Example pathway with three possible inputs and three possible outputs. Any of the output proteins trigger a different functionality of the pathway. The connection matrix shows how input and output can be connected through 5 different sub-pathways. Any sub-pathway can be traversed by different paths. For example, the sub-pathway connecting ProtA to ProtH can be traversed by two different paths, represented by two sequences of nodes (that, for the sake of the simplicity are here equivalent to proteins): ProtA, ProtB, ProtD, ProtF, ProtH or ProtA, ProtB, ProtD, ProtG, ProtH. On the right, the two interactions among proteins: top right represents activation, with an arrowhead line, and bottom right represents repression with a line with no arrow. In the lower part there is an example to illustrate the way in which the probability of activation of a sub-pathway can be calculated from the combined activation of the corresponding nodes. From top to bottom: i) Probability of the transmission of the signal through an activation action, ii) Probability of the transmission of the signal through a repression action, iii) An example of a simple bifurcating sub-pathway and iv) the probability of signal transmission along this pathway.