A persistent challenge lies in the interpretation of consensus and discord from 
functional genomics experimentation. Harmonizing and analyzing this data will 
enable investigators to discover relations of many genes to many diseases, and 
from many phenotypes and experimental paradigms to many diseases through their 
genomic substrates. The GeneWeaver.org system provides a platform for 
cross-species integration and interrogation of heterogeneous curated and 
experimentally derived functional genomics data. GeneWeaver enables researchers 
to store, share, analyze, and compare results of their own genome-wide 
functional genomics experiments in an environment containing rich companion data 
obtained from major curated repositories, including the Mouse Genome Database 
and other model organism databases, along with derived data from highly 
specialized resources, publications, and user submissions. The data, largely 
consisting of gene sets and putative biological networks, are mapped onto one 
another through gene identifiers and homology across species. A versatile suite 
of interactive tools enables investigators to perform a variety of set analysis 
operations to find consilience among these often noisy experimental results. 
Fast algorithms enable real-time analysis of large queries. Specific 
applications include prioritizing candidate genes for quantitative trait loci, 
identifying biologically valid mouse models and phenotypic assays for human 
disease, finding the common biological substrates of related diseases, 
classifying experiments and the biological concepts they represent from 
empirical data, and applying patterns of genomic evidence to implicate novel 
genes in disease. These results illustrate an alternative to strict emphasis on 
replicability, whereby researchers classify experimental results to identify the 
conditions that lead to their similarity.