Motivation: Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking. Results: INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design.

de Pretis, S., Kress, T., Morelli, M., Melloni, G., Riva, L., Amati, B., et al. (2015). INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. BIOINFORMATICS, 31(17), 2829-2835 [10.1093/bioinformatics/btv288].

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

Pelizzola M
Ultimo
2015

Abstract

Motivation: Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking. Results: INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design.
Articolo in rivista - Articolo scientifico
RNA dynamics, nascent RNA, mathematical modelling, transcriptional profiling
English
2015
31
17
2829
2835
reserved
de Pretis, S., Kress, T., Morelli, M., Melloni, G., Riva, L., Amati, B., et al. (2015). INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. BIOINFORMATICS, 31(17), 2829-2835 [10.1093/bioinformatics/btv288].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/447278
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