Review
Combining many interaction networks to predict gene function and analyze gene lists
Sara Mostafavi,
Quaid Morris,
Sara Mostafavi
Department of Computer Science, Stanford University, Stanford, CA, USA
Search for more papers by this authorCorresponding Author
Quaid Morris
Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
Departments of Molecular Genetics and Computer Science, University of Toronto, Ontario, Canada
The Donnelly Centre, University of Toronto, Ontario, Canada
Correspondence: Dr. Quaid Morris, Banting and Best Department of Medical Research, Univesity of Toronto, 160 College St., Rm 616, Toronto, Ontario, M5S3E1, Canda
E-mail:[email protected]
Search for more papers by this authorSara Mostafavi,
Quaid Morris,
Sara Mostafavi
Department of Computer Science, Stanford University, Stanford, CA, USA
Search for more papers by this authorCorresponding Author
Quaid Morris
Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
Departments of Molecular Genetics and Computer Science, University of Toronto, Ontario, Canada
The Donnelly Centre, University of Toronto, Ontario, Canada
Correspondence: Dr. Quaid Morris, Banting and Best Department of Medical Research, Univesity of Toronto, 160 College St., Rm 616, Toronto, Ontario, M5S3E1, Canda
E-mail:[email protected]
Search for more papers by this authorColour Online: See article online to view Figs. 1‒3 in colour.
Abstract
In this article, we review how interaction networks can be used alone or in combination in an automated fashion to provide insight into gene and protein function. We describe the concept of a “gene-recommender system” that can be applied to any large collection of interaction networks to make predictions about gene or protein function based on a query list of proteins that share a function of interest. We discuss these systems in general and focus on one specific system, GeneMANIA, that has unique features and uses different algorithms from the majority of other systems.
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