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

Detalhes bibliográficos
Autor(a) principal: Pinto, Jose P.
Data de Publicação: 2015
Outros Autores: Kalathur, Ravi Kiran Reddy, Oliveira, Daniel V., Barata, Tania, Machado, Rui, Machado, Susana, Pacheco-Leyva, Ivette, Duarte, Isabel, Futschik, Matthias E.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.1/11446
Resumo: Stem 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.
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spelling StemChecker: a web-based tool to discover and explore stemness signatures in gene setsPancreatic Ductal AdenocarcinomaCell molecular signatureRnai screenPluripotentIdentityRenewalDiseaseCancerStem 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.Oxford University PressSapientiaPinto, Jose P.Kalathur, Ravi Kiran ReddyOliveira, Daniel V.Barata, TaniaMachado, RuiMachado, SusanaPacheco-Leyva, IvetteDuarte, IsabelFutschik, Matthias E.2018-12-07T14:53:18Z2015-072015-07-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.1/11446eng0305-10481362-496210.1093/nar/gkv529info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-11-29T10:27:53Zoai:sapientia.ualg.pt:10400.1/11446Portal AgregadorONGhttps://www.rcaap.pt/oai/openairemluisa.alvim@gmail.comopendoar:71602024-11-29T10:27:53Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
title StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
spellingShingle StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
Pinto, Jose P.
Pancreatic Ductal Adenocarcinoma
Cell molecular signature
Rnai screen
Pluripotent
Identity
Renewal
Disease
Cancer
title_short StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
title_full StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
title_fullStr StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
title_full_unstemmed StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
title_sort StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
author Pinto, Jose P.
author_facet Pinto, Jose P.
Kalathur, Ravi Kiran Reddy
Oliveira, Daniel V.
Barata, Tania
Machado, Rui
Machado, Susana
Pacheco-Leyva, Ivette
Duarte, Isabel
Futschik, Matthias E.
author_role author
author2 Kalathur, Ravi Kiran Reddy
Oliveira, Daniel V.
Barata, Tania
Machado, Rui
Machado, Susana
Pacheco-Leyva, Ivette
Duarte, Isabel
Futschik, Matthias E.
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Sapientia
dc.contributor.author.fl_str_mv Pinto, Jose P.
Kalathur, Ravi Kiran Reddy
Oliveira, Daniel V.
Barata, Tania
Machado, Rui
Machado, Susana
Pacheco-Leyva, Ivette
Duarte, Isabel
Futschik, Matthias E.
dc.subject.por.fl_str_mv Pancreatic Ductal Adenocarcinoma
Cell molecular signature
Rnai screen
Pluripotent
Identity
Renewal
Disease
Cancer
topic Pancreatic Ductal Adenocarcinoma
Cell molecular signature
Rnai screen
Pluripotent
Identity
Renewal
Disease
Cancer
description Stem 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.
publishDate 2015
dc.date.none.fl_str_mv 2015-07
2015-07-01T00:00:00Z
2018-12-07T14:53:18Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.1/11446
url http://hdl.handle.net/10400.1/11446
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 0305-1048
1362-4962
10.1093/nar/gkv529
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv mluisa.alvim@gmail.com
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