Consensus network of the 9 primate replicates in the example dataset. For each edge, the consensus adjacency was calculated as the weighted average of replicate-wise adjacencies using weights that correct for 1) the phylogenetic distances between species and 2) the different numbers of replicates per species. If an edge was not detected in certain replicate, the adjacency of that replicate was regarded as 0 for the calculation of the consensus. The directionality of each edge was determined based on a modified Spearman's correlation between the corresponding 2 genes' expression profiles (positive expression correlation - activating interaction, negative expression correlation - repressing interaction). The correlations were calculated per replicate, then the mean correlation was taken across all replicates.
Format
An [igraph] object with 300 nodes, and has 1 node attribute and 3 edge attributes:
Node attributes:
- name
Name of the node (gene).
Edge attributes:
- weight
Consensus edge weight/adjacency, the weighted average of replicate-wise adjacencies.
- rho
Approximate Spearman's correlation coefficient of the 2 genes' expression profiles that form the edge.
- p.adj
BH-corrected approximate p-value of rho.
- direction
Direction of the interaction between the 2 genes that form the edge ("+" or "-").