title: StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.
abstract: 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.
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal jppinto@ualg.pt.
authors.forename: José P
authors.initials: JP
authors.lastname: Pinto
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal Experimental and Clinical Cell Therapy Institute, Spinal Cord and Tissue Regeneration Center Salzburg, Paracelsus Medizinische Privatuniversität, Salzburg, A-5020, Austria.
authors.forename: Ravi K
authors.initials: RK
authors.lastname: Kalathur
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal.
authors.forename: Daniel V
authors.initials: DV
authors.lastname: Oliveira
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal.
authors.forename: Tânia
authors.initials: T
authors.lastname: Barata
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal.
authors.forename: Rui S R
authors.initials: RS
authors.lastname: Machado
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal.
authors.forename: Susana
authors.initials: S
authors.lastname: Machado
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal.
authors.forename: Ivette
authors.initials: I
authors.lastname: Pacheco-Leyva
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal.
authors.forename: Isabel
authors.initials: I
authors.lastname: Duarte
authors.affiliation: Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, 8005-139, Portugal mfutschik@ualg.pt.
authors.forename: Matthias E
authors.initials: ME
authors.lastname: Futschik
mesh_terms: D000818:Animals; D001665:Binding Sites; D002454:Cell Differentiation / Q000235:genetics; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D051379:Mice; D010190:Pancreatic Neoplasms / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D012984:Software; D013234:Stem Cells / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors