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AURA 2: Empowering discovery of post-transcriptional networks

Post-transcriptional regulation (PTR) of gene expression is now recognized as a major determinant of cell phenotypes. The recent availability of methods to map protein-RNA interactions in entire transcriptomes such as RIP, CLIP and their variants, together with global polysomal and ribosome profilin...

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Autores principales: Dassi, Erik, Re, Angela, Leo, Sara, Tebaldi, Toma, Pasini, Luigi, Peroni, Daniele, Quattrone, Alessandro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705823/
https://www.ncbi.nlm.nih.gov/pubmed/26779400
http://dx.doi.org/10.4161/trla.27738
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author Dassi, Erik
Re, Angela
Leo, Sara
Tebaldi, Toma
Pasini, Luigi
Peroni, Daniele
Quattrone, Alessandro
author_facet Dassi, Erik
Re, Angela
Leo, Sara
Tebaldi, Toma
Pasini, Luigi
Peroni, Daniele
Quattrone, Alessandro
author_sort Dassi, Erik
collection PubMed
description Post-transcriptional regulation (PTR) of gene expression is now recognized as a major determinant of cell phenotypes. The recent availability of methods to map protein-RNA interactions in entire transcriptomes such as RIP, CLIP and their variants, together with global polysomal and ribosome profiling techniques, are driving the exponential accumulation of vast amounts of data on mRNA contacts in cells, and of corresponding predictions of PTR events. However, this exceptional quantity of information cannot be exploited at its best to reconstruct potential PTR networks, as it still lies scattered throughout several databases and in isolated reports of single interactions. To address this issue, we developed the second and vastly enhanced version of the Atlas of UTR Regulatory Activity (AURA 2), a meta-database centered on mapping interaction of trans-factors with human and mouse UTRs. AURA 2 includes experimentally demonstrated binding sites for RBPs, ncRNAs, thousands of cis-elements, variations, RNA epigenetics data and more. Its user-friendly interface offers various data-mining features including co-regulation search, network generation and regulatory enrichment testing. Gene expression profiles for many tissues and cell lines can be also combined with these analyses to display only the interactions possible in the system under study. AURA 2 aims at becoming a valuable toolbox for PTR studies and at tracing the road for how PTR network-building tools should be designed. AURA 2 is available at http://aura.science.unitn.it.
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spelling pubmed-47058232016-01-15 AURA 2: Empowering discovery of post-transcriptional networks Dassi, Erik Re, Angela Leo, Sara Tebaldi, Toma Pasini, Luigi Peroni, Daniele Quattrone, Alessandro Translation (Austin) Research Paper Post-transcriptional regulation (PTR) of gene expression is now recognized as a major determinant of cell phenotypes. The recent availability of methods to map protein-RNA interactions in entire transcriptomes such as RIP, CLIP and their variants, together with global polysomal and ribosome profiling techniques, are driving the exponential accumulation of vast amounts of data on mRNA contacts in cells, and of corresponding predictions of PTR events. However, this exceptional quantity of information cannot be exploited at its best to reconstruct potential PTR networks, as it still lies scattered throughout several databases and in isolated reports of single interactions. To address this issue, we developed the second and vastly enhanced version of the Atlas of UTR Regulatory Activity (AURA 2), a meta-database centered on mapping interaction of trans-factors with human and mouse UTRs. AURA 2 includes experimentally demonstrated binding sites for RBPs, ncRNAs, thousands of cis-elements, variations, RNA epigenetics data and more. Its user-friendly interface offers various data-mining features including co-regulation search, network generation and regulatory enrichment testing. Gene expression profiles for many tissues and cell lines can be also combined with these analyses to display only the interactions possible in the system under study. AURA 2 aims at becoming a valuable toolbox for PTR studies and at tracing the road for how PTR network-building tools should be designed. AURA 2 is available at http://aura.science.unitn.it. Taylor & Francis 2014-01-29 /pmc/articles/PMC4705823/ /pubmed/26779400 http://dx.doi.org/10.4161/trla.27738 Text en Copyright © 2014 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
spellingShingle Research Paper
Dassi, Erik
Re, Angela
Leo, Sara
Tebaldi, Toma
Pasini, Luigi
Peroni, Daniele
Quattrone, Alessandro
AURA 2: Empowering discovery of post-transcriptional networks
title AURA 2: Empowering discovery of post-transcriptional networks
title_full AURA 2: Empowering discovery of post-transcriptional networks
title_fullStr AURA 2: Empowering discovery of post-transcriptional networks
title_full_unstemmed AURA 2: Empowering discovery of post-transcriptional networks
title_short AURA 2: Empowering discovery of post-transcriptional networks
title_sort aura 2: empowering discovery of post-transcriptional networks
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705823/
https://www.ncbi.nlm.nih.gov/pubmed/26779400
http://dx.doi.org/10.4161/trla.27738
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