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By interacting tissue with the gene in the model (adding tissue to the right most box), the interaction p-value may provide a method of discovering categories where total expression is might not changed significantly but the pattern of gene expression with the category is altered or disrupted. Within a functional group, the interaction p-value represents how similar the patterns of gene expression are between the different tissues. One example of a functional group identified by a tissue*gene interaction might include a category such as ion transfer. Ion transfer is equally important to both nerve and muscle function, but the distribution of ion channels and many of the responsible genes may be quite different between the two.

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