Model-based extension of high-throughput to high-content data.
BACKGROUND
High-quality quantitative data is a major limitation in systems biology. The experimental data used in systems biology can be assigned to one of the following categories: assays yielding average data of a cell population, high-content single cell measurements and high-throughput techniques generating single cell data for large cell populations. For modeling purposes, a combination of data from different categories is highly desirable in order to increase the number of observable species and processes and thereby maximize the identifiability of parameters.


RESULTS
In this article we present a method that combines the power of high-content single cell measurements with the efficiency of high-throughput techniques. A calibration on the basis of identical cell populations measured by both approaches connects the two techniques. We develop a mathematical model to relate quantities exclusively observable by high-content single cell techniques to those measurable with high-content as well as high-throughput methods. The latter are defined as free variables, while the variables measurable with only one technique are described in dependence of those. It is the combination of data calibration and model into a single method that makes it possible to determine quantities only accessible by single cell assays but using high-throughput techniques. As an example, we apply our approach to the nucleocytoplasmic transport of STAT5B in eukaryotic cells.


CONCLUSIONS
The presented procedure can be generally applied to systems that allow for dividing observables into sets of free quantities, which are easily measurable, and variables dependent on those. Hence, it extends the information content of high-throughput methods by incorporating data from high-content measurements.
Pfeifer
Andrea C
AC
Division Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Kaschek
Daniel
D
Bachmann
Julie
J
Klingmüller
Ursula
U
Timmer
Jens
J
D021581:Active Transport, Cell Nucleus; D000818:Animals; D002138:Calibration; D002467:Cell Nucleus / Q000378:metabolism; D048429:Cell Size; D005434:Flow Cytometry; D036681:Fluorescence Recovery After Photobleaching; D051379:Mice; D008853:Microscopy; D008954:Models, Biological; D041681:NIH 3T3 Cells; D050799:STAT5 Transcription Factor / Q000378:metabolism; D059010:Single-Cell Analysis; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors
D050799:STAT5 Transcription Factor