A novel community driven software for functional enrichment analysis of extracellular vesicles data

Mohashin Pathan, Shivakumar Keerthikumar, David Chisanga, Riccardo Alessandro, Ching Seng Ang, Philip Askenase, Arsen O. Batagov, Alberto Benito-Martin, Giovanni Camussi, Aled Clayton, Federica Collino, Dolores di Vizio, Juan Manuel Falcon-Perez, Pedro Fonseca, Pamali Fonseka, Simona Fontana, Yong Song Gho, An Hendrix, Esther Nolte-’T Hoen, Nunzio IraciKenneth Kastaniegaard, Thomas Kislinger, Joanna Kowal, Igor V. Kurochkin, Tommaso Leonardi, Yaxuan Liang, Alicia Llorente, Taral R. Lunavat, Sayantan Maji, Francesca Monteleone, Anders Øverbye, Theocharis Panaretakis, Tushar C Patel, Héctor Peinado, Stefano Pluchino, Simona Principe, Goran Ronquist, Felix Royo, Susmita Sahoo, Cristiana Spinelli, Allan Stensballe, Clotilde Théry, Martijn J.C. van Herwijnen, Marca Wauben, Joanne L. Welton, Kening Zhao, Suresh Mathivanan

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number1321455
JournalJournal of Extracellular Vesicles
Volume6
Issue number1
DOIs
StatePublished - Jan 1 2017

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Software
Research Personnel
Computational Biology
Databases
Extracellular Vesicles
Community Participation

Keywords

  • Bioinformatics
  • Extracellular vesicles
  • FunRich

ASJC Scopus subject areas

  • Histology
  • Cell Biology

Cite this

Pathan, M., Keerthikumar, S., Chisanga, D., Alessandro, R., Ang, C. S., Askenase, P., ... Mathivanan, S. (2017). A novel community driven software for functional enrichment analysis of extracellular vesicles data. Journal of Extracellular Vesicles, 6(1), [1321455]. https://doi.org/10.1080/20013078.2017.1321455

A novel community driven software for functional enrichment analysis of extracellular vesicles data. / Pathan, Mohashin; Keerthikumar, Shivakumar; Chisanga, David; Alessandro, Riccardo; Ang, Ching Seng; Askenase, Philip; Batagov, Arsen O.; Benito-Martin, Alberto; Camussi, Giovanni; Clayton, Aled; Collino, Federica; di Vizio, Dolores; Falcon-Perez, Juan Manuel; Fonseca, Pedro; Fonseka, Pamali; Fontana, Simona; Gho, Yong Song; Hendrix, An; Nolte-’T Hoen, Esther; Iraci, Nunzio; Kastaniegaard, Kenneth; Kislinger, Thomas; Kowal, Joanna; Kurochkin, Igor V.; Leonardi, Tommaso; Liang, Yaxuan; Llorente, Alicia; Lunavat, Taral R.; Maji, Sayantan; Monteleone, Francesca; Øverbye, Anders; Panaretakis, Theocharis; Patel, Tushar C; Peinado, Héctor; Pluchino, Stefano; Principe, Simona; Ronquist, Goran; Royo, Felix; Sahoo, Susmita; Spinelli, Cristiana; Stensballe, Allan; Théry, Clotilde; van Herwijnen, Martijn J.C.; Wauben, Marca; Welton, Joanne L.; Zhao, Kening; Mathivanan, Suresh.

In: Journal of Extracellular Vesicles, Vol. 6, No. 1, 1321455, 01.01.2017.

Research output: Contribution to journalArticle

Pathan, M, Keerthikumar, S, Chisanga, D, Alessandro, R, Ang, CS, Askenase, P, Batagov, AO, Benito-Martin, A, Camussi, G, Clayton, A, Collino, F, di Vizio, D, Falcon-Perez, JM, Fonseca, P, Fonseka, P, Fontana, S, Gho, YS, Hendrix, A, Nolte-’T Hoen, E, Iraci, N, Kastaniegaard, K, Kislinger, T, Kowal, J, Kurochkin, IV, Leonardi, T, Liang, Y, Llorente, A, Lunavat, TR, Maji, S, Monteleone, F, Øverbye, A, Panaretakis, T, Patel, TC, Peinado, H, Pluchino, S, Principe, S, Ronquist, G, Royo, F, Sahoo, S, Spinelli, C, Stensballe, A, Théry, C, van Herwijnen, MJC, Wauben, M, Welton, JL, Zhao, K & Mathivanan, S 2017, 'A novel community driven software for functional enrichment analysis of extracellular vesicles data', Journal of Extracellular Vesicles, vol. 6, no. 1, 1321455. https://doi.org/10.1080/20013078.2017.1321455
Pathan, Mohashin ; Keerthikumar, Shivakumar ; Chisanga, David ; Alessandro, Riccardo ; Ang, Ching Seng ; Askenase, Philip ; Batagov, Arsen O. ; Benito-Martin, Alberto ; Camussi, Giovanni ; Clayton, Aled ; Collino, Federica ; di Vizio, Dolores ; Falcon-Perez, Juan Manuel ; Fonseca, Pedro ; Fonseka, Pamali ; Fontana, Simona ; Gho, Yong Song ; Hendrix, An ; Nolte-’T Hoen, Esther ; Iraci, Nunzio ; Kastaniegaard, Kenneth ; Kislinger, Thomas ; Kowal, Joanna ; Kurochkin, Igor V. ; Leonardi, Tommaso ; Liang, Yaxuan ; Llorente, Alicia ; Lunavat, Taral R. ; Maji, Sayantan ; Monteleone, Francesca ; Øverbye, Anders ; Panaretakis, Theocharis ; Patel, Tushar C ; Peinado, Héctor ; Pluchino, Stefano ; Principe, Simona ; Ronquist, Goran ; Royo, Felix ; Sahoo, Susmita ; Spinelli, Cristiana ; Stensballe, Allan ; Théry, Clotilde ; van Herwijnen, Martijn J.C. ; Wauben, Marca ; Welton, Joanne L. ; Zhao, Kening ; Mathivanan, Suresh. / A novel community driven software for functional enrichment analysis of extracellular vesicles data. In: Journal of Extracellular Vesicles. 2017 ; Vol. 6, No. 1.
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