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA
- 26. Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norw
- 27. Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA; Microenvironment and Metastasis Group, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- 28. Department of Clinical Neurosciences, Wellcome Trust-Medical Research Council Stem Cell Institute and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK
- 29. Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- 30. Department of Biomedical Sciences, Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
Description
Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture “what the community needs in a tool”. Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines.