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Protocols

LNCipedia specifications

Information


Unique identifier OMICS_04193
Name LNCipedia
Restrictions to use Academic or non-commercial use
Community driven No
Data access File download, Browse, Application programming interface
User data submission Allowed
Version 5.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Pieter-Jan Volders

Additional information


https://lncipedia.org/info

Publications for LNCipedia

LNCipedia citations

 (41)
library_books

The use of long non coding RNAs as prognostic biomarkers and therapeutic targets in prostate cancer

2018
Oncotarget
PMCID: 5945524
PMID: 29755696
DOI: 10.18632/oncotarget.25038

[…] n a boom in the development of databases that are designed specifically for lncRNAs. There are several databases that are dedicated to the curation of novel reported lncRNAs, including LncRNABase [], LNCipedia [], lncRNAdb [], LncRNAWiki [], NONCODE [], TANRIC [] and the ncRNA expression database []. Sequencing technology has evolved rapidly enough to allow lncRNA profiling at a single-cell resolu […]

library_books

The hypoxia responsive lncRNA NDRG OT1 promotes NDRG1 degradation via ubiquitin mediated proteolysis in breast cancer cells

2017
Oncotarget
PMCID: 5828211
PMID: 29535820
DOI: 10.18632/oncotarget.23732

[…] , and TopHat 2 (https://ccb.jhu.edu/software/tophat/indshex.tml) was used to align sequencing reads to human genome references (GRCh37/hg19). Then, these mapped reads were matched to lncRNAs from the Lncipedia database (http://www.lnciedia.org/) and were normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM) as the expression level of a given lncRNA using Cufflink (http […]

library_books

Alcohol and hepatitis virus dysregulated lncRNAs as potential biomarkers for hepatocellular carcinoma

2017
Oncotarget
PMCID: 5787460
PMID: 29416609
DOI: 10.18632/oncotarget.22921

[…] lncRNA read counts were generated from RNA-sequencing datasets via BEDtools coverageBed (https://github.com/arq5x/bedtools2) [] using lncRNA annotation files obtained from LNCipedia 3.0 (http://lncipedia.org/) [], a database curating 113,438 lncRNA transcripts from sources including the Broad Institute, Ensembl, Gencode, Refseq, and NONCODE. The read count tables were i […]

call_split

A Novel Y Specific Long Non Coding RNA Associated with Cellular Lipid Accumulation in HepG2 cells and Atherosclerosis related Genes

2017
Sci Rep
PMCID: 5711902
PMID: 29196750
DOI: 10.1038/s41598-017-17165-9
call_split See protocol

[…] ndations for probe melting temperature (Tm) values, GC content, and amplicon length provided by Thornton & Basu. All the primers for lincRNAs were designed from the DNA template sequence annotated on LNCipedia, the database for human lncRNA genes and transcripts. Primer sequences are available in Supplementary Table¬†. […]

library_books

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

2017
Sci Rep
PMCID: 5686184
PMID: 29138457
DOI: 10.1038/s41598-017-15822-7

[…] resulting set of candidate lncRNAs was used to build the final gene set and annotate novel lncRNAs as follows: candidate lncRNAs were merged with previous lncRNA annotations from both GENCODE V19 and LNCipedia (V2.1) using cuffmerge. The merged lncRNA annotation was further filtered to remove transcripts that had significant exonic overlap with GENCODE protein-coding genes. Specifically, we employ […]

library_books

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment

2017
Sci Rep
PMCID: 5656573
PMID: 29070806
DOI: 10.1038/s41598-017-14451-4

[…] AT. The transcripts that were not predicted as protein coding by either of the two methods were retained as candidate lncRNAs. The candidate lncRNAs were merged with previous lncRNAs from Gencode and Lncipedia to build a final lncRNA reference. This final lncRNA reference consisted of a total of 31,885 lncRNAs, which included 63 novel lncRNAs not annotated in the existing lncRNA databases (Fig.¬†, […]

Citations

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LNCipedia institution(s)
Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
LNCipedia funding source(s)
Supported by Ghent University; UGent-GOA LNCCA; Fund for Scientific Research Flanders [FWO].

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