The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs. In particular, it allows to: (i) interactively visualize gene-level RNA dynamics; (ii) refine the model fit of experimental data; (iii) test alternative regulatory models; (iv) explore, independently from the availability of data, how the combined action of the RNA kinetic rates impacts on premature and mature RNA. INSPEcT-GUI is freely available within the R/Bioconductor package INSPEcT at http://bioconductor.org/packages/INSPEcT/. An HTML vignette including documentation on the tool startup and usage, executable examples, and a video demonstration, are available at: http://bioconductor.org/packages/release/bioc/vignettes/INSPEcT/inst/doc/INSPEcT_GUI.html.

de Pretis, S., Furlan, M., Pelizzola, M. (2020). INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. FRONTIERS IN GENETICS, 11 [10.3389/fgene.2020.00759].

INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species

Pelizzola M
Ultimo
2020

Abstract

The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs. In particular, it allows to: (i) interactively visualize gene-level RNA dynamics; (ii) refine the model fit of experimental data; (iii) test alternative regulatory models; (iv) explore, independently from the availability of data, how the combined action of the RNA kinetic rates impacts on premature and mature RNA. INSPEcT-GUI is freely available within the R/Bioconductor package INSPEcT at http://bioconductor.org/packages/INSPEcT/. An HTML vignette including documentation on the tool startup and usage, executable examples, and a video demonstration, are available at: http://bioconductor.org/packages/release/bioc/vignettes/INSPEcT/inst/doc/INSPEcT_GUI.html.
Articolo in rivista - Articolo scientifico
graphical user interface (GUI); mathematical modeling; RNA degradation; RNA processing; RNA synthesis; transcription;
English
2020
11
759
open
de Pretis, S., Furlan, M., Pelizzola, M. (2020). INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. FRONTIERS IN GENETICS, 11 [10.3389/fgene.2020.00759].
File in questo prodotto:
File Dimensione Formato  
Pretis-2020-Front Genet-VoR.pdf

accesso aperto

Descrizione: Article
Tipologia di allegato: Publisher’s Version (Version of Record, VoR)
Licenza: Creative Commons
Dimensione 1.91 MB
Formato Adobe PDF
1.91 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/446719
Citazioni
  • Scopus 3
  • ???jsp.display-item.citation.isi??? 4
Social impact