A novel community driven software for functional enrichment analysis of extracellular vesicles data
Identifieur interne : 001278 ( Main/Exploration ); précédent : 001277; suivant : 001279A novel community driven software for functional enrichment analysis of extracellular vesicles data
Auteurs : 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- 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 Verbye ; 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 MathivananSource :
- Journal of Extracellular Vesicles [ 2001-3078 ] ; 2017.
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.
Url:
DOI: 10.1080/20013078.2017.1321455
PubMed: 28717418
PubMed Central: 5505018
Affiliations:
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Le document en format XML
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</affiliation>
</author>
<author><name sortKey="Maji, Sayantan" sort="Maji, Sayantan" uniqKey="Maji S" first="Sayantan" last="Maji">Sayantan Maji</name>
<affiliation><nlm:aff id="AFF0027"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Monteleone, Francesca" sort="Monteleone, Francesca" uniqKey="Monteleone F" first="Francesca" last="Monteleone">Francesca Monteleone</name>
<affiliation><nlm:aff id="AFF0003"></nlm:aff>
</affiliation>
</author>
<author><name sortKey=" Verbye, Anders" sort=" Verbye, Anders" uniqKey=" Verbye A" first="Anders" last=" Verbye">Anders Verbye</name>
<affiliation><nlm:aff id="AFF0024"></nlm:aff>
</affiliation>
<affiliation><nlm:aff id="AFF0025"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Panaretakis, Theocharis" sort="Panaretakis, Theocharis" uniqKey="Panaretakis T" first="Theocharis" last="Panaretakis">Theocharis Panaretakis</name>
<affiliation><nlm:aff id="AFF0013"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Patel, Tushar" sort="Patel, Tushar" uniqKey="Patel T" first="Tushar" last="Patel">Tushar Patel</name>
<affiliation><nlm:aff id="AFF0027"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Peinado, Hector" sort="Peinado, Hector" uniqKey="Peinado H" first="Héctor" last="Peinado">Héctor Peinado</name>
<affiliation><nlm:aff id="AFF0007"></nlm:aff>
</affiliation>
<affiliation><nlm:aff id="AFF0028"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pluchino, Stefano" sort="Pluchino, Stefano" uniqKey="Pluchino S" first="Stefano" last="Pluchino">Stefano Pluchino</name>
<affiliation><nlm:aff id="AFF0018"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Principe, Simona" sort="Principe, Simona" uniqKey="Principe S" first="Simona" last="Principe">Simona Principe</name>
<affiliation><nlm:aff id="AFF0020"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ronquist, Goran" sort="Ronquist, Goran" uniqKey="Ronquist G" first="Goran" last="Ronquist">Goran Ronquist</name>
<affiliation><nlm:aff id="AFF0029"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Royo, Felix" sort="Royo, Felix" uniqKey="Royo F" first="Felix" last="Royo">Felix Royo</name>
<affiliation><nlm:aff id="AFF0012"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sahoo, Susmita" sort="Sahoo, Susmita" uniqKey="Sahoo S" first="Susmita" last="Sahoo">Susmita Sahoo</name>
<affiliation><nlm:aff id="AFF0023"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Spinelli, Cristiana" sort="Spinelli, Cristiana" uniqKey="Spinelli C" first="Cristiana" last="Spinelli">Cristiana Spinelli</name>
