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

Journal Article

TitleStemChecker: a web-based tool to discover and explore stemness signatures in gene sets.
Publication TypeJournal Article
AuthorsPinto, JP, Kalathur, RK, Oliveira, DV, Barata, T, Machado, RSR, Machado, S, Pacheco-Leyva, I, Duarte, I, Futschik, ME
Year of Publication2015
JournalNucleic Acids Res
Date Published2015 Jul 1
KeywordsAnimals, Binding Sites, Cell Differentiation, Embryonic Stem Cells, Gene Expression Profiling, Humans, Internet, Mice, Pancreatic Neoplasms, RNA Interference, Software, Stem Cells, Transcription Factors

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


Alternate JournalNucleic Acids Res.
PubMed ID26007653
PubMed Central IDPMC4489266
CCMAR Authors