FIGURE 1 

Illustrating the analogy between Ohm's Law and 'Omes Law'. The work of Nguyen and D'haeseleer extends a class of linear models for gene expression regulation that has a very direct and useful analogy to basic electricity theory. (A) In an electrical circuit, Ohm's Law, I=GV, describes the linear relation that exists between the current (I) through a resistor and the voltage (V) that drives it, the constant of proportionality being the conductivity (G) of the resistor. We use a color-coding scheme where a scale from white (G=0) to dark brown (G>0) represents conductivity, green (I<0) to red (I>0) via black (I=0) represents current, and blue (V<0) to yellow (V>0) via black (V=0) represents voltage. (B) In a gene regulatory network, changes in 'hidden' post-translational TF activity play the role of the voltage, while the resulting changes in mRNA expression level play that of the current. For any given TF, the regulatory strength of DNA binding sites in the upstream region, or 'conductivity', varies greatly between genes. The change in mRNA expression for a given gene is a weighted combination of the changes in activity of the TFs that bind to its upstream region. In the example shown, gene X is only controlled by factor A, while gene Y is controlled by both factor A and factor B. Therefore, while gene X is upregulated (red) in response to the increase in the activity of factor A (yellow), the decrease in the activity of factor B (blue) causes the net change in expression of gene Y to be zero (black). The many-to-many relationship between TF activities and mRNA expression levels can be summarized in the form of a linear matrix equation ('Omes Law'). (C) Schematic depiction of the iterative procedure used by Nguyen and D'heaseleer to simultaneously infer a matrix of condition-specific TF activity changes (blue/yellow) and a matrix of gene-specific motif strengths (white/brown), which together optimally explain the observed mRNA expression changes (green/red).