A face-face incidence matrix (FFIM) is proposed to describe the relationship between modules in detail.
The intrinsic association relationship between modules 12 and 17 was suggested by their correlation in the organizational structure of coexpression modules (Figure 5) inferred by estimating the partial correlation coefficients of the 27 modules.
Thus, we directly surveyed regulation relationship between modules or sub-modules for each dimension using heat map such as the upper part of Figure 3.
Both the ML and Bayesian trees for the C domains also support a strong relationship between modules 1 and 2 (Fig. 5B, see Additional files 4Di ii and 6).
Considering such characteristics of the modules and directions of the arcs between modules, we observe that the obtained network codes a partially consistent regulatory relationship between modules recalled from the time sequence of the phase in cell cycle.
In fact, we define a tree-based parent child relationship between modules such that along each path from the root to a leaf, the module size is increasing, whereas the module density is monotonically decreasing.
