LncATLAS database for subcellular localization of long noncoding RNAs
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- dc.contributor.author Mas Ponte, Davidca
- dc.contributor.author Carlevaro-Fita, Joanaca
- dc.contributor.author Palumbo, Emilioca
- dc.contributor.author Hermoso Pulido, Antonioca
- dc.contributor.author Guigó Serra, Rodericca
- dc.contributor.author Johnson, Roryca
- dc.date.accessioned 2018-03-22T08:44:34Z
- dc.date.issued 2017
- dc.description.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.
- dc.format.mimetype application/pdf
- dc.identifier.citation Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA. 2017 Jul;23(7):1080-7. DOI: 10.1261/rna.060814.117
- dc.identifier.doi http://dx.doi.org/10.1261/rna.060814.117
- dc.identifier.issn 1355-8382
- dc.identifier.uri http://hdl.handle.net/10230/34239
- dc.language.iso eng
- dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)ca
- dc.relation.ispartof RNA. 2017 Jul;23(7):1080-7
- dc.rights Copyright © 2017, RNA by RNA Society. Published version available at http://www.rnajournal.org/cgi/doi/10.1261/rna.060814.117
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.subject.keyword Long noncoding RNA
- dc.subject.keyword lncRNA
- dc.subject.keyword Subcellular localization
- dc.subject.keyword Cytoplasm
- dc.subject.keyword Chromatin
- dc.subject.keyword Nucleus
- dc.title LncATLAS database for subcellular localization of long noncoding RNAsca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion