About GN


GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher-order gene functions and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists, sequence data (SNPs), and massive transcriptome data sets (expression genetic or eQTL data sets). The quantitative trait locus (QTL) mapping module built into GN is optimized for fast online analysis of traits controlled by combinations of gene variants and environmental factors. GeneNetwork can be used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Most of these population data sets are linked with dense genetic maps (genotypes) that can be used to locate the genetic modifiers that cause differences in expression and phenotypes, including disease susceptibility.


GeneNetwork (GN) contains data from different groups of mice. The BXD genetic reference panel (GRP) will be your best bet if you are just exploring GN. All groups must have a genotype data set (under Type) and most also have a phenotype data set (also under Type). The phenotype in this case usually means classical trait data that we have gathered from various publications. Molecular expression data, when available, are listed with the suffix "mRNA."

Here are the groups to select for access to particular types of data:

  • AKXD: Expression data for mammary tumors generated by Kent Hunter at NCI.
  • AXB/BXA: Classical phenotypes that have usually been collected from the literature.
  • B6BTBRF2: Expression data for liver generated by Alan Attie and colleagues.
  • B6D2F2: Expression data for the whole brain generated by Robert Hitzemann and colleagues.
  • BDF2-2005: Expression data for striatum generated by Robert Hitzemann and colleagues. The striatum is a large forebrain region involved in learning and movement control that is severely affected by Huntington's and Parkinson's diseases.
  • BXD: Expression data for the brain and several brain regions, including the cerebellum, hippocampus, and striatum. BXD expression data for whole eye, liver, and hematopoietic stem cells. Classical phenotypes have usually been collected from the literature.
  • BHF2: F2 cross of BXH. Expression data for adipose, brain, liver, and muscle tissue generated by Jake Lusis at UCLA and Eric Schadt at Rosetta.
  • BXH: Only classical phenotypes have usually been collected from the literature.
  • CXB: Expression data for the hippocampus; a brain region involved in learning and memory, epilepsy, and neurodegenerative diseases. Classical phenotypes have also been collected from the literature.
  • Heterogeneous Stock (HS) mice: Three expression data sets for hippocampus, lung, and liver are currently available. Phenotype and genotype data are also available at http://gscan.well.ox.ac.uk/.
  • LXS: Phenotypes that have usually been generated by investigators at the Institute of Behavior Genetics and at the University of Tennessee over the last few years. We expect the addition of several large brain expression data sets late in 2006.
  • MDP: The great majority of data on the Mouse Diversity Panel is taken from the Phenome Project. Unlike the PHone Project, the MDP also includes limited data from the older literature. If you would like to add phenotypes, please submit your data to RW Williams and colleagues.