Associação Portuguesa de Investigação em Cancro
StemCellNet: A new and unique resource to decipher molecular networks in stem cell biology
StemCellNet: A new and unique resource to decipher molecular networks in stem cell biology
In recent years, numerous scientific breakthroughs have expanded our knowledge of stem cell biology, and inspired intense research efforts in this field. Aside from the evident importance of stem cells in developmental processes, their potential for clinical and medical applications has attracted much interest.
Although research has produced a considerable amount of data for stem cell biology, the exploration and exploitation of these data is restricted by the lack of dedicated computational resources. Furthermore, the complexity of the underlying processes make it difficult to interpret the data.
To overcome this dilemma and to provide the research a powerful tool for the study of stem cells, members of the Systems Biology and Bioinformatics Laboratory of the University of Algarve have developed a unique computational source: StemCellNet. It is an interactive platform for network-oriented investigations in stem cell biology and can be publicly accessed at http://stemcellnet.sysbiolab.eu. Thanks to its comprehensive coverage, StemCellNet will also be useful for biomedical researcher in areas, where different types of stem cells play a role, such as in the study of regenerative medicine, degenerative diseases or cancer.
Dr. José Pedro Pinto, who recently received a FCT postdoc scholarship has been the main developer. Dr. Matthias Futschik, FCT Investigator and project leader: «We believe that StemCellNet will help a broad community in gaining a understanding of stem cells and using stem cells in biomedicine. StemCellNet is only our first computational tool dedicated to stem cell biology, and various other tools can be expected to be released in the near future.»
Authors and Affiliations:
José Pedro Pinto: CBME/IBB, LA, University of Algarve, Faro
Ravi Kiran Reddy Kalathur: CBME/IBB, LA, University of Algarve, Faro
Rui S. R. Machado: CBME/IBB, LA, University of Algarve, Faro
Joana M. Xavier: CBME/IBB, LA, University of Algarve, Faro
José Bragança: CBME/IBB e DCBM, LA, University of Algarve, Faro.
Matthias E. Futschik: CBME/IBB e CCMAR, LA, University of Algarve, Faro.
Abstract:
Stem cells are characterized by their potential for self-renewal and their capacity to differentiate into mature cells. These two key features emerge through the interplay of various factors within complex molecular networks. To provide researchers with a dedicated tool to investigate these networks, we have developed StemCellNet, a versatile web server for interactive network analysis and visualization. It rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer.
Journal:
Nucleic Acids Research
Link:
