Program scripts were developed for the use of ActivePerl and R statistical software (version 2.6.1) in text processing, parsing networks (svg files), analyzing and comparing the gene lists, linking gene-specific information and chromosomal coordinates, and transforming gene-gene interactions into matrices for networks topological analyses.
For example, the transition rate matrix for network system (1) with r operation modes can be expressed as [ π 11 ? … ? π 21 ? … π 2 r ⋮ ⋮ ⋱ ⋮ ? π r 2 … π r r ], where '?' represents the unknown transition rate.
We used uncorrected- p distances as input for P OFAD and made use of the standardized matrix for network reconstruction.
The MOO-DSp procedure was always more effective than SOO (up to 11% increase, p < 10 -3) and gave higher AUC values than the simple DSp matrix for networks of size 50 (8% increase, p < 0.05).
Each exchanger in the network is represented algebraically using the effectiveness-NTU methodology The properties of the resulting structural disturbance matrices for the network play a vital role in this model.
Finally, we introduce notation for vectors and matrices stacking together the network-level outcome vectors, covariate matrices and adjacency matrices for all networks in the data.
The e-matrix for this network can be reconstructed from the frequencies of inter-color edges, and be used to grow networks that not only have the same degree distribution as the original network, but mimic the connection pattern between functional types as well.
The specification of this network in SBML format is available as Additional File 1. Figure 1(a) shows the DAG matrix for this network using a colour scale to represent numerical values of the matrix elements.
The coupling matrix for the network can be asymmetric.
Like Laplacian matrix for any network the vector (1,1,1,…) is an eigenvector of the modularity matrix with eigenvalue zero but the eigenvalues of the modularity matrix are not necessarily all of one sign i.e. matrix has both positive and negative eigenvalues [39].
