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

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 regulat...

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Bibliographic Details
Published in:Bioinformatics 2015-09, Vol.31 (17), p.2829-2835
Main Authors: de Pretis, Stefano, Kress, Theresia, Morelli, Marco J, Melloni, Giorgio E M, Riva, Laura, Amati, Bruno, Pelizzola, Mattia
Format: Article
Language:English
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Summary: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. 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. INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1. mattia.pelizzola@iit.it Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv288