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

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

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

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

Biomedicina, Neuroscienze e Diagnostica avanzata

Research output: Contribution to journal › Article › peer-review

224 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
Number of pages	4
Journal	Journal of Extracellular Vesicles
Volume	6
Publication status	Published - 2017

All Science Journal Classification (ASJC) codes

Histology
Cell Biology

Cite this

Fontana, S., Alessandro, R., Mathivanan, S., Øverbye, A., Hendrix, A., Van Herwijnen, M. J. C., Collino, F., Ang, C-S., Benito-Martin, A., Keerthikumar, S., Welton, J. L., Principe, S., Panaretakis, T., Ronquist, G., Leonardi, T., Iraci, N., Gho, Y. S., Kowal, J., Liang, Y., ... Clayton, A. (2017). A novel community driven software for functional enrichment analysis of extracellular vesicles data. Journal of Extracellular Vesicles, 6.

Fontana, S , Alessandro, R, Mathivanan, S, Øverbye, A, Hendrix, A, Van Herwijnen, MJC, Collino, F, Ang, C-S, Benito-Martin, A, Keerthikumar, S, Welton, JL, Principe, S, Panaretakis, T, Ronquist, G, Leonardi, T, Iraci, N, Gho, YS, Kowal, J, Liang, Y, Maji, S, Royo, F, Spinelli, C, Pathan, M, Fonseca, P, Lunavat, TR, Kastaniegaard, K, Zhao, K, Chisanga, D, Nolte-’T Hoen, E, Camussi, G, Patel, T, Kurochkin, IV, Fonseka, P, Van Herwijnen, MJC, Nolte-’T Hoen, E, Camussi, G, Batagov, AO, Peinado, H, Falcon-Perez, JM, Stensballe, A, Kislinger, T, Di Vizio, D, Pluchino, S, Llorente, A, Théry, C, Askenase, P, Wauben, M, Camussi, G, Sahoo, S & Clayton, A 2017, 'A novel community driven software for functional enrichment analysis of extracellular vesicles data', Journal of Extracellular Vesicles, vol. 6.

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title = "A novel community driven software for functional enrichment analysis of extracellular vesicles data",

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.",

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language = "English",

volume = "6",

journal = "Journal of Extracellular Vesicles",

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

AU - Fontana, Simona

AU - Alessandro, Riccardo

AU - Mathivanan, Suresh

AU - Øverbye, Anders

AU - Hendrix, An

AU - Van Herwijnen, Martijn J. C.

AU - Collino, Federica

AU - Ang, Ching-Seng

AU - Benito-Martin, Alberto

AU - Keerthikumar, Shivakumar

AU - Welton, Joanne L.

AU - Principe, Simona

AU - Panaretakis, Theocharis

AU - Ronquist, Goran

AU - Leonardi, Tommaso

AU - Iraci, Nunzio

AU - Gho, Yong Song

AU - Kowal, Joanna

AU - Liang, Yaxuan

AU - Maji, Sayantan

AU - Royo, Felix

AU - Spinelli, Cristiana

AU - Pathan, Mohashin

AU - Fonseca, Pedro

AU - Lunavat, Taral R.

AU - Kastaniegaard, Kenneth

AU - Zhao, Kening

AU - Chisanga, David

AU - Nolte-’T Hoen, Esther

AU - Camussi, Giovanni

AU - Patel, Tushar

AU - Kurochkin, Igor V.

AU - Fonseka, Pamali

AU - Van Herwijnen, Martijn J. C.

AU - Nolte-’T Hoen, Esther

AU - Camussi, Giovanni

AU - Batagov, Arsen O.

AU - Peinado, Héctor

AU - Falcon-Perez, Juan Manuel

AU - Stensballe, Allan

AU - Kislinger, Thomas

AU - Di Vizio, Dolores

AU - Pluchino, Stefano

AU - Llorente, Alicia

AU - Théry, Clotilde

AU - Askenase, Philip

AU - Wauben, Marca

AU - Camussi, Giovanni

AU - Sahoo, Susmita

AU - Clayton, Aled

PY - 2017

Y1 - 2017

N2 - 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.

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 - Extracellular vesicles

KW - FunRich

KW - bioinformatics

KW - Extracellular vesicles

KW - FunRich

KW - bioinformatics

UR - http://hdl.handle.net/10447/239035

M3 - Article

SN - 2001-3078

VL - 6

JO - Journal of Extracellular Vesicles

JF - Journal of Extracellular Vesicles

ER -

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

Abstract

All Science Journal Classification (ASJC) codes

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