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StemChecker: a web-based tool to discover and explore stemness signatures in gene sets

2015-07Journal article Open Access
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dc.contributor.authorPinto, Jose P.
dc.contributor.authorKalathur, Ravi Kiran Reddy
dc.contributor.authorOliveira, Daniel V.
dc.contributor.authorBarata, Tania
dc.contributor.authorMachado, Rui
dc.contributor.authorMachado, Susana
dc.contributor.authorPacheco-Leyva, Ivette
dc.contributor.authorDuarte, Isabel
dc.contributor.authorFutschik, Matthias E.
dc.date.accessioned2018-12-07T14:53:18Z
dc.date.available2018-12-07T14:53:18Z
dc.date.issued2015-07
dc.description.abstractStem cells present unique regenerative abilities, offering great potential for treatment of prevalent pathologies such as diabetes, neurodegenerative and heart diseases. Various research groups dedicated significant effort to identify sets of genes-so-called stemness signatures-considered essential to define stem cells. However, their usage has been hindered by the lack of comprehensive resources and easy-to-use tools. For this we developed StemChecker, a novel stemness analysis tool, based on the curation of nearly fifty published stemness signatures defined by gene expression, RNAi screens, Transcription Factor (TF) binding sites, literature reviews and computational approaches. StemChecker allows researchers to explore the presence of stemness signatures in user-defined gene sets, without carrying-out lengthy literature curation or data processing. To assist in exploring underlying regulatory mechanisms, we collected over 80 target gene sets of TFs associated with pluri- or multipotency. StemChecker presents an intuitive graphical display, as well as detailed statistical results in table format, which helps revealing transcriptionally regulatory programs, indicating the putative involvement of stemness-associated processes in diseases like cancer. Overall, StemChecker substantially expands the available repertoire of online tools, designed to assist the stem cell biology, developmental biology, regenerative medicine and human disease research community. StemChecker is freely accessible at http://stemchecker.sysbiolab.eu.
dc.description.sponsorshipPortuguese Fundacao para a Ciencia e Tecnologia (FCT) [RH/BPD/96890/2013, SFRH/BPD/70718/2010, PTDC/BIA/GEN/116519/2010, IF/00881/2013, PTDC/BIA-GEN/116519/2010]; Programa Doutoral ProRegeM-Mecanismos de Doenca e Medicina Regenerativa [PD/00117/2012]
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1093/nar/gkv529
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttp://hdl.handle.net/10400.1/11446
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.relationSYSTEMS BIOLOGY APPROACH TO UNRAVEL THE MOLECULAR MECHANISMS INVOLVED IN T-CELL ACUTE LYMPHOBLASTIC LEUKAEMIA
dc.relationAlternative splicing and its impact on molecular networks during stem cell differentiation
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectPancreatic Ductal Adenocarcinoma
dc.subjectCell molecular signature
dc.subjectRnai screen
dc.subjectPluripotent
dc.subjectIdentity
dc.subjectRenewal
dc.subjectDisease
dc.subjectCancer
dc.titleStemChecker: a web-based tool to discover and explore stemness signatures in gene sets
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleDEVELOPMENT OF SOFTWARE TOOLS FOR THE PREDICTION OF CELULAR FATE IN STEM CELL DIFERENTIATION
oaire.awardTitleSYSTEMS BIOLOGY APPROACH TO UNRAVEL THE MOLECULAR MECHANISMS INVOLVED IN T-CELL ACUTE LYMPHOBLASTIC LEUKAEMIA
oaire.awardTitleAlternative splicing and its impact on molecular networks during stem cell differentiation
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F96890%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F70718%2F2010/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-GEN%2F116519%2F2010/PT
oaire.citation.endPageW77
oaire.citation.issueW1
oaire.citation.startPageW72
oaire.citation.titleNucleic Acids Research
oaire.citation.volume43
oaire.fundingStream3599-PPCDT
person.familyNameKalathur
person.familyNameMachado
person.familyNameMachado
person.familyNamePacheco-Leyva
person.familyNamedos Santos Duarte
person.familyNameFutschik
person.givenNameRavi Kiran Reddy
person.givenNameRui
person.givenNameSusana
person.givenNameIvette
person.givenNameGuilhermina Isabel
person.givenNameMatthias
person.identifier.ciencia-id5D19-8F5F-3CE1
person.identifier.ciencia-idB812-0D5C-4983
person.identifier.ciencia-idED15-7F67-7B64
person.identifier.ciencia-idA71B-AD01-3501
person.identifier.orcid0000-0003-2894-3345
person.identifier.orcid0000-0002-4080-2353
person.identifier.orcid0000-0002-3152-1701
person.identifier.orcid0000-0003-3006-2264
person.identifier.orcid0000-0003-0060-2936
person.identifier.orcid0000-0002-6245-8071
person.identifier.ridK-4033-2012
person.identifier.scopus-author-id22940879800
person.identifier.scopus-author-id55991033900
person.identifier.scopus-author-id56201414700
person.identifier.scopus-author-id56524572200
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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