<affiliation><nlm:aff id="AFF0011"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stensballe, Allan" sort="Stensballe, Allan" uniqKey="Stensballe A" first="Allan" last="Stensballe">Allan Stensballe</name>
<affiliation><nlm:aff id="AFF0019"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Thery, Clotilde" sort="Thery, Clotilde" uniqKey="Thery C" first="Clotilde" last="Théry">Clotilde Théry</name>
<affiliation><nlm:aff id="AFF0021"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Van Herwijnen, Martijn J C" sort="Van Herwijnen, Martijn J C" uniqKey="Van Herwijnen M" first="Martijn J. C." last="Van Herwijnen">Martijn J. C. Van Herwijnen</name>
<affiliation><nlm:aff id="AFF0016"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wauben, Marca" sort="Wauben, Marca" uniqKey="Wauben M" first="Marca" last="Wauben">Marca Wauben</name>
<affiliation><nlm:aff id="AFF0016"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Welton, Joanne L" sort="Welton, Joanne L" uniqKey="Welton J" first="Joanne L." last="Welton">Joanne L. Welton</name>
<affiliation><nlm:aff id="AFF0030"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zhao, Kening" sort="Zhao, Kening" uniqKey="Zhao K" first="Kening" last="Zhao">Kening Zhao</name>
<affiliation><nlm:aff id="AFF0001"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mathivanan, Suresh" sort="Mathivanan, Suresh" uniqKey="Mathivanan S" first="Suresh" last="Mathivanan">Suresh Mathivanan</name>
<affiliation><nlm:aff id="AFF0001"></nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of Extracellular Vesicles</title>
<idno type="eISSN">2001-3078</idno>
<imprint><date when="2017">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><title>ABSTRACT</title>
<p>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.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhang, B" uniqKey="Zhang B">B Zhang</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gerstein, Mb" uniqKey="Gerstein M">MB Gerstein</name>
</author>
<author><name sortKey="Rozowsky, J" uniqKey="Rozowsky J">J Rozowsky</name>
</author>
<author><name sortKey="Yan, K K" uniqKey="Yan ">-K-K Yan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, P" uniqKey="Bailey P">P Bailey</name>
</author>
<author><name sortKey="Chang, Dk" uniqKey="Chang D">DK Chang</name>
</author>
<author><name sortKey="Nones, K" uniqKey="Nones K">K Nones</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Muir, P" uniqKey="Muir P">P Muir</name>
</author>
<author><name sortKey="Li, S" uniqKey="Li S">S Li</name>
</author>
<author><name sortKey="Lou, S" uniqKey="Lou S">S Lou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Subramanian, A" uniqKey="Subramanian A">A Subramanian</name>
</author>
<author><name sortKey="Tamayo, P" uniqKey="Tamayo P">P Tamayo</name>
</author>
<author><name sortKey="Mootha, Vk" uniqKey="Mootha V">VK Mootha</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Benito Martin, A" uniqKey="Benito Martin A">A Benito-Martin</name>
</author>
<author><name sortKey="Peinado, H" uniqKey="Peinado H">H. Peinado</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pathan, M" uniqKey="Pathan M">M Pathan</name>
</author>
<author><name sortKey="Keerthikumar, S" uniqKey="Keerthikumar S">S Keerthikumar</name>
</author>
<author><name sortKey="Ang, C S" uniqKey="Ang C">C-S Ang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wadi, L" uniqKey="Wadi L">L Wadi</name>
</author>
<author><name sortKey="Meyer, M" uniqKey="Meyer M">M Meyer</name>
