AURA 2: Empowering discovery of post-transcriptional networks

Translation
E DassiAlessandro Quattrone

Abstract

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 line...Continue Reading

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Citations

Jun 14, 2014·Cell Death and Differentiation·S ZaccaraA Inga
Nov 26, 2015·Nucleic Acids Research·Jörg FallmannIvo L Hofacker
Aug 9, 2015·Nucleic Acids Research·Erik Dassi, Alessandro Quattrone
Apr 22, 2015·Nucleic Acids Research·Damian SmedleyArek Kasprzyk
Feb 6, 2015·BMC Genomics·Yu-Cheng T YangZhi John Lu
Nov 5, 2014·Frontiers in Cell and Developmental Biology·Erik Dassi, Alessandro Quattrone
Aug 10, 2016·Bioinformatics·Gianluca CorradoAndrea Passerini
May 10, 2017·Cancer Biology & Therapy·Shruti BhargavaKumaravel Somasundaram
Sep 25, 2015·Scientific Reports·Erik DassiAlessandro Quattrone
Dec 28, 2018·Nucleic Acids Research·Hui YuYu Shyr
May 9, 2019·Wiley Interdisciplinary Reviews. RNA·Xiaoyong PanHong-Bin Shen
May 4, 2018·Frontiers in Immunology·Theresa KordaßStefan B Eichmüller
Jan 27, 2017·Non-coding RNA·Ying YiDong Wang
Oct 17, 2017·Frontiers in Molecular Biosciences·Erik Dassi
Aug 19, 2020·Briefings in Bioinformatics·Haitao YangJing Wu
Oct 3, 2020·Frontiers in Molecular Biosciences·Paola ZuccottiErik Dassi
Nov 22, 2020·Pharmacological Reviews·Torsten Schöneberg, Ines Liebscher
Oct 16, 2020·Proceedings of the National Academy of Sciences of the United States of America·Biljana Culjkovic-KraljacicKatherine L B Borden
Jul 22, 2021·The Journal of Experimental Medicine·Roberto VendraminEleonora Leucci
Dec 21, 2021·Briefings in Bioinformatics·Junkang WeiYu Li

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Methods Mentioned

BETA
CLIP
CLASH
RNA-seq

Software Mentioned

AURA
Ensembl
Cufflinks
UTR Browser
UCSC Genome Browser
BioMart
AURAlight
CytoscapeWeb
MySQL Community Server
VARNA

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