On Observability and Reconstruction of Promoter Activity Statistics from Reporter Protein Mean and Variance Profiles
Reporter protein systems are widely used in biology for the indirect quantitative monitoring of gene expression activity over time. At the level of population averages, the relationship between the observed reporter concentration profile and gene promoter activity is established, and effective methods have been introduced to reconstruct this information from the data. At single-cell level, the relationship between population distribution time profiles and the statistics of promoter activation is still not fully investigated, and adequate reconstruction methods are lacking.
This paper develops new results for the reconstruction of promoter activity statistics from mean and variance profiles of a reporter protein. Based on stochastic modelling of gene expression dynamics, it discusses the observability of mean and autocovariance function of an arbitrary random binary promoter activity process. Mathematical relationships developed are explicit and nonparametric, i.e. free of a priori assumptions on the laws governing the promoter process, thus allowing for the decoupled analysis of the switching dynamics in a subsequent step. The results of this work constitute the essential tools for the development of promoter statistics and regulatory mechanism inference algorithms.
KeywordsGene regulation Doubly stochastic process Spectral analysis
- 2.Cinquemani, E.: Reconstruction of promoter activity statistics from reporter protein population snapshot data. In: 2015 54th IEEE Conference on Decision and Control (CDC), pp. 1471–1476, December 2015Google Scholar
- 13.Munsky, B., Trinh, B., Khammash, M.: Listening to the noise: Random fluctuations reveal gene network parameters. Mol. Syst. Biol. 5 (2009). Article ID 318Google Scholar