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StemCellNet: an interactive platform for network-oriented investigations in stem cell biology

2014-07Journal article Open access
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dc.contributor.authorPinto, Jose P.
dc.contributor.authorKalathur, Ravi Kiran Reddy
dc.contributor.authorMachado, Rui
dc.contributor.authorJM Xavier
dc.contributor.authorBragança, José
dc.contributor.authorFutschik, Matthias E.
dc.date.accessioned2018-12-07T14:53:19Z
dc.date.available2018-12-07T14:53:19Z
dc.date.issued2014-07
dc.description.abstractStem cells are characterized by their potential for self-renewal and their capacity to differentiate into mature cells. These two key features emerge through the interplay of various factors within complex molecular networks. To provide researchers with a dedicated tool to investigate these networks, we have developed StemCellNet, a versatile web server for interactive network analysis and visualization. It rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer. The StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu.
dc.description.sponsorshipPortuguese Fundacao para a Ciencia e a Tecnologia [PTDC/BIA-GEN/116519/2010, SFRH/BPD/70718/2010, SFRH/BPD/96890/2013, PEst-OE/EQB/LA0023/2013]
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1093/nar/gku455
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttp://hdl.handle.net/10400.1/11455
dc.language.isoeng
dc.peerreviewedyes
dc.publisherOxford University Press
dc.relationAlternative splicing and its impact on molecular networks during stem cell differentiation
dc.relationSYSTEMS BIOLOGY APPROACH TO UNRAVEL THE MOLECULAR MECHANISMS INVOLVED IN T-CELL ACUTE LYMPHOBLASTIC LEUKAEMIA
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.subjectSomatic-cells
dc.subjectRnai screen
dc.subjectMolecular signature
dc.subjectDatabase
dc.subjectDisease
dc.subjectPluripotency
dc.subjectIntegration
dc.subjectLeukemia
dc.subjectIdentity
dc.subjectRenewal
dc.titleStemCellNet: an interactive platform for network-oriented investigations in stem cell biology
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleAlternative splicing and its impact on molecular networks during stem cell differentiation
oaire.awardTitleSYSTEMS BIOLOGY APPROACH TO UNRAVEL THE MOLECULAR MECHANISMS INVOLVED IN T-CELL ACUTE LYMPHOBLASTIC LEUKAEMIA
oaire.awardTitleDEVELOPMENT OF SOFTWARE TOOLS FOR THE PREDICTION OF CELULAR FATE IN STEM CELL DIFERENTIATION
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-GEN%2F116519%2F2010/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F70718%2F2010/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F96890%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PEst-OE%2FEQB%2FLA0023%2F2013/PT
oaire.citation.endPageW160
oaire.citation.issueW1
oaire.citation.startPageW154
oaire.citation.titleNucleic Acids Research
oaire.citation.volume42
oaire.fundingStream3599-PPCDT
oaire.fundingStream3599-PPCDT
person.familyNameKalathur
person.familyNameMachado
person.familyNameGonçalves de Gouveia Maia Xavier
person.familyNameBragança
person.familyNameFutschik
person.givenNameRavi Kiran Reddy
person.givenNameRui
person.givenNameJoana
person.givenNameJosé
person.givenNameMatthias
person.identifier1489493
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person.identifier.orcid0000-0003-2894-3345
person.identifier.orcid0000-0002-4080-2353
person.identifier.orcid0000-0002-0702-6700
person.identifier.orcid0000-0001-9566-400X
person.identifier.orcid0000-0002-6245-8071
person.identifier.ridI-4676-2014
person.identifier.scopus-author-id22940879800
person.identifier.scopus-author-id55991033900
person.identifier.scopus-author-id36061472900
person.identifier.scopus-author-id6602220001
person.identifier.scopus-author-id14017989400
project.funder.identifierhttp://doi.org/10.13039/501100001871
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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
project.funder.nameFundação para a CiĂȘncia e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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