Data sets in GeneNetwork are typically made up of large collections of genotypes (e.g., SNPs) and phenotypes from groups of individuals, including humans, strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley.
Development of GeneNetwork started at the University of Tennessee Health Science Center in 1994 as a web-based version of the Portable Dictionary of the Mouse Genome (1994).
[4] In early 2003, the first large Affymetrix gene expression data sets (whole mouse brain mRNA and hematopoietic stem cells) were incorporated and the system was renamed WebQTL.
Production services are hosted on systems at University of Tennessee Health Science Center with a backup instance in Europe.
[11] Researchers and students typically retrieve sets of genotypes and phenotypes from one or more families and use built-in statistical and mapping functions to explore relations among variables and to assemble networks of associations.
There are tools on the site for a wide range of functions that range from simple graphical displays of variation in gene expression or other phenotypes, scatter plots of pairs of traits (Pearson or rank order), construction of both simple and complex network graphs, analysis of principal components and synthetic traits, QTL mapping using marker regression, interval mapping, and pair scans for epistatic interactions.
Users can also download the primary data sets as text files, Excel, or in the case of network graphs, as SBML.