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ReTrOS : a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.
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Minas, Giorgos, Momiji, Hiroshi, Jenkins, Dafyd J., Costa, Maria J. (Maria João), Rand, David A. and Finkenstädt, Bärbel (2017) ReTrOS : a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. BMC Bioinformatics, 18 (316). doi:10.1186/s12859-017-1695-8 ISSN 1471-2105.
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Official URL: https://doi.org/10.1186/s12859-017-1695-8
Abstract
Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to researchers. The ReTrOS toolbox (Reconstructing Transcription Open Software) provides MATLAB-based implementations of two related methods, namely ReTrOS-Smooth and ReTrOS-Switch, for reconstructing the temporal transcriptional activity profile of a gene from given mRNA expression time series or protein reporter time series. The methods are based on fitting a differential equation model incorporating the processes of transcription, translation and degradation.The toolbox provides a framework for model fitting along with statistical analyses of the model with a graphical interface and model visualisation. We highlight several applications of the toolbox, including the reconstruction of the temporal cascade of transcriptional activity inferred from mRNA expression data and protein reporter data in the core circadian clock in Arabidopsis thaliana, and how such reconstructed transcription profiles can be used to study the effects of different cell lines and conditions.The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.
| Item Type: | Journal Article | ||||||
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Mathematics Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre |
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| SWORD Depositor: | Library Publications Router | ||||||
| Journal or Publication Title: | BMC Bioinformatics | ||||||
| Publisher: | BioMed Central Ltd. | ||||||
| ISSN: | 1471-2105 | ||||||
| Official Date: | 26 June 2017 | ||||||
| Dates: |
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| Volume: | 18 | ||||||
| Number: | 316 | ||||||
| Number of Pages: | 11 | ||||||
| DOI: | 10.1186/s12859-017-1695-8 | ||||||
| Status: | Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Reuse Statement (publisher, data, author rights): | ** From Europe PMC via Jisc Publications Router. ** Licence for this article: cc by | ||||||
| Access rights to Published version: | Open Access (Creative Commons) |
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