PMC:1481596 / 18003-19187 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, after connecting all pairs of weak siblings, the resulting graph is not chordal, the COD method attempts to transform it to chordal by adding some additional edges. Consistently with our assumption that we connect only nodes corresponding to proteins that could be put in the same functional group, we impose restrictions on this \"fill-in\" process. Namely, we require that, each introduced edge connects a pair of nodes which are close to being weak siblings. In such case the new edge is a diagonal of one or more squares in the graph. We emphasize that adding edges between nodes of longer cycles has no such justification. To summarize our edge addition procedure, our method attempts to eliminate all the squares in the protein interaction network by adding a limited set of diagonals that satisfies following conditions (i) connects potentially functionally equivalent proteins, as measured by the overlap in neighborhoods or distance from being a pair of weak siblings; (ii) ensures that functional groups correspond to cographs; we argue that this condition is guaranteed if the set of added edges does not form a P4 in a maximal clique of the modified graph (cf. Methods);","tracks":[]}