International Workshop on Hybrid Systems Biology

Hybrid Systems Biology pp 3-19

Reconstructing Statistics of Promoter Switching from Reporter Protein Population Snapshot Data

Conference paper

DOI: 10.1007/978-3-319-26916-0_1

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9271)
Cite this paper as:
Cinquemani E. (2015) Reconstructing Statistics of Promoter Switching from Reporter Protein Population Snapshot Data. In: Abate A., Šafránek D. (eds) Hybrid Systems Biology. Lecture Notes in Computer Science, vol 9271. Springer, Cham

Abstract

The use of fluorescent reporter proteins is an established experimental approach for dynamic quantification of gene expression over time. Yet, the observed fluorescence levels are only indirect measurements of the relevant promoter activity. At the level of population averages, reconstruction of mean activity profiles from mean fluorescence profiles has been addressed with satisfactory results. At the single cell level, however, promoter activity is generally different from cell to cell. Making sense of this variability is at the core of single-cell modelling, but complicates the reconstruction task. Here we discuss reconstruction of promoter activity statistics from time-lapse population snapshots of fluorescent reporter statistics, as obtained e.g. by flow-cytometric measurements of a dynamical gene expression experiment. After discussing the problem in the framework of stochastic modelling, we provide an estimation method based on convex optimization. We then instantiate it in the fundamental case of a single promoter switch, reflecting a typical random promoter activation or deactivation, and discuss estimation results from in silico experiments.

Keywords

Identification Gene regulatory networks Doubly stochastic process 

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.INRIA Grenoble – Rhône-AlpesSaint-Ismier CEDEXFrance

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