In this paper we will outline a proposal for an irreversible thermodynamic theory of gene regulation. This theory would allow us to have a proper integration of molecular biophysical data for both, normal and abnormal gene function within the cell, hence enabling biomedical applications. The formalism is based on ideas taken from Extended Irreversible Thermodynamics. We describe how to deal with experimental data (mRNA levels) for high throughput gene expression experiments (microarrays) in order to extract information relevant for the biological characterization of gene regulatory phenomena. We then derive explicit expressions for the gene expression intensity, the chemical potentials of transcription and their associated affinities, as well as the corresponding Maxwell relations. With the aid of these, we were able to show that a change in the expression level of a single gene may affect the expression levels of the other genes and therefore of the whole genome. (C) 2010 Elsevier B.V. All rights reserved.