Author: Dr. Masahiro Ono
Date: 14 November 2024
Introduction: Fluorescent Timer as Experimental Tool and Development of the Tocky Concept
The potential of Fluorescent Timer proteins
Fluorescent Timer proteins uniquely alter their emission spectra over time, making them powerful tools for monitoring dynamic cellular processes. These proteins are pivotal for understanding the intricate temporal dynamics of cellular events. Despite their potential, analyzing Timer fluorescence data in flow cytometry is often hampered by variability in instrument settings and the lack of standardized data preprocessing methods.
Tocky: A Breakthrough in Fluorescent Timer Analysis
A significant advancement was made in 2018 when the Ono lab introduced Tocky, a novel concept for analyzing Fluorescent Timer data. This approach encompasses data normalization and transformation methods (see Introduction). However, a computational implementation of this methodology was not yet available.
The breakthrough in the anslysis of Fluorescent Timer data was the introduction of the polar coordinate, or trigonometric transformation of Timer fluorescence data, which produces the key variables: Timer Angle and Timer Intensity.
However, to effectively use the approach, a dedicated computational tool was required to normalize and transform Timer fluorescence data. To address these challenges, we have recently developed the TockyPrep package. This R package provides a comprehensive suite of tools designed to automate the preprocessing, normalization, and trigonometric transformation of Timer fluorescence data. TockyPrep specifically addresses the normalization of immature and mature Timer fluorescence as a critical step for robust downstream analysis.
TockyLocus: The R Package for Quantitative Analysis of Fluorescent Timer Data
Aim of the TockyLocus Package
The aim of the TockyLocus package is to standardize quantitative analysis and visualization techniques for flow cytometric Fluorescent Timer data. It focuses on data categorization using Timer Angle data, which represents the temporal maturation dynamics of Timer proteins.
Features of the TockyLocus Package
Timer Data Categorization Method:
- This feature enables quantitative analysis and effective visualization of Timer fluorescence dynamics. Precisely, Timer Angle data is categorized into the five loci. This allows quantitative analysis of cell dynamics across Timer loci, enabling effective visualization and statistical analysis.
Visualization Tools:
- The package includes functions to visualize Tocky Locus.
Statistical Analysis Methods:
- Dedicated statistical methods are implemented for group-wise comparison of Tocky Locus data.
Availability
- TockyLocus is freely available for distribution via GitHub:
Link to the repository: TockyLocus on GitHub
Getting Started with TockyLocus
To begin using TockyLocus, install the package from GitHub using the following command:
# Install TockyLocus from GitHub
devtools::install_github("MonoTockyLab/TockyLocus")Package Documentation
The TockyLocus package documentation is available online:
This site includes all the function reference manuals and vignettes (tutorials).
In addition to the HTML manual pages, a PDF manual for the TockyLocus package is available. You can find it in the installed package directory under doc/, or you can access it directly from GitHub.
Copyright, License, and Citation Guidelines
Copyright
All code and original graphical content within the TockyPrep package, including anime-like characters and logos, are copyrighted by Masahiro Ono.
License
The distribution and modification are governed by the Apache License 2.0, which ensures that all users have the freedom to use and change the software in a way that respects the original authorship. See the LICENSE file for more information.
Citing TockyLocus
If you use TockyLocus in your research, please cite:
Masahiro Ono (2024). TockyLocus: Quantitative Analysis Methods for Flow Cytometric Fluorescent Timer Data. arXiv:2411.09386 [q-bio.QM]. Available at:https://arxiv.org/abs/2411.04111.
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Further Resources
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The Ono Lab (MonoTockyLab)
The Masahiro Ono Lab (MonoTockyLab) offers innovative approaches to analyzing omics and flow cytometric data. The lab is particularly well-known for their development of Timer-of-cell-kinetics-and-Activity (Tocky) and integrated analysis of immunological data using both experiments and computational analysis.
Principal Investigator: Dr. Masahiro Ono, Reader in Immunology at Imperial College London.
Dr. Ono is the creator and developer of Tocky. He innovated the transgenic and computational technologies that constitute Tocky.
In 2008, Dr. Ono initiated his pioneering transition from molecular immunology to becoming an Integrated Experimental and Computational Immunologist, demonstrating his visionary leadership and pioneering spirit in the development and application of multidimensional analysis and computational methods to address experimental and immunological problems. Tocky represents one of the fusion technologies that Dr. Ono has both created and developed.
Tocky employs the Fluorescent Timer protein to analyze the temporal dynamics of cell activities and development in vivo. His lab integrates molecular biology, immunology, and computational analysis to develop novel research tools, thereby enhancing the understanding of immune cell biology.
Contact and More
Email: 
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BlueSky: 
Professional Homepage: Imperial College London - Masahiro Ono