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## Figure 5.
Distribution of mutual information for different lengths of the shortest path between
genes for the scale-free topology. Here we plot the log of the empirical probability that MI for a given separation
between genes is above some value (in nats) marked on the horizontal axis. High MI
values are significantly more probable for closer genes. Statistical significance
threshold of 10^{-4 }for the background MI distribution, corresponding to I_{0 }= 0.0175 nats, is marked on the graph. As shown, this threshold retains a large number
of indirect candidate interactions, and there is no threshold that would be able to
separate indirect and direct interactions; a threshold that eliminates most of the
former (red arrows) also eliminates the majority of the latter. This severely degrades
performance of RNs. (Inset) Expanded log-log view of the MI distribution for 934 gene
pairs with 3 or more intermediaries and the background distribution computed by Monte
Carlo. The curves are virtually indistinguishable, indicating that the background
distribution can be used to obtain reliable estimates of statistical significance
thresholds for filtering genes with higher degrees of connectivity. Similar results
apply for the Erdös-Rényi topology (see 3: MI distribution for different shortest path lengths for the Erdös-Rényi topology).
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