The development of quantitative models of signal transduction, as well as parameter estimation to improve existing models, depends on the ability to obtain quantitative information about various proteins that are part of the signaling pathway. However, commonly-used measurement techniques such as Western blots and mobility shift assays provide only qualitative or semi-quantitative data which cannot be used for estimating parameters. This paper presents a solution of an inverse problem for quantitatively determining transcription factor profiles from green fluorescent protein (GFP) reporter data. We have used this technique to quantitatively characterize activation of the transcription factor NF-kB by the cytokine TNF-a. The obtained results are in good agreement with qualitative descriptions of NF-kB activation as well as semi-quantitative experimental data from the literature. While the presented approach has been applied to NF-kB and TNF-a signaling, it can be used to determine the profile of other transcription factors with only minor modifications.
Proceedings of the 2009 American Control Conference, St. Louis, Missouri, pp. 1688-1693 (2009)