Tag Archives: database

EVLncRNAs – the current largest database for experimentally validated lncRNAs

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few ...

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Identification of long non-coding RNA in the horse transcriptome

Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet to be characterized in the horse. The most recent equine transcriptome based on RNA-seq from several tissues was a prime opportunity to obtain a concurrent long non-coding RNA (lncRNA) database. ...

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LncATLAS – a database for subcellular localisation of long noncoding RNAs

lncRNA

The subcellular localisation of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localisation of newly-discovered lncRNAs involves time-consuming and costly experimental methods. Researchers from the Centre for Genomic Regulation and the University of Bern have created “LncATLAS”, a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. Altogether, 6768 GENCODE-annotated lncRNAs are ...

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KTCNlncDB – a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas

lncRNA

Keratoconus (KTCN, OMIM 148300) is a degenerative eye disorder characterized by progressive stromal thinning that leads to a conical shape of the cornea, resulting in optical aberrations and even loss of visual function. The biochemical background of the disease is poorly understood, which motivated researchers from the Medical University of Warsaw to perform RNA-Seq experiment, aimed at better characterizing the ...

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LincSNP 2.0 – an updated database for linking disease-associated SNPs to human long non-coding RNAs

lncrna

Researchers from Harbin Medical University describe LincSNP 2.0, an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, the researchers have updated the database with more data and several new features, including: expanding disease-associated SNPs in human lncRNAs; ...

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Logic programming to infer complex RNA expression patterns from RNA-seq data

lncRNA

To meet the increasing demand in the field, numerous long noncoding RNA (lncRNA) databases are available. Given many lncRNAs are specifically expressed in certain cell types and/or time-dependent manners, most lncRNA databases fall short of providing such profiles. Researchers at the University of Louisville have developed a strategy using logic programming to handle the complex organization of organs, their tissues ...

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FARNA – knowledgebase of inferred functions of non-coding RNA transcripts

lncRNA

Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, researchers from the King Abdullah University of Science and Technology present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and ...

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Navigating the dynamic landscape of long noncoding RNA and protein-coding gene annotations in GENCODE

lncRNA

Our understanding of the transcriptional potential of the genome and its functional consequences has undergone a significant change in the last decade. This has been largely contributed by the improvements in technology which could annotate and in many cases functionally characterize a number of novel gene loci in the human genome. Keeping pace with advancements in this dynamic environment and ...

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LncVar – a database of genetic variation associated with long noncoding genes

Long noncoding RNAs (lncRNAs) are essential in many molecular pathways, and are frequently associated with disease, but the mechanisms of most lncRNAs have not yet been characterized. Genetic variations, including SNPs and structural variations, are widely distributed in the genome, including lncRNA gene regions. As the number of studies on lncRNAs grows rapidly, it is necessary to evaluate the effects ...

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Long non-coding RNA Databases in Cardiovascular Research

lncrna

With rising interest in the regulatory functions of long non-coding RNAs (lncRNAs) in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories specialized in lncRNAs have been developed, which make use of huge high-throughput data ...

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