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 Iraci; Kenneth 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 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

doi:10.1080/20013078.2017.1321455

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 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 journal › Article › Research › peer-review

285 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 language	English
Article number	1321455
Number of pages	4
Journal	Journal of Extracellular Vesicles
Volume	6
Issue number	1
DOIs	https://doi.org/10.1080/20013078.2017.1321455
Publication status	Published - 2017
Externally published	Yes

Keywords

Bioinformatics
Extracellular vesicles
FunRich

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10.1080/20013078.2017.1321455Licence: CC BY-NC

Cite this

Pathan, M., Keerthikumar, S., Chisanga, D., Alessandro, R., Ang, C.-S., Askenase, P., Batagov, A. O., Benito-Martin, A., Camussi, G., Clayton, A., Collino, F., di Vizio, D., Falcon-Perez, J. M., Fonseca, P., Fonseka, P., Fontana, S., Gho, Y. S., Hendrix, A., Nolte-’T Hoen, E., ... Mathivanan, S. (2017). A novel community driven software for functional enrichment analysis of extracellular vesicles data. Journal of Extracellular Vesicles, 6(1), Article 1321455. https://doi.org/10.1080/20013078.2017.1321455

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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.",

keywords = "Bioinformatics, Extracellular vesicles, FunRich",

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

note = "Publisher Copyright: {\textcopyright} 2017 The Author(s).",

year = "2017",

doi = "10.1080/20013078.2017.1321455",

language = "English",

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journal = "Journal of Extracellular Vesicles",

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Pathan, M, Keerthikumar, S, Chisanga, D, Alessandro, R, Ang, C-S, 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, T, 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

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T1 - A novel community driven software for functional enrichment analysis of extracellular vesicles data

AU - Pathan, Mohashin

AU - Keerthikumar, Shivakumar

AU - Chisanga, David

AU - Alessandro, Riccardo

AU - Ang, Ching-Seng

AU - Askenase, Philip

AU - Batagov, Arsen O.

AU - Benito-Martin, Alberto

AU - Camussi, Giovanni

AU - Clayton, Aled

AU - Collino, Federica

AU - di Vizio, Dolores

AU - Falcon-Perez, Juan Manuel

AU - Fonseca, Pedro

AU - Fonseka, Pamali

AU - Fontana, Simona

AU - Gho, Yong Song

AU - Hendrix, An

AU - Nolte-’T Hoen, Esther

AU - Iraci, Nunzio

AU - Kastaniegaard, Kenneth

AU - Kislinger, Thomas

AU - Kowal, Joanna

AU - Kurochkin, Igor V.

AU - Leonardi, Tommaso

AU - Liang, Yaxuan

AU - Llorente, Alicia

AU - Lunavat, Taral R.

AU - Maji, Sayantan

AU - Monteleone, Francesca

AU - Øverbye, Anders

AU - Panaretakis, Theocharis

AU - Patel, Tushar

AU - Peinado, Héctor

AU - Pluchino, Stefano

AU - Principe, Simona

AU - Ronquist, Goran

AU - Royo, Felix

AU - Sahoo, Susmita

AU - Spinelli, Cristiana

AU - Stensballe, Allan

AU - Théry, Clotilde

AU - van Herwijnen, Martijn J.C.

AU - Wauben, Marca

AU - Welton, Joanne L.

AU - Zhao, Kening

AU - Mathivanan, Suresh

PY - 2017

Y1 - 2017

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AB - 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.

KW - Bioinformatics

KW - Extracellular vesicles

KW - FunRich

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U2 - 10.1080/20013078.2017.1321455

DO - 10.1080/20013078.2017.1321455

M3 - Article

C2 - 28717418

AN - SCOPUS:85022097961

SN - 2001-3078

VL - 6

JO - Journal of Extracellular Vesicles

JF - Journal of Extracellular Vesicles

IS - 1

M1 - 1321455

ER -

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

Abstract

Keywords

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