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To model the active transcriptional programs, a co-regulation network is built by setting an edge between two significantly cooperative TF (details in Supplementary Information).
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In a gene set network (GSN), a node represents a gene set and an edge represents a relationship between two gene sets.
Let G = (V, E) be a graph with a vertex set V and an edge set E of V, the set of some pairs of vertices in V.
A G GTN) contains a vertex set V GTN) and an edge set E GTN).
The minimal cut set (MC, an edge set) is one of the major and fundamental tools for evaluating network reliability.
A subgraph of G is a graph with a vertex set V′⊆ V and an edge set E′⊆ E. A subgraph G′ = (V′, E′) of G is said to be induced by a vertex set V′⊆ V when an edge is in E′ if and only if the edge is in E. The subgraph induced by a clique is complete (all possible edges between vertices in clique are included in the edge set).
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A tree T is a connected graph with no cycles, consisting of a node set V(T) and an edge set E(T).
Definition 4 (seeds graph): A seeds graph G is a tuple (V,E), where V is a vertex set and E is a edge set.
A subset of vertices is termed "independent" provided that no two vertices in the set have an edge between them.
4. Connect a pair of gene sets with an edge if the edge is rejected by the Benjamini-Hochberg procedure and thus considered as a significant edge.
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