This column shows the neighborhood of protein interactions surrounding the selected gene. The neighborhood is computed from a genome-wide protein-protein interaction network. The network connects genes if the proteins they encode have been detected to physically interact in high-throughput experiments.
The network distance listed in the column shows the number of interactions between a gene and the selected gene. For example, genes whose protein products have been detected to directly interact are listed with a network distance of one. Genes that share a direct interaction with a protein that also directly interacts with the selected gene are listed with a distance of 2. For example, if the protein of gene X interacts with the protein of gene Y (but not the protein of the selected gene), and Y's protein interacts with the selected gene, then gene X will have a distance of 2.
Because the protein interaction network is highly connected (i.e. most genes are connected to one another by some distance), we limited the size of the neighborhood to contain only those genes within a pre-specified distance (2 by default).
The interaction data were created by the Erich Wanker laboratory, MDC-Berlin.
Stelzl, U. et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell. 2005 Sept 23;122(6):957-68.