StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.
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. The StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu.
Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal jppinto@ualg.pt.
José P
JP
Pinto
Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal.
Ravi Kiran
RK
Reddy Kalathur
Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal.
Rui S R
RS
Machado
Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal.
Joana M
JM
Xavier
Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Algarve 8005-139, Portugal.
José
J
Bragança
Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, University of Algarve, Faro, Algarve 8005-139, Portugal Centre of Marine Science, University of Algarve, Faro, Algarve 8005-139, Portugal jppinto@ualg.pt.
Matthias E
ME
Futschik
D000818:Animals; D015870:Gene Expression; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D051379:Mice; D025941:Protein Interaction Mapping; D020543:Proteome; D012984:Software; D013234:Stem Cells / Q000378:metabolism*
D020543:Proteome