TockyLocus: Quantitative Analysis Methods for Flow Cytometric Fluorescent Timer Data

TL;DR

This paper introduces the TockyLocus R package with algorithms for quantitative analysis of Fluorescent Timer data, improving the interpretation of cellular dynamics captured by Tocky tools in flow cytometry.

Contribution

It presents a novel data categorization method and an R package for standardized, quantitative analysis of Fluorescent Timer flow cytometry data, enhancing biological insights.

Findings

The five-locus approach effectively captures Timer profile dynamics.

The TockyLocus package enables standardized data analysis and visualization.

Algorithms improve the interpretation of cellular temporal changes.

Abstract

Fluorescent Timer proteins, which spontaneously change their emission spectra over time, are valuable tools for analyzing temporal changes in cellular activities at the single-cell level. Traditional analysis of Fluorescent Timer data has mostly relied on conventional flow cytometric methods, which lacks the sophistication needed for detailed quantitative analysis. Recently, we developed the Timer-of-Cell-Kinetics-and-Activity (Tocky) tools, employing transgenic reporter systems using an mCherry mutant Timer protein, Fast-FT, to analyze these changes, implementing data preprocessing methods for Timer fluorescence. Despite this advancement, the computational implementation of effective quantitative analysis methods for Fluorescent Timer data has been lacking. In this study, we introduce rigorous algorithms for a data categorization method, designated as the Tocky locus approach, which uses normalized and trigonometric-transformed Fluorescent Timer data, suitable for quantitative analysis. We found that the five-locus approach, which categorizes Timer fluorescence into five categories, optimally captures the dynamics of Timer profiles, thus enabling effective quantitative statistical analysis and biological interpretation. The current study has developed comprehensive tools for data categorization, visualization, and statistical analysis optimized to Tocky Locus data. These algorithms have been implemented in the TockyLocus package, a new R package designed to facilitate the quantitative analysis of Timer fluorescence data. This toolkit is expected to significantly enhance the utility of experimental systems using Fluorescent Timer proteins, particularly the Tocky tools, by standardizing methods for analyzing dynamic cellular events and responses.