LNCipedia 5: towards a reference set of human long non-coding RNAs
Open accessAbstract
While long non-coding RNA (lncRNA) research in the past has primarily focused on the discovery of novel genes, today it has shifted towards functional annotation of this large class of genes. With thousands of lncRNA studies published every year, the current challenge lies in keeping track of which lncRNAs are functionally described. This is further complicated by the fact that lncRNA nomenclature is not straightforward and lncRNA annotation is scattered across different resources with their own quality metrics and definition of a lncRNA. To overcome this issue, large scale curation and annotation is needed. Here, we present the fifth release of the human lncRNA database LNCipedia (https://lncipedia.org). The most notable improvements include manual literature curation of 2482 lncRNA articles and the use of official gene symbols when available. In addition, an improved filtering pipeline results in a higher quality reference lncRNA gene set.
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The lncRNA class gene LOC100506023 originally associated by proximity with CpG cg11091478 was subsequently annotated as lnc-TNFSF4-3.
“The lncRNA class gene LOC100506023 originally associated by proximity with CpG cg11091478 was subsequently annotated as lnc-TNFSF4-3 (Volders et al., 2019).”
From Epigenome-wide DNA methylation in unipolar depression: predictive biomarker of antidepressant treatment response? (2024) · cites this paper as Volders et al., 2019
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- Authors
- Volders, P.-J., Anckaert, J., Verheggen, K., Nuytens, J., Martens, L., Mestdagh, P., & Vandesompele, J.
- Affiliations
- Ghent University (BE)
- Corresponding author
- Volders, Pieter-Jan
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-29
- Volume
- 47
- Issue
- D1
- Pages
- D135-D139
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6323963
- OpenAlex
- W2899028887
- Cited by
- 547
- References
- 29
- Citations by year
- 2026: 30 · 2025: 43 · 2024: 61 · 2023: 95 · 2022: 101 · 2021: 97 · 2020: 85 · 2019: 34 · 2018: 1
- FWCI
- 17.76
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
- Funders
- Ghent University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- long non-coding RNA, lncRNA database, lncRNA annotation, functional annotation, literature curation, gene symbols
- MeSH terms
- Humans, Computational Biology, Genomics, Databases, Nucleic Acid, Molecular Sequence Annotation, RNA, Long Noncoding, Web Browser
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