Figure 5

SPIKE visualization of signaling networks. The different types of biological entities are represented in SPIKE maps by nodes of different colors: violet nodes correspond to protein-coding genes, turquoise nodes to non protein-coding genes (e.g., micro-RNAs, rRNAs, tRNAs), green nodes to protein complexes, and yellow nodes to protein families. Small molecules are displayed in orange (not included in this map). Blue directed edges represent regulations: arrows correspond to activation, T shape edges to inhibition, and open circles denote regulations whose effect is still not clear (e.g., ATM was reported to phosphorylate MCM2, but the effect of this modification is not known yet). Blue undirected edges represent protein-protein interactions (not included in this map). Green edges represent containment relations between nodes (e.g., a complex and its components). Red and green dots within a node indicate that not all regulation and containment relations stored in the DB for the node are displayed in the map. This map represents the ATM-regulated network which is set off by the cell in response to double-strand breaks in the DNA.