LncATLAS database for subcellular localization of long noncoding RNAs

  1. Rory Johnson3,4
  1. 1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
  2. 2Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
  3. 3Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
  4. 4Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
  5. 5Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain
  1. Corresponding author: rory.johnson{at}dkf.unibe.ch
  1. 6These authors contributed equally to this work.

Abstract

The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created “lncATLAS,” a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.

Keywords

  • Received January 23, 2017.
  • Accepted March 31, 2017.

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

| Table of Contents