Each element in the correlation matrix represents a measure of dependencies between corresponding gene pairs, with zero indicates independence.
The dependency matrix of the interaction graph (computed for time scale 1, Figure 2) displays all functional dependencies between each pair of species.
Furthermore, MX1 was included to assess the effect of IFN-ß therapy, although it does not influence T-cell activation, and we found that it did not affect the dependency matrix of the T-cell activation network, reinforcing the specificity of the analysis.
This is further supported by the dependency matrix of the network, which is based solely on the underlying network interaction graph without information on Boolean functions.
For example, the dependency matrix of the T-cell model tells us, that LAT-phosp exerts purely positive effects on ERK, JNK, IKK, and NFAT, because there are only positive paths from LAT-phosp to these species and no negative feedback is involved.
The main reason may be that these two types of dependencies employ the matrices D x (x ∈ {Y, U, V}) to reflect intra- and inter-block dependencies.
Though the mechanism of extra-matrix Ca2+ dependency of mitochondrial Ca2+ uptake has been well characterized, the mechanism of membrane potential dependency of mitochondrial Ca2+ uptake has not been completely characterized.
Though the mechanism of extra-matrix Ca2+ dependency of mitochondrial Ca2+ uptake has been well characterized both experimentally and mathematically, the mechanism of membrane potential dependency of mitochondrial Ca2+ uptake has not been completely characterized.
Collinearity of independent variables was assessed by using the variance/covariance matrix from PROC LOGISTIC (SAS Institute, Inc., Cary, NC) generate condition indices and a matrix of variance decomposition proportions to detect dependencies among the variables (9).
