Pruned modules created by the dynamic pruning of the initial modules via the "UIK_adj_kIM" method. The initial module members were filtered in successive steps based on their adjacency to the regulator and their intramodular connectivitiy alternately. In each step, the cumulative sum curve based on one of these two characteristics was calculated per module, then the targets below the knee point of the curve were kept. This process was continued until the module sizes became as small as possible without the median falling below a pre-defined minimum of 20 genes.
Format
A data frame with 225 rows and 9 columns:
- regulator
Character, transcriptional regulator.
- target
Character, target gene of the transcriptional regulator (member of the regulator's pruned module).
- weight
Numeric, 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
Character specifying the direction of regulation between the regulator and the target, either "+" or "-".
- module_size
Module size, the numer of target genes assigned to a regulator.