Database

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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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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The Non-Coding RNA Ontology (NCRO) – a comprehensive resource for the unification of non-coding RNA biology

lncRNA

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this ...

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NPInter v3.0 – an upgraded database of noncoding RNA-associated interactions

Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs’ functions, researchers from the Chinese Academy of Sciences updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and ...

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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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CANTATAdb – a Collection of Plant Long Non-coding RNAs

lncRNA

Long non-coding RNAs (lncRNAs) represent a class of potent regulators of gene expression that are found in a wide array of eukaryotes, however, our knowledge about these molecules in plants is still very limited. In particular, a number of model plant species still lack comprehensive datasets of lncRNAs and their annotations and very little is known about their biological roles. ...

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deepBase v2.0 – identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

lncRNA

Small non-coding RNAs (e.g. miRNAs) and long non-coding RNAs (e.g. lincRNAs and circRNAs) are emerging as key regulators of various cellular processes. However, only a very small fraction of these enigmatic RNAs have been well functionally characterized. In this study, we describe deepBase v2.0, an updated platform, to decode evolution, expression patterns and functions of diverse ncRNAs across 19 species. ...

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