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Intergenic distance between two genes are defined as the closest distance between them, using 5' or 3' end.
Correlation-based network inference methods assume that correlated expression levels between two genes are indicative of a regulatory interaction.
Given that the grapevine genome is still a work in progress with many unanchored scaffolds and whole regions with unsecure orientations, we can anticipate that scaffolds will be inserted or re-oriented and that the chosen numbering method will not lead to the risk of running out of numbers in the case that the gaps between two genes are larger than foreseen.
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Interaction between two genes is mediated by gene products.
A natural distance between two genes is the distance between their corresponding natural vectors.
Quantifying the functional relatedness between two genes is not trivial; often existing information about gene function are exploited to infer functional relationships among genes.
In the context of synthetic lethal interaction data alone, the global similarity of synthetic lethal interaction patterns between two genes is used to predict gene function.
However, the ability to demonstrate interactions between two genes is restricted to those that result in a measurable change in phenotype, such as fitness.
Each gene loci is a range of base pairs and the distance between two genes was defined as the head to tail distance except when a miRNA is in the intron of an mRNA.
This approach helps discard spurious correlation co-efficients i.e. arrangements where a large proportion of the correlation between two genes is actually attributable to the presence of a third gene.
The remaining inter-gene variants between two genes were grouped together.
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