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RWRH considers the following heterogeneous network: c = G λ P λP T Q where G is the entire gene-gene interactions matrix, Q is the phenotype-phenotype similarity matrix, and λ is the probability that the random walker jumps from a gene node to a phenotype node (or vice versa).
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Formally, we define E to be the set of edges that can appear in ℐ: all undirected edges between two protein nodes, and directed edges from a protein (TF) node to a gene node.
For each eQTL node, we connected it to Ni gene nodes: with probability p, a gene node randomly selected from the same module was connected to the eQTL; otherwise a gene node randomly selected from the whole gene node set was connected to the eQTL.
Calpains −13 and −14 are derived from a gene duplication at node G.
After that, each gene was marked with a unique age index from oldest Opisthokonta node to the latest human node.
We searched for seed modules within a range of m (the number of eQTL nodes) from 2 to 6 and n (the number of gene nodes) from 4 to 14.
The constructed network contained 215115 interactions ranging from 1 to 494 for each gene node (Supplementary Table 5).
In this system a special "token" packet is passed from node to node.
Predicted gene nodes without direct interactions to anchor genes were excluded from the network diagram.
The final mapping from gene symbol to node id is generated by merging the above three kinds of mapping data.
Local /tmp storage is available on most nodes, but size varies from node to node.
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