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Edges were added between the xref nodes based on the interaction network.
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In addition, each pathway node was connected to each of the xref nodes that are associated with that pathway.
In this study, parameter nb was set to 5, limiting the number of edges between xref nodes in a path to maximal three.
Secondly, edge weights were assigned based on the transformed T statistic f(T) of the target xref nodes they connect to, or to the maximum value of 1 if no data was available for the target xref.
For each permutation, Pr was generated by reconnecting the endpoints of its adjacent edges (which are the nodes representing the xrefs associated to the pathway) to different xref nodes from the interaction network that have a similar strength (also weighted degree [ 43]) as the original xref node.
For xref nodes that were connected to both Pn and Pm, the edge to Pm was removed to prevent paths to go directly through an overlapping xref. 5.
Excluding xref nodes that are present in pathways other than Pm and Pn is necessary to prevent detection of false interactions between Pn and Pm that cross other pathways.
The stem is solid at the nodes, but between the nodes the central pith breaks down to form an internodal lacuna and the stem is hollow.
The weight of the edges is proportional to the P-value between the respective nodes.
The algorithms are variations on a theme, the theme being several layers of nodes, with different types of communications between the nodes and the layers.
Primal graphs are concerned with information at street intersections: street junctions are the nodes in the graph, and streets as the links between the nodes.
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