NRED: a database of long noncoding RNA expression

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.
Nucleic Acids Research (Impact Factor: 9.11). 11/2008; 37(Database issue):D122-6. DOI: 10.1093/nar/gkn617
Source: PubMed


In mammals, thousands of long non-protein-coding RNAs (ncRNAs) (>200 nt) have recently been described. However, the biological significance and function of the vast majority of these transcripts
remain unclear. We have constructed a public repository, the Noncoding RNA Expression Database (NRED), which provides gene
expression information for thousands of long ncRNAs in human and mouse. The database contains both microarray and in situ hybridization data, much of which is described here for the first time. NRED also supplies a rich tapestry of ancillary information
for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense
relationships. The database is available at, and the web interface enables both advanced searches and data downloads. Taken together, NRED should significantly advance
the study and understanding of long ncRNAs, and provides a timely and valuable resource to the scientific community.

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Available from: Marcel Dinger,
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    • "Notably, lncRNA-specific databases have been recently emerging. These public repositories can be listed as follows: LncRNAdb (Amaral et al., 2011), LNCipedia (Volders et al., 2013), PlantNATsDB (Chen et al., 2012), NRED (Dinger et al., 2009), and PLncDB (Jin et al., 2013). Of these, PlantNATsDB and PLncDB are specifically programmed for plant lncRNAs. "
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    ABSTRACT: Accumulating published reports have confirmed the critical biological role (e.g., cell differentiation, gene regulation, stress response) for plant long non-coding RNAs (lncRNAs). However, a literature-derived database with the aim of lncRNA curation, data deposit and further distribution remains still absent for this particular lncRNA clade. PLNlncRbase has been designed as an easy-to-use resource to provide detailed information for experimentally identified plant lncRNAs. In the current version, PLNlncRbase has manually collected data from nearly 200 published literature, covering a total of 1187 plant lncRNAs in 43 plant species. The user can retrieve plant lncRNA entries from a well-organized interface through a keyword search by using the name of plant species or a lncRNA identifier. Each entry upon a query will be returned with detailed information for a specific plant lncRNA, including the species name, a lncRNA identifier, a brief description of the potential biological role, the lncRNA sequence, the lncRNA classification, an expression pattern of the lncRNA, the tissue/developmental stage/condition for lncRNA expression, the detection method for lncRNA expression, a reference literature, and the potential target gene(s) of the lncRNA extracted from the original reference. This database will be regularly updated to greatly facilitate future investigations of plant lncRNAs pertaining to their biological significance. The PLNlncRbase database is now freely available at Copyright © 2015. Published by Elsevier B.V.
    Gene 07/2015; 573(2). DOI:10.1016/j.gene.2015.07.069 · 2.14 Impact Factor
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    • "LncRNAs are usually divided into five categories: sense, antisense, bidirectional, intronic, and intergenic. In recent years, a large number of lncRNAs have been identified, prompting the creation of the human lncRNA database, which provides lncRNA expression profiles and other important information [8]. The abnormal expression of lncRNAs has been implicated in a range of diseases, including cancer [9]. "
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    ABSTRACT: Background Long noncoding RNAs (lncRNAs) have been shown to be involved in the development and progression of lung cancer. However, the roles of lncRNAs in lung cancer are not well understood. Methodology/Principal Findings We used a high-throughput microarray to compare the lncRNA and messenger RNA (mRNA) expression profiles in lung adenocarcinoma and normal tissue (NT) samples. Several candidate adenocarcinoma-associated lncRNAs were verified by real-time quantitative reverse transcription polymerase chain reaction (PCR) analysis. Using abundant and varied probes, we were able to assess 30,586 lncRNAs and 26,109 mRNAs in our microarray. We found that 2,420 lncRNAs and 1,109 mRNAs were differentially expressed (≥2-fold change) in lung adenocarcinoma samples and NT, indicating that many lncRNAs were significantly upregulated or downregulated in lung adenocarcinoma. We also found, via quantitative PCR, that 19 lncRNAs were aberrantly expressed in lung adenocarcinoma compared with matched histologically normal lung tissues. Among these, LOC100132354 and RPLP0P2 were the most aberrantly expressed lncRNAs, as estimated by quantitative PCR in 100 pairs of lung adenocarcinoma and NT samples. Conclusions/Significance Our study ascertained the expression patterns of lncRNAs in lung adenocarcinoma by microarray. The results revealed that many lncRNAs were differentially expressed in lung adenocarcinoma tissues and NT, suggesting that they may play a key role in tumor development.
    PLoS ONE 08/2014; 9(8):e104044. DOI:10.1371/journal.pone.0104044 · 3.23 Impact Factor
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    • "It was observed that lncRNAs are highly abundant in cells, but their importance for the regulation of gene function is still argued (Wang et al., 2004; Dinger et al., 2009). There are not many examples of functional lncRNAs for which the mechanisms of action are known, but this number is growing. "
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    ABSTRACT: Long non-coding RNAs (lncRNAs) are ubiquitously expressed RNA molecules of more than 200 nucleotides without substantial ORFs. LncRNAs could act as epigenetic regulators of gene expression affecting transcription, mRNA stability and transport, and translation, although, precise functions have been attributed to only few of them. Competing endogenous RNAs (ceRNAs) represent one recently emerged type of functional lncRNAs that share microRNA recognition sequences with mRNAs and may compete for microRNA binding and thus affect regulation and function of target mRNAs. We studied the epigenetic regulation of the BARD1 gene. The BARD1 protein acts as tumor suppressor with BRCA1. In cancer, mRNAs encoding the tumor suppressor full length BARD1 are often down-regulated while the expression of oncogenic truncated isoforms is boosted. We found that the BARD1 3'UTR is almost 3000 nt long and harbors a large number of microRNA binding elements. In addition we discovered a novel lncRNA, BARD1 9'L, which is transcribed from an alternative promoter in intron 9 of the BARD1 gene and shares part of the 3'UTR with the protein coding BARD1 mRNAs. We demonstrate with the example of two microRNAs, miR-203 and miR-101, that they down-regulate the expression of FL BARD1 and cancer-associated BARD1 mRNAs, and that BARD1 9'L counteracts the effect of miR-203 and miR-101, As BARD1 9'L is abnormally over-expressed in human cancers, we suggest it might be a tumor promoting factor and treatment target.
    The International Journal of Biochemistry & Cell Biology 07/2014; 54. DOI:10.1016/j.biocel.2014.06.018 · 4.05 Impact Factor
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