3. The method of claim 1 wherein said mutual information is pairwise mutual information.
1. A computer-implemented method for identifying a regulatory interaction between a transcription factor and a gene target of said transcription factor, the method comprising: a) providing a compendium of biochemical expression measurements reflecting gene expression for a set of biochemical species in an organism wherein at least a subset of said species are transcription factors and a second subset of said species are gene targets of transcription factors; b) in a specifically programmed computer, computing mutual information between members of said set of biochemical species; c) in a specifically programmed computer, applying a background correction to each said mutual information value so as to identify a set of those mutual information values that are significantly higher than background mutual information values, wherein the step of applying a background correction comprises the step of estimating a likelihood of the mutual information score, MI, for each possible pair of genes, by comparing the mutual information score for that pair to a background distribution of mutual information values, and wherein said set of mutual information values identified in step (c) identifies a regulatory interaction between a transcription factor and a gene target of said transcription factor; and d) outputting the identified regulatory interaction to a user interface.