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Finally, a functional similarity score (funSim) between two pathways was computed via cosine measure.
The co-expression value between two pathways was measured by combining Jaccard coefficient (JC) and overlap coefficient (OC) defined as: (7) J C = E 12 E 1 + E 2 - E 12 and O C = E 12 min (E 1, E 2 ) Where E 1 and E 2 denote the number of tissues in which pathway 1 and 2 are expressed, respectively, and E 12 denotes the number of common tissues where both pathways are expressed.
Specifically, the interaction score between two pathways is estimated by their overlapping status of weighted pathways in the following formula: The overlapping score is the summation of the scores of overlapping edges between pathways.
The number of edges in each interaction network that have a weight smaller than the maximum path length (see methods) and hence may contribute to a path between two pathways is shown in Table 1.
No significant correlation in FC contamination between any two pathways was found (Table 3).
However, when WT-Ras-expressing tumor cells were stimulated by TNFα, cooperativity between the two pathways was obtained.
A novel RTK-independent crosstalk between these two pathways was found in an intriguing study by Zmajkovicova et al (2013).
The interaction between the two pathways was revealed only recently by our previous study (Hillman et al., 2011).
However, the asymmetry between the two pathways was fairly small and it is obvious that the WUS-repressing signal is dependent on both pathways.
The absolute connection between the two pathways was confirmed by examining the flux correlations of both pathways (see Additional File 5).
