title: LncATLAS database for subcellular localization of long noncoding RNAs.
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.
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
authors.forename: David
authors.identifier: 0000-0001-7409-305X
authors.initials: D
authors.lastname: Mas-Ponte
authors.affiliation: Department of Clinical Research, University of Bern, 3008 Bern, Switzerland.|Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.
authors.forename: Joana
authors.identifier: 0000-0002-1674-2055
authors.initials: J
authors.lastname: Carlevaro-Fita
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.
authors.forename: Emilio
authors.initials: E
authors.lastname: Palumbo
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.
authors.forename: Toni
authors.identifier: 0000-0003-2016-6465
authors.initials: T
authors.lastname: Hermoso Pulido
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.|Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain.
authors.forename: Roderic
authors.identifier: 0000-0002-5738-4477
authors.initials: R
authors.lastname: Guigo
authors.affiliation: Department of Clinical Research, University of Bern, 3008 Bern, Switzerland.|Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.
authors.forename: Rory
authors.identifier: 0000-0003-4607-2782
authors.initials: R
authors.lastname: Johnson
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003593:Cytoplasm / Q000235:genetics*; D030541:Databases, Genetic; D006801:Humans; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D062085:RNA, Long Noncoding
keywords: chromatin; cytoplasm; lncRNA; long noncoding RNA; nucleus; subcellular localization