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

We have developed StemChecker (http://stemchecker.sysbiolab.eu), a publicly accessible web server to analyze the presence of stemness signatures in gene sets provided by the user. Stemness signatures are sets of genes, which have been associated with the capabilities of stem cells to proliferate and differentiate. Particularly for cancer researchers, stemness signatures have proven to be valuable tool for the classification of tumors and might indicate the presence of malignant stem cells - the so called cancer stem cells. Our tool verifies the overlaps between a list of genes provided by the user and a large number of manually curated stemness signatures and calculates the statistical significance. As case studies demonstrated, StemChecker is a powerful tool to detect and dissect the activity of stemness-related processes in developmental biology as well as in human diseases such as cancer.

Authors an Affiliations:

José P. Pinto^1,*, Ravi K. Kalathur^1,2, Daniel V. Oliveira¹,Tânia Barata¹, Rui S.R. Machado¹, Susana Machado¹, Ivette Pacheco-Leyva¹, Isabel Duarte¹ and Matthias E. Futschik^1,3,*

¹ Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, 8005-139, Portugal,

² Experimental and Clinical Cell Therapy Institute, Spinal Cord and Tissue Regeneration Center Salzburg, Paracelsus Medizinische Privatuniversit¨at, Salzburg, A-5020, Austria

³ Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Algarve, 8005-139, Portugal

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/.

Journal: Nucleic Acids Research (NAS)

Link: http://nar.oxfordjournals.org/content/early/2015/05/24/nar.gkv529.long