PMC:1481596 / 19188-21168 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1481596","sourcedb":"PMC","sourceid":"1481596","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1481596","text":"If the modification step succeeds, i.e., the modified graph is chordal, all the clique tree representations of the modified graph are computed and then each clique tree is extended to a Tree of Complexes representation of the original graph. The COD algorithm keeps track of all the edge additions and uses this information to delineate functional groups by projecting each maximal clique onto original network and removing all introduced edges contained in the clique. For example, in the modified graph of Figure 1 a maximal clique with four nodes, {1, 2, 5, 8}, is projected to a functional group by removing an edge connecting proteins 5 and 8. This functional group contains two variants of a protein complex, {1, 2, 5} and {1, 2, 8}, which are compactly represented by a (1 ∧ 2) ∧ (5 ∨ 8) Boolean expression. If, on the other hand, the modified graph is not chordal, the COD method stops without producing the representation. Since the clique tree representation for a chordal graph is not unique, the Tree of Complexes representation that derives from it is not unique either. As all clique trees of a chordal graph have the same set of nodes (the nodes are the maximal cliques in the graph), the difference between clique trees comes from the topology of the tree. The clique tree topology is determined by the \"connected subgraph\" constraints and restriction power of these constraints depends on the structure of the underlying graph, i.e., there are graphs with a unique clique tree representation and there are graphs for which almost any tree that spans all the maximal cliques in the graph is a valid clique tree. As a result a protein interaction network may have several Tree of Complexes representations; all such representations will have the same functional groups but will differ in the way these functional groups are interconnected. For every protein interaction network analyzed bellow we explicitly state all the possible Tree of Complexes representations.","tracks":[]}