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Figure 4 | Genome Biology

Figure 4

From: Coverage and error models of protein-protein interaction data by directed graph analysis

Figure 4

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 [10]. 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.

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