Preservation statistics of the original and jackknifed pruned modules

Correlation of intramodular connectivities (cor_kIM) per replicate pair for the original and all jackknifed versions of the pruned modules. The jackknifed versions of the modules were created by removing each target gene assigned to a module (the regulators were never excluded). The preservation statistic cor.kIM was then calculated for the original module as well as each jackknife module version by comparing each replicate to all others, both within and across species. cor.kIM quantifies how well the connectivity patterns are preserved between the networks of two replicates, mathematically it is the correlation of the intramodular connectivities per module member gene in the network of the 1st replicate VS the intramodular connectivities per module member gene in the network of the 2nd replicate.

Usage

pres_stats_jk

Format

A data frame with 8352 rows and 8 columns:

regulator

Character, transcriptional regulator.

module_size

Integer, the numer of target genes assigned to a regulator.

type

Character, module type (orig = original or jk = jackknifed).

id

Character, the unique ID of the module version (format: nameOfRegulator_jk_nameOfGeneRemoved in case of module type 'jk' and nameOfRegulator_orig in case of module type 'orig').

gene_removed

Character, the name of the gene removed by jackknifing (NA in case of module type 'orig').

replicate1, replicate2

Character, the names of the replicates compared.

species1, species2

Character, the names of the species replicate1 and replicate2 belong to, respectively.

cor_adj

Numeric, correlation of adjacencies.

cor_kIM

Numeric, correlation of intramodular connectivities.