A means to assess functional impact of x-hub perturbations
xHubEnrich(ig, go2eg)
| ig | An igraph network object output from either
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|---|---|
| go2eg | Named list where the names denote a biological process (e.g. Gene Ontology ID) and the elements of the list is a vector of members belonging to the biological process. The list ought to be non-redundant in names. |
Data.frame with each x-hub, out-degree, and the neighborhood percentage.
A x-hub is defined to be any x node with at least one edge to a y node. A x neighborhood comprises all y nodes that are directly connected to a x-hub by an edge. x neighborhoods are of interest because they represent direct perturbations to y nodes. To quantitatively assess how much those perturbations are functionally meaningful, we compute a score called the GO-neighbor percentage. Two y nodes are called GO-neighbors if they share a common Gene Ontology (GO) term in the same x neighborhood. We postulate that a high percentage of GO-neighbors within an x neighborhood associates the x-hub with more functional meaning. These scores, as presented in figure 5 of the spaceMap publication, can be generated with a GO mapping