Figure 6

Superposition of ' omics ' data on maps. By allowing the user to superimpose functional genomic or proteomic data on pathway maps, SPIKE facilitates improved interpretation of such datasets. The color of the bar above each gene's node indicates its response. Upregulated genes are shades of red: the darker the red the greater the fold of induction. Similarly, downregulated genes are in shades of green. Genes whose expression was not changed are yellow, and genes for which data are not available (e.g., genes not present on the microarray) are grey. In this example, superimposing gene expression data measured in human lymphocyte cells exposed to ionizing radiation on the signaling map shows the activation of the p53 network (top-left part of the network) and the down-regulation of genes that function in the cell cycle G2-M phase transition (bottom-right part of the network). Superimposing the data on this map clearly shows that a large fraction of the p53 network was activated in the analyzed condition. SPIKE also allows superimposition of clustering data: any partition of the genes into groups (e.g., according to GO annotation, cellular compartment, clustering, or user-specific definitions) can be viewed on the pathway map. The color scheme can be adjusted by the user.