The abundance of existing functional genomics studies permits an integrative 
approach to interpreting and resolving the results of diverse systems genetics 
studies. However, a major challenge lies in assembling and harmonizing 
heterogeneous data sets across species for facile comparison to the positional 
candidate genes and coexpression networks that come from systems genetic 
studies. GeneWeaver is an online database and suite of tools at 
www.geneweaver.org that allows for fast aggregation and analysis of gene 
set-centric data. GeneWeaver contains curated experimental data together with 
resource-level data such as GO annotations, MP annotations, and KEGG pathways, 
along with persistent stores of user entered data sets. These can be entered 
directly into GeneWeaver or transferred from widely used resources such as 
GeneNetwork.org. Data are analyzed using statistical tools and advanced graph 
algorithms to discover new relations, prioritize candidate genes, and generate 
function hypotheses. Here we use GeneWeaver to find genes common to multiple 
gene sets, prioritize candidate genes from a quantitative trait locus, and 
characterize a set of differentially expressed genes. Coupling a large 
multispecies repository curated and empirical functional genomics data to fast 
computational tools allows for the rapid integrative analysis of heterogeneous 
data for interpreting and extrapolating systems genetics results.