Cross-species conservation measures of the target genes in the POU5F1 module

Cross-species conservation measures of the 21 target genes in the POU5F1 module in the subsetted early neuronal differentiation dataset.

Usage

POU5F1_target_conservation

Format

A data frame with 23 rows and 12 columns:

focus: Character, the focus of interest in terms of cross-species conservation ("overall").
regulator: Character, transcriptional regulator.
module_size: Integer, the numer of target genes assigned to a regulator.
type: Character, module type (orig = original, jk = jackknifed or summary = the summary across all jackknife module versions).
id: Character, the unique ID of the module version (format: nameOfRegulator_jk_nameOfGeneRemoved in case of module type 'jk', nameOfRegulator_orig in case of module type 'orig' and nameOfRegulator_summary in case of module type 'summary').
gene_removed: Character, the name of the gene removed by jackknifing (NA in case of module types 'orig' and 'summary').
total_tree_length: Numeric, total tree length per jackknife module version.
within_species_diversity: Numeric, within-species diversity per jackknife module version.
fit: Numeric, the fitted total tree length at the within-species diversity value of a jackknife module version.
lwr_fit: Numeric, the lower bound of the prediction interval of the fit.
upr_fit: Numeric, the upper bound of the prediction interval of the fit.
residual: Numeric, the residual of the jackknife module version in the linear model. It is calculated as the difference between the observed and expected (fitted) total tree lengths.
contribution: Numeric, the contribution score of the removed target gene.

Details

To determine which target genes are the most responsible for the divergence of the POU5F1 module, the same statistics were be used as for the identification of conserved/diverged modules but in combination with jackknifing. This means that each target gene in the module was removed and all statistics, including the tree-based statistics that carry information about cross-species conservation, were re-calculated (please see calculatePresStats, reconstructTrees and calculateTreeStats). Our working hypothesis is that if removing a target gene from the diverged POU5F1 module makes the module more conserved, then this gene contributed to the divergence of the original module in the first place. This can be quantified using the residuals compared to the regression line between the total tree lengths and within-species diversities of the tree representations across all modules (please see fitTreeStatsLm and findConservedDivergedTargets. The jackknifed versions of the POU5F1 module that have the lowest residuals are the most conserved, therefore the corresponding target genes are considered the most diverged.