R spider implements the Global Network statistical framework to analyze gene list using as reference knowledge a global gene network constructed by combining signaling and metabolic pathways from Reactome and KEGG databases. Reactome is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways. Reactome database model specifies protein-protein interaction pairs. The meaning of "interaction" is broad: 2 protein sequences occur in the same complex or they occur in the same or neighbouring reaction(s). Both, Reactome signaling network and KEGG metabolic network were united into the integral network. For the human genome, the resulting integral network covers about 4000 genes involved in approximately 50,000 unique pairwise gene interactions.
Reference: if you will find the results produced by R spider usefull, please cite:
1. Antonov A.V., Schmidt E., Dietmann S., Krestyaninova M.,Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases Nucleic Acids Research, 2010, Vol. 38, No. suppl_2 W118-W123