StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
Autor(a) principal: | |
---|---|
Data de Publicação: | 2015 |
Outros Autores: | , , , , , , , |
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. |
id |
RCAP_82e933f617a3aa31305f1363dcbdf03b |
---|---|
oai_identifier_str |
oai:sapientia.ualg.pt:10400.1/11446 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
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 |
_version_ |
1817549706716250112 |