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Table 3 Network and model properties calculated to characterise simulations

From: Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Label

Description

Type

Mapping

Avg num input TFs

Average number of input genes co-regulating the differentially regulated target.

Network

1-to-1

Clust coef (g)

Ratio of cliques over all possible cliques in the network. Large values are indicative of small-world networks. Calculated on the undirected regulatory network.

Network

1-to-1

Clust coef (l)

Average of clustering coefficients calculated per node. Calculated on the undirected network.

Network

1-to-1

Density diffnet

Network density of the true differential network. Here the differential association network is used.

Network

1-to-1

Density source

Network density of the source regulatory network. Density is calculated as the ratio of observed edges over the total number of possible edges (N choose 2) for N edges.

Network

1-to-1

Diameter

Calculated as the longest of all shortest paths in the network and is indicative of the linear size of the network. Calculated on the undirected network.

Network

1-to-1

Eigen centrality

Eigen centrality of each perturbed (knockdown) node. Calculated on the undirected network.

Network

1-to-many

Input means

Mean value of the distribution each input gene

Model

1-to-many

Input vars

Variance of the distribution of each input gene

Model

1-to-many

KD sample props

The smaller proportion of the population resulting from a knockdown. 0.2 if the proportions are 0.2 and 0.8.

Model

1-to-many

Num co-targeted

Number of differentially regulated targets

Network

1-to-1

Num inputs

Number of input nodes in the source regulatory network.

Network

1-to-1

Num KD genes

Number of perturbed genes (knockdown).

Model

1-to-1

Num TFs

Number of regulators in the source regulatory network (both inputs and downstream).

Network

1-to-1

Radius

Minimum eccentricity of any node where eccentricity of a node is the shortest distance to the farthest node. Calculated on the undirected network.

Network

1-to-1

Var of input cors

Variance of the correlations between relative abundances of input genes.

Model

1-to-1