Tree-based statistics of the original and jackknifed pruned modules

Tree-based statistics calculated for the original and all jackknifed versions of the pruned modules. For each module version, a tree was reconstructed based on the module preservation scores within and across species. The tips of resulting tree represent the replicates and the branch lengths represent the dissimilarity of connectivity patterns between the replicates. Branches between replicates of different species carry information about cross-species differences, while the branches between replicates of the same species carry information about the within-species diversity.

Usage

tree_stats_jk

Format

A data frame with 232 rows and 16 columns:

regulator

Character, transcriptional regulator.

module_size

Module size, 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

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

within_species_diversity

Numeric, the sum of the human, gorilla and cynomolgus diversity.

total_tree_length

Numeric, the sum of all branch lengths in the tree.

human_diversity

Numeric, the sum of the branch lengths in the subtree that contains only the human tips.

gorilla_diversity

Numeric, the sum of the branch lengths in the subtree that contains only the gorilla tips.

cynomolgus_diversity

Numeric, the sum of the branch lengths in the subtree that contains only the cynomolgus tips.

human_monophyl

Logical indicating whether the tree is monophyletic for the human replicates.

gorilla_monophyl

Logical indicating whether the tree is monophyletic for the gorilla replicates.

cynomolgus_monophyl

Logical indicating whether the tree is monophyletic for the cynomolgus replicates.

human_subtree_length

Numeric, the sum of the branch lengths in the subtree that is defined by the human replicates and includes the internal branch connecting the human replicates to the rest of the tree. NA if the tree is not monophyletic for the human replicates.

gorilla_subtree_length

Numeric, the sum of the branch lengths in the subtree that is defined by the gorilla replicates and includes the internal branch connecting the gorilla replicates to the rest of the tree. NA if the tree is not monophyletic for the gorilla replicates.

cynomolgus_subtree_length

Numeric, the sum of the branch lengths in the subtree that is defined by the cynomolgus replicates and includes the internal branch connecting the cynomolgus replicates to the rest of the tree. NA if the tree is not monophyletic for the cynomolgus replicates.