LncATLAS database for subcellular localization of long noncoding RNAs.

Mas-Ponte, David; Carlevaro Fita, Joana; Palumbo, Emilio; Hermoso Pulido, Toni; Guigo, Roderic; Johnson, Rory (2017). LncATLAS database for subcellular localization of long noncoding RNAs. RNA - a publication of the RNA Society, 23(7), pp. 1080-1087. Cold Spring Harbor Laboratory Press 10.1261/rna.060814.117

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Medical Oncology
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Carlevaro Fita, Joana and Johnson, Rory Baldwin

Subjects:

600 Technology > 610 Medicine & health
000 Computer science, knowledge & systems
500 Science
500 Science > 570 Life sciences; biology

ISSN:

1355-8382

Publisher:

Cold Spring Harbor Laboratory Press

Language:

English

Submitter:

Joana Carlevaro Fita

Date Deposited:

29 May 2018 12:26

Last Modified:

29 May 2018 12:35

Publisher DOI:

10.1261/rna.060814.117

PubMed ID:

28386015

Uncontrolled Keywords:

chromatin cytoplasm lncRNA long noncoding RNA nucleus subcellular localization

BORIS DOI:

10.7892/boris.112921

URI:

https://boris.unibe.ch/id/eprint/112921

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