Figure 2

Sample schemas. Examples of network schemas. Unlabeled schema proteins are considered to be 'wildcards' and can match any protein in the interaction network. (a) A signaling pathway schema. This schema matches all sets of proteins such that a protein in the cell membrane physically interacts with a succession of anywhere between one and three kinases, the last of which physically interacts with a protein that is a transcription factor. (b) A MAP kinase schema, specified by particular yeast proteins making up a canonical MAPK signaling pathway. (c) A feed-forward loop network motif [8] schema. The unlabeled nodes can match any protein in the network. (d) A 'kinate' feedback loop network motif schema [13]. (e) An SH3 domain interaction schema. This schema matches all interacting pairs of proteins such that one contains a Pfam SH3 domain and the other has one of the specified patterns, corresponding to SH3 binding sites, in its underlying amino acid sequence. Amino acids in the pattern are specified by their one letter code, and 'x' denotes a match to any amino acid. (f) A specific protein schema. This schema matches all proteins with a synthetic lethal relationship to yeast protein ACT1.