title: AURA 2: Empowering discovery of post-transcriptional networks.
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 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.
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Erik
authors.initials: E
authors.lastname: Dassi
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Angela
authors.initials: A
authors.lastname: Re
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Leo
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Toma
authors.initials: T
authors.lastname: Tebaldi
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Pasini
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Peroni
authors.affiliation: Laboratory of Translational Genomics; Centre for Integrative Biology; University of Trento; Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Quattrone
keywords: CLIP; RNA modification; RNA-binding protein; UTR; cis-element; database; non-coding RNA; post-transcriptional regulation; regulatory network; translatome