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A larger PCC between two genes indicates that the genes have greater similarity.
A high Kendall tau between two genes indicates that their levels of expression vary in the same way: when the expression level of the first gene increases, the expression level of the other one increases also.
The correlation between the expression profiles in a gene expression dataset is modeled as a coexpression graph in which nodes represent genes and an unweighted edge between two genes indicates significant correlation between the two genes' expression profiles.
In contrast to relevance networks (where a missing edge between two genes indicates marginal independence), the absence of an edge between genes g1 and g2 in a GGM means that g1 and g2 are conditionally independent.
A functional relationship between two genes indicates that their products are used by the cell to perform a particular biological process (for example, two proteins both participating in the DNA damage response).
In the course of making these predictions, we constructed multiple functional linkage networks [FLNs where an edge between two genes indicates some level of shared function (Lee et al. 2004)], capturing different categories of biological relationships.
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Pairwise comparisons showed dS>dN and are almost equal between the two genes, indicating that both genes are in states of purifying and neutral selection.
Furthermore, although the very limited amount of change between all four genes indicates that their functions are conserved, we do observe that GH1 and GH2 may potentially have different subfunctions.
For gene co-expression networks, an edge between two genes may indicate that the corresponding expression traits are correlated in a given population of interest.
In our directed networks, each node correspond to a gene and the co-expression between two genes is indicated by an arc that connects the nodes corresponding to the two genes.
Note that this dynamic time order relation does not imply any causal relation between two genes but only indicates which one is expressed after the other.
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