Illustration of the different disease networks based on genome-wide association data.A: The bipartite graph constructed from all association data. The two disjoint node sets are diseases (n = 111) and loci (n = 734; 508 gene loci and 226 intergenic loci), connected to each other by an edge if a variant (n = 1,120) within the respective locus is associated with the corresponding trait. B: The SLN (shared locus network) consisting of 84 traits and 157 loci, retrieved by removing isolated traits and loci that are associated with a single trait only. C: The SVN (shared variant network) that corresponds to a variant-based representation of the data. Here, a trait and a locus are linked if the locus contains a variant comprising associations with this and at least one other trait. The network consists of 175 SNPs located in 94 loci that are associated with 55 diseases (see also Additional file 2: Table S1). The colors of the disease nodes correspond to disease classes according to the MeSH ontology, multi-colored nodes indicate an association with different disease classes; loci are depicted as transparent, diamond-shaped nodes. The node size reflects the number of loci a disease is associated with. In C, the edge color reflects the allelic information: gray indicates agonistic variant(s), red corresponds to antagonistic variant(s), and blue mark both agonistic and antagonistic signals.
Arnold et al. BMC Genomics 2012 13:490 doi:10.1186/1471-2164-13-490