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StemMapper: a curated gene expression database for stem cell lineage analysis

2018-01Journal article Open Access
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dc.contributor.authorPinto, Jose P.
dc.contributor.authorMachado, Rui S. R.
dc.contributor.authorMagno, Ramiro
dc.contributor.authorOliveira, Daniel V.
dc.contributor.authorMachado, Susana
dc.contributor.authorAndrade, Raquel P.
dc.contributor.authorBraganca, Jose
dc.contributor.authorDuarte, Isabel
dc.contributor.authorFutschik, Matthias E.
dc.date.accessioned2018-12-07T14:53:04Z
dc.date.available2018-12-07T14:53:04Z
dc.date.issued2018-01
dc.description.abstractTranscriptomic data have become a fundamental resource for stem cell (SC) biologists as well as for a wider research audience studying SC-related processes such as aging, embryonic development and prevalent diseases including cancer, diabetes and neurodegenerative diseases. Access and analysis of the growing amount of freely available transcriptomics datasets for SCs, however, are not trivial tasks. Here, we present StemMapper, a manually curated gene expression database and comprehensive resource for SC research, built on integrated data for different lineages of human and mouse SCs. It is based on careful selection, standardized processing and stringent quality control of relevant transcriptomics datasets to minimize artefacts, and includes currently over 960 transcriptomes covering a broad range of SC types. Each of the integrated datasets was individually inspected andmanually curated. StemMapper's user-friendly interface enables fast querying, comparison, and interactive visualization of quality-controlled SC gene expression data in a comprehensive manner. A proof-of-principle analysis discovering novel putative astrocyte/neural SC lineage markers exemplifies the utility of the integrated data resource. We believe that StemMapper can open the way for new insights and advances in SC research by greatly simplifying the access and analysis of SC transcriptomic data.
dc.description.sponsorshipPortuguese Fundacao para a Ciencia e Tecnologia (FCT) [SFRH/BPD/96890/2013, PTDC/BEX-BID/5410/2014, IF/00881/2013, UID/BIM/04773/2013, UID/Multi/04326/2013]; Programa Doutoral ProRegeM-Mecanismos de Doenca e Medicina Regenerativa [PD/00117/2012]; Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, Devon, UK
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1093/nar/gkx921
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttp://hdl.handle.net/10400.1/11338
dc.language.isoeng
dc.peerreviewedyes
dc.publisherOxford University Press
dc.relationDEVELOPMENT OF SOFTWARE TOOLS FOR THE PREDICTION OF CELULAR FATE IN STEM CELL DIFERENTIATION
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectRegenerative medicine
dc.subjectDifferentiation
dc.subjectHematopoiesis
dc.subjectProfiles
dc.subjectNetwork
dc.subjectBiology
dc.subjectUpdate
dc.subjectAtlas
dc.subjectSets
dc.titleStemMapper: a curated gene expression database for stem cell lineage analysis
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleDEVELOPMENT OF SOFTWARE TOOLS FOR THE PREDICTION OF CELULAR FATE IN STEM CELL DIFERENTIATION
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F96890%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FBIM%2F04773%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FMulti%2F04326%2F2013/PT
oaire.citation.endPageD793
oaire.citation.issueD1
oaire.citation.startPageD788
oaire.citation.titleNucleic Acids Research
oaire.citation.volume46
oaire.fundingStream5876
oaire.fundingStream5876
person.familyNameMachado
person.familyNameMagno
person.familyNameOliveira
person.familyNameMachado
person.familyNameAndrade
person.familyNameBragança
person.familyNamedos Santos Duarte
person.familyNameFutschik
person.givenNameRui
person.givenNameRamiro
person.givenNameDaniel
person.givenNameSusana
person.givenNameRaquel
person.givenNameJosé
person.givenNameGuilhermina Isabel
person.givenNameMatthias
person.identifier222659
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person.identifier.ciencia-idA71B-AD01-3501
person.identifier.orcid0000-0002-4080-2353
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person.identifier.orcid0000-0003-0622-2934
person.identifier.orcid0000-0002-3152-1701
person.identifier.orcid0000-0002-0397-5917
person.identifier.orcid0000-0001-9566-400X
person.identifier.orcid0000-0003-0060-2936
person.identifier.orcid0000-0002-6245-8071
person.identifier.ridK-4033-2012
person.identifier.scopus-author-id55991033900
person.identifier.scopus-author-id55253361100
person.identifier.scopus-author-id56201414700
person.identifier.scopus-author-id7103114918
person.identifier.scopus-author-id6602220001
person.identifier.scopus-author-id14017989400
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a CiĂȘncia e a Tecnologia
project.funder.nameFundação para a CiĂȘncia e a Tecnologia
project.funder.nameFundação para a CiĂȘncia e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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