For example, Barrera et al. use mutual information for dimension reduction [ 17], with mutual information between genes being computed and then, the highest mutual informations selected.
The shortest paths between two genes were computed using Dijkstra's algorithm (Dijkstra, 1959).
In addition, overlaps between lists of genes were computed by using MatchMiner web tool, which also takes into account gene aliases and/or different types of gene identifiers [ 83].
To determine the gene expression fold changes in response to UV-irradiation, the ΔΔCT values of specified genes were computed between the UV-treated and untreated groups (i.e., Δ Δ C T[gene] = Δ C T[gene] (treated samples) - Δ C T[gene] (controls) ), followed by the use of the empirical formula 2-ΔΔCT for calculating the fold-changes.
The score between two genes is computed as ∑ f i 2, where f i is the frequency of the i-th feature shared by both genes.
To estimate the age since gene duplication, the synonymous substitution rate (Ks) between two duplicates genes was computed using a ML algorithm using the program Codeml in PAML (Yang 1997).
The enrichment, or overlap, between two sets of genes is computed by assuming an underlying hyper-geometric model.
Quantitative scores describing the strength of association between each GO term and human gene were computed (for a total of 4333⋅21,341 ~ 92 × 10 gene/term scores).
Interaction effects between genes were not computed, due to the fact that the sample size did not yield sufficient statistical power.
