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To evaluate whether network discordances were driven exclusively by changes in species abundances, we carried out a Procrustes analysis based on relative (instead of absolute) interaction frequencies.
For each pair of bins, the number of paired-end tags was set as the absolute interaction value (IV).
Note that our aim is not the evaluation of accurate absolute interaction energies but merely the relative values for different complexes.
Alternatively spliced events are declared if p-AC < = 10^-8 and the maximum absolute interaction effect (maxik|ACik|) is greater than or equal to 2. A p-AC < = 10^-8 corresponds to less than 1% false discovery rate (FDR) using the method of Benjamini and Hochberg [ 18].
This shift of span size characteristics is not accompanied by a general decrease of absolute interaction frequencies (red curve in Figure 3) and also lacks any symmetry around the gaps (owed to SDs with high sequence similarity) within the Hi-C data set, which would be expected if the observed changes in average span size are a consequence of mapping problems associated with the presence of SDs.
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Absolute frequency of interaction.
Our new metric is based on neighborhood overlap and the absolute frequency of interaction among researchers.
We now analyze the relationship between neighborhood and absolute frequency of interaction on DBLP, PubMed, and APS.
Such study considers three different networks and the two main metrics: neighborhood overlap (NO) and absolute frequency of interaction (W).
Next, we analyze the linear and non-linear correlation between neighborhood overlap (NO) and absolute frequency of interaction (W).
We also introduce a nominal scale to tieness based on the values of a modified neighborhood overlap and absolute frequency of interaction.
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