Lantern: an integrative repository of functional annotations for lncRNAs in the human genome.

Szczegóły
Abstrakt

Tytuł:: Lantern: an integrative repository of functional annotations for lncRNAs in the human genome.
Autorzy:: Daulatabad SV; Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA.
Srivastava R; Department of Surgery, Indiana Center for Regenerative Medicine and Engineering (ICRME), Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Janga SC; Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA. .; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, 975 West Walnut Street, Indianapolis, IN, 46202, USA. .; Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA. .
Źródło:: BMC bioinformatics [BMC Bioinformatics] 2021 May 26; Vol. 22 (1), pp. 279. Date of Electronic Publication: 2021 May 26.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Original Publication: [London] : BioMed Central, 2000-
MeSH Terms:: RNA, Long Noncoding*/genetics
Genome, Human ; Humans ; Molecular Sequence Annotation
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Grant Information:: R01 GM123314 United States GM NIGMS NIH HHS; R01GM123314 United States GM NIGMS NIH HHS
Contributed Indexing:: Keywords: Coding potential; Expression; Interaction; LncRNA; Ontology; Snps; eCLIP; eQTL
Substance Nomenclature:: 0 (RNA, Long Noncoding)
Entry Date(s):: Date Created: 20210527 Date Completed: 20210528 Latest Revision: 20230920
Update Code:: 20240105
PubMed Central ID:: PMC8157669
DOI:: 10.1186/s12859-021-04207-3
PMID:: 34039271
: Czasopismo naukowe

Pełny tekst

Background: With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare.
Results: We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Lantern's annotations were benchmarked against lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform.
Conclusions: Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.

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