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CoExp: A Web Tool for the Exploitation of Co-expression Networks

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dc.contributor.authorGarcía-Ruiz, Sonia
dc.contributor.authorCisterna, Alejandro
dc.contributor.authorJurado-Ruiz, Federico
dc.contributor.authorReynolds, Regina H.
dc.contributor.authorNABEC (North American Brain Expression Consortium)
dc.contributor.authorCookson, Mark R.
dc.contributor.authorHardy, John
dc.contributor.authorRyten, Mina
dc.contributor.authorGil Martínez, Ana Luisa
dc.contributor.authorBotía Blaya, Juan Antonio
dc.contributor.departmentIngeniería de la Información y las Comunicaciones
dc.date.accessioned2026-02-24T13:36:26Z
dc.date.available2026-02-24T13:36:26Z
dc.date.copyright© 2021 García-Ruiz, Gil-Martínez, Cisterna, Jurado-Ruiz, Reynolds, Cookson, Hardy, Ryten and Botía.
dc.date.created2021
dc.date.issued2021-02-24
dc.description.abstractGene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels are highly correlated across samples. Subsequent annotation of modules often reveals biological functions and/or evidence of cellular specificity for cell types implicated in the tissue being studied. There are multiple ways to perform such analyses with weighted gene co-expression network analysis (WGCNA) amongst one of the most widely used R packages. While managing a few network models can be done manually, it is often more advantageous to study a wider set of models derived from multiple independently generated transcriptomic data sets (e.g., multiple networks built from many transcriptomic sources). However, there is no software tool available that allows this to be easily achieved. Furthermore, the visual nature of co-expression networks in combination with the coding skills required to explore networks, makes the construction of a web-based platform for their management highly desirable. Here, we present the CoExp Web application, a user-friendly online tool that allows the exploitation of the full collection of 109 co-expression networks provided by the CoExpNets suite of R packages. We describe the usage of CoExp, including its contents and the functionality available through the family of CoExpNets packages. All the tools presented, including the web front- and back-ends are available for the research community so any research group can build its own suite of networks and make them accessible through their own CoExp Web application. Therefore, this paper is of interest to both researchers wishing to annotate their genes of interest across different brain network models and specialists interested in the creation of GCNs looking for a tool to appropriately manage, use, publish, and share their networks in a consistent and productive manner.
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dc.identifier.citationFront. Genet., Sec. Computational Genomics, Volume 12 - 2021
dc.identifier.doihttps://doi.org/10.3389/fgene.2021.630187
dc.identifier.eissn1664-8021
dc.identifier.urihttp://hdl.handle.net/10201/212361
dc.languageeng
dc.publisherFrontiers Media SA
dc.relationNational Institute on Aging (NIH), Intramural Research Program; Leonard Wolfson Doctoral Training Fellowship; Medical Research Council (MR/N026004/, MR/N008324/1); UK Dementia Research Institute; Wellcome Trust (202903/Z/16/Z); NIHR Biomedical Research Centre; Fundación Séneca (20762/FPI/18; 00007/COVI/20; 21230/PD/19).
dc.relation.publisherversionhttps://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.630187/full
dc.rightsAttribution 4.0 International*
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectGuilt by association
dc.subjectWeb app for neuroscience
dc.subjectTranscriptomics
dc.subjectBrain
dc.subjectCo-expression network
dc.subject.odsNo relacionado con ningún objetivo de desarrollo sostenible
dc.titleCoExp: A Web Tool for the Exploitation of Co-expression Networks
dc.typeinfo:eu-repo/semantics/article
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dspace.entity.typePublicationes
relation.isAuthorOfPublication848746a7-05ac-4d08-82cb-e6a80680c24f
relation.isAuthorOfPublicationee187cf4-aebe-4d10-bfe0-09dedbc8daaf
relation.isAuthorOfPublication.latestForDiscovery848746a7-05ac-4d08-82cb-e6a80680c24f
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