</author>
<author><name sortKey="Weiser, J" uniqKey="Weiser J">J Weiser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kalra, H" uniqKey="Kalra H">H Kalra</name>
</author>
<author><name sortKey="Simpson, Rj" uniqKey="Simpson R">RJ Simpson</name>
</author>
<author><name sortKey="Hong, J" uniqKey="Hong J">J Hong</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list></list>
<tree><noCountry><name sortKey=" Verbye, Anders" sort=" Verbye, Anders" uniqKey=" Verbye A" first="Anders" last=" Verbye">Anders Verbye</name>
<name sortKey="Alessandro, Riccardo" sort="Alessandro, Riccardo" uniqKey="Alessandro R" first="Riccardo" last="Alessandro">Riccardo Alessandro</name>
<name sortKey="Ang, Ching Seng" sort="Ang, Ching Seng" uniqKey="Ang C" first="Ching-Seng" last="Ang">Ching-Seng Ang</name>
<name sortKey="Askenase, Philip" sort="Askenase, Philip" uniqKey="Askenase P" first="Philip" last="Askenase">Philip Askenase</name>
<name sortKey="Batagov, Arsen O" sort="Batagov, Arsen O" uniqKey="Batagov A" first="Arsen O." last="Batagov">Arsen O. Batagov</name>
<name sortKey="Benito Martin, Alberto" sort="Benito Martin, Alberto" uniqKey="Benito Martin A" first="Alberto" last="Benito-Martin">Alberto Benito-Martin</name>
<name sortKey="Camussi, Giovanni" sort="Camussi, Giovanni" uniqKey="Camussi G" first="Giovanni" last="Camussi">Giovanni Camussi</name>
<name sortKey="Chisanga, David" sort="Chisanga, David" uniqKey="Chisanga D" first="David" last="Chisanga">David Chisanga</name>
<name sortKey="Clayton, Aled" sort="Clayton, Aled" uniqKey="Clayton A" first="Aled" last="Clayton">Aled Clayton</name>
<name sortKey="Collino, Federica" sort="Collino, Federica" uniqKey="Collino F" first="Federica" last="Collino">Federica Collino</name>
<name sortKey="Di Vizio, Dolores" sort="Di Vizio, Dolores" uniqKey="Di Vizio D" first="Dolores" last="Di Vizio">Dolores Di Vizio</name>
<name sortKey="Falcon Perez, Juan Manuel" sort="Falcon Perez, Juan Manuel" uniqKey="Falcon Perez J" first="Juan Manuel" last="Falcon-Perez">Juan Manuel Falcon-Perez</name>
<name sortKey="Fonseca, Pedro" sort="Fonseca, Pedro" uniqKey="Fonseca P" first="Pedro" last="Fonseca">Pedro Fonseca</name>
<name sortKey="Fonseka, Pamali" sort="Fonseka, Pamali" uniqKey="Fonseka P" first="Pamali" last="Fonseka">Pamali Fonseka</name>
<name sortKey="Fontana, Simona" sort="Fontana, Simona" uniqKey="Fontana S" first="Simona" last="Fontana">Simona Fontana</name>
<name sortKey="Gho, Yong Song" sort="Gho, Yong Song" uniqKey="Gho Y" first="Yong Song" last="Gho">Yong Song Gho</name>
<name sortKey="Hendrix, An" sort="Hendrix, An" uniqKey="Hendrix A" first="An" last="Hendrix">An Hendrix</name>
<name sortKey="Hoen, Esther Nolte" sort="Hoen, Esther Nolte" uniqKey="Hoen E" first="Esther Nolte-" last="Hoen">Esther Nolte- Hoen</name>
<name sortKey="Iraci, Nunzio" sort="Iraci, Nunzio" uniqKey="Iraci N" first="Nunzio" last="Iraci">Nunzio Iraci</name>
<name sortKey="Kastaniegaard, Kenneth" sort="Kastaniegaard, Kenneth" uniqKey="Kastaniegaard K" first="Kenneth" last="Kastaniegaard">Kenneth Kastaniegaard</name>
<name sortKey="Keerthikumar, Shivakumar" sort="Keerthikumar, Shivakumar" uniqKey="Keerthikumar S" first="Shivakumar" last="Keerthikumar">Shivakumar Keerthikumar</name>
<name sortKey="Kislinger, Thomas" sort="Kislinger, Thomas" uniqKey="Kislinger T" first="Thomas" last="Kislinger">Thomas Kislinger</name>
