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While SNP changes must be upstream (causal) of gene expression and phenotype manifestations, this does not preclude some SNPs from modifying the action of other SNPs, and the effect of such modifiers may become apparent only in particular contexts.
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High-throughput technologies enable nowadays to tackle the problem of causal inference of gene networks from experimental data [ 3, 26- 28] on a genomic scale.
Correlations between ED parameters make it difficult to ascertain the causal factor of gene expression change from the parameter selected in a model.
Bi-allelic alteration, such as homozygous deletion, or concerted genetic and epigenetic changes, are well documented causal mechanisms of gene disruption.
For gene expression data the causal effect of gene X on gene Y can be defined as the number of units gene Y changes in expression, if the expression of gene X is experimentally altered by one unit.
The transcript polymorphisms discovered here should greatly facilitate identification of the causal genes and gene variants.
Uncovering causal relations of genes from static, observational data alone is challenging due to the ambiguities of transferring associations into causal information.
He later defined epigenetics as "causal interactions of genes and their products which bring the phenotype into being' (Waddington 1975).
For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products.
But, the argument goes, in biological systems the causal role of genes is in fact tightly interconnected with the roles of many other factors (often loosely lumped together as "environmental").
Our approach utilizes the causal membership of genes and the hierarchical organization of the transcriptional regulatory network leading to two groups of periodic genes with a well defined direction of information flow.
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