ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

Area of Science:

• Computational Biology
• Systems Biology
• Bioinformatics

Background:

• High-throughput techniques generate extensive gene transcription profiling time series data.
• Researchers require tools to analyze temporal gene expression dynamics.
• Existing methods may lack the flexibility to handle diverse data types.

Purpose of the Study:

• To introduce the ReTrOS toolbox for reconstructing temporal transcriptional activity.
• To provide MATLAB-based implementations of ReTrOS-Smooth and ReTrOS-Switch methods.
• To facilitate the analysis of gene and protein expression time series data.

Main Methods:

• Utilizes differential equation models integrating transcription, translation, and degradation.
• Employs fitting procedures for time series data (mRNA or protein reporter).
• Incorporates statistical analyses, graphical interface, and model visualization.

Main Results:

• Successfully reconstructed temporal transcriptional activity from mRNA and protein reporter data.
• Demonstrated application in analyzing the circadian clock in Arabidopsis thaliana.
• Showcased the utility of reconstructed profiles for studying cell lines and conditions.

Conclusions:

• ReTrOS toolbox enables inference of transcriptional activity changes from expression time series.
• Flexible model accommodates data from any organism and various technologies.
• Provides valuable time series analysis for further modeling and hypothesis generation.