<name sortKey="Kowal, Joanna" sort="Kowal, Joanna" uniqKey="Kowal J" first="Joanna" last="Kowal">Joanna Kowal</name>
<name sortKey="Kurochkin, Igor V" sort="Kurochkin, Igor V" uniqKey="Kurochkin I" first="Igor V." last="Kurochkin">Igor V. Kurochkin</name>
<name sortKey="Leonardi, Tommaso" sort="Leonardi, Tommaso" uniqKey="Leonardi T" first="Tommaso" last="Leonardi">Tommaso Leonardi</name>
<name sortKey="Liang, Yaxuan" sort="Liang, Yaxuan" uniqKey="Liang Y" first="Yaxuan" last="Liang">Yaxuan Liang</name>
<name sortKey="Llorente, Alicia" sort="Llorente, Alicia" uniqKey="Llorente A" first="Alicia" last="Llorente">Alicia Llorente</name>
<name sortKey="Lunavat, Taral R" sort="Lunavat, Taral R" uniqKey="Lunavat T" first="Taral R." last="Lunavat">Taral R. Lunavat</name>
<name sortKey="Maji, Sayantan" sort="Maji, Sayantan" uniqKey="Maji S" first="Sayantan" last="Maji">Sayantan Maji</name>
<name sortKey="Mathivanan, Suresh" sort="Mathivanan, Suresh" uniqKey="Mathivanan S" first="Suresh" last="Mathivanan">Suresh Mathivanan</name>
<name sortKey="Monteleone, Francesca" sort="Monteleone, Francesca" uniqKey="Monteleone F" first="Francesca" last="Monteleone">Francesca Monteleone</name>
<name sortKey="Panaretakis, Theocharis" sort="Panaretakis, Theocharis" uniqKey="Panaretakis T" first="Theocharis" last="Panaretakis">Theocharis Panaretakis</name>
<name sortKey="Patel, Tushar" sort="Patel, Tushar" uniqKey="Patel T" first="Tushar" last="Patel">Tushar Patel</name>
<name sortKey="Pathan, Mohashin" sort="Pathan, Mohashin" uniqKey="Pathan M" first="Mohashin" last="Pathan">Mohashin Pathan</name>
<name sortKey="Peinado, Hector" sort="Peinado, Hector" uniqKey="Peinado H" first="Héctor" last="Peinado">Héctor Peinado</name>
<name sortKey="Pluchino, Stefano" sort="Pluchino, Stefano" uniqKey="Pluchino S" first="Stefano" last="Pluchino">Stefano Pluchino</name>
<name sortKey="Principe, Simona" sort="Principe, Simona" uniqKey="Principe S" first="Simona" last="Principe">Simona Principe</name>
<name sortKey="Ronquist, Goran" sort="Ronquist, Goran" uniqKey="Ronquist G" first="Goran" last="Ronquist">Goran Ronquist</name>
<name sortKey="Royo, Felix" sort="Royo, Felix" uniqKey="Royo F" first="Felix" last="Royo">Felix Royo</name>
<name sortKey="Sahoo, Susmita" sort="Sahoo, Susmita" uniqKey="Sahoo S" first="Susmita" last="Sahoo">Susmita Sahoo</name>
<name sortKey="Spinelli, Cristiana" sort="Spinelli, Cristiana" uniqKey="Spinelli C" first="Cristiana" last="Spinelli">Cristiana Spinelli</name>
<name sortKey="Stensballe, Allan" sort="Stensballe, Allan" uniqKey="Stensballe A" first="Allan" last="Stensballe">Allan Stensballe</name>
<name sortKey="Thery, Clotilde" sort="Thery, Clotilde" uniqKey="Thery C" first="Clotilde" last="Théry">Clotilde Théry</name>
<name sortKey="Van Herwijnen, Martijn J C" sort="Van Herwijnen, Martijn J C" uniqKey="Van Herwijnen M" first="Martijn J. C." last="Van Herwijnen">Martijn J. C. Van Herwijnen</name>
<name sortKey="Wauben, Marca" sort="Wauben, Marca" uniqKey="Wauben M" first="Marca" last="Wauben">Marca Wauben</name>
<name sortKey="Welton, Joanne L" sort="Welton, Joanne L" uniqKey="Welton J" first="Joanne L." last="Welton">Joanne L. Welton</name>
<name sortKey="Zhao, Kening" sort="Zhao, Kening" uniqKey="Zhao K" first="Kening" last="Zhao">Kening Zhao</name>
</noCountry>
</tree>
</affiliations>
</record>
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