LncATLAS database for subcellular localization of long noncoding RNAs

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 lncRN...

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Bibliographic Details
Published in:RNA (Cambridge) 2017-07, Vol.23 (7), p.1080-1087
Main Authors: Mas-Ponte, David, Carlevaro-Fita, Joana, Palumbo, Emilio, Hermoso Pulido, Toni, Guigo, Roderic, Johnson, Rory
Format: Article
Language:English
Subjects:
Cell lines
Cell Nucleus - genetics
Chromatin
Computational Biology - methods
Cytoplasm
Cytoplasm - genetics
Databases, Genetic
Humans
lncRNA
Localization
Long noncoding RNA
Molecular Sequence Annotation
Nucleus
Organelles
Research methodology
Ribonucleic acid
RNA
RNA, Long Noncoding - metabolism
Sequence Analysis, RNA
Software
Subcellular localization
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Summary: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.
ISSN:1355-8382
1469-9001
DOI:10.1261/rna.060814.117