Genetical Genomic Analysis of Complex Phenotypes Using the PhenoGen Website

Our laboratory has developed an online interactive resource called PhenoGen (http://phenogen.ucdenver.edu) which provides an archive of brain and other organ gene expression data from a panel of 20 common inbred mouse strains, and three recombinant inbred (RI) panels (two mouse and one rat). DNA microarray data can also be uploaded to the site where numerous analytical tools can be implemented. An important advantage to the archived data is that each array represents data from a single animal and each strain was sampled 4–7 times, providing an estimate of genetic variance (heritability) of individual transcript levels. These panels also allow genetic mapping of expression QTLs. Overlap of eQTLs with phenotypic QTLs provides a powerful approach to candidate gene identification. These methods are briefly described here and we encourage the use of our site for both scientific discovery and as a teaching tool in quantitative genetics.