Adjacency matrices: random versus ascending CAI. These plots present a view of the adjacency matrix for the viable bait/prey (VBP) derived from the report from Gavin and coworkers . An interaction between bait b and prey p is recorded by a dark pixel in (b,p)th position of the matrix. (a) Rows and columns are randomly ordered; (b) rows and columns are ordered by ascending values of each protein's codon adaptation index (CAI). Contrasting these two figures, we can ascertain that there is a relationship between bait/prey interactions and CAI. The relationship is based on proteins with large un-reciprocated in-degree because panel b shows a dark vertical band. Had unreciprocated out-degree also been associated with CAI, then there would be a similar horizontal band reflected across the main diagonal of the matrix.
Chiang et al. Genome Biology 2007 8:R186 doi:10.1186/gb-2007-8-9-r186