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In this situation, n ¯ 1, 3 (or at least its first coordinate) will be large even if there is no direct interaction from N 3 on N 1.
This new network detects not only the direct interaction from the original protein association network, but also all indirect interactions via other genes.
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Probably, SSB might also be caused by direct interactions from the low energy electrons from 99mTc even at high doses up to 500 Gy.
Kim et al. [ 12] proposed a new method to distinguish direct interactions from indirect ones.
Therefore, the ability to distinguish direct interactions from indirect ones is of much interest.
However, they did not investigate the performance of their method on detecting direct interactions from AP-MS data.
The advantage of partial correlations over the conventional pairwise correlations is its ability to distinguish direct interactions from indirect ones.
In addition, there are direct interactions from two key residues positioned at 74/101 and 84/111 in the RAMPs.
We first propose a simple probabilistic model for the interactions captured by AP-MS experiments, under which the problem of separating direct interactions from indirect ones is formulated.
Although these assumptions are clearly unrealistic, they provide a useful starting point for separating direct interactions from indirect ones (see Discussion for possible relaxation of these assumptions).
The modelling and algorithm proposed here is only a first step toward an accurate detection of direct interactions from AP-MS data.
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