Database

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

lncvar-feat

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

database

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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Integrating Large-Scale RNA-Seq and CLIP-Seq Datasets Enables Study of lncRNA

lncRNA

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown. Recent advances in high-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq) provide powerful ways to identify biologically relevant protein-lncRNA interactions. In this study, researchers at Sun Yat-sen University analyzed millions of ...

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C-It-Loci – a knowledge database for tissue-enriched loci

lncRNA

Increasing evidences suggest that most of the genome is transcribed into RNAs, but many of them are not translated into proteins. All those RNAs that do not become proteins are called ‘non-coding RNAs (ncRNAs)’, which outnumbers protein-coding genes. Interestingly, these ncRNAs are shown to be more tissue specifically expressed than protein-coding genes. Given that tissue-specific expressions of transcripts suggest their ...

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Co-LncRNA – investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

lncRNA

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, researchers at Harbin Medical University, China have developed Co-LncRNA, which is a ...

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LncReg – a reference resource for lncRNA-associated regulatory networks

lncRNA

Long non-coding RNAs (lncRNAs) are critical in the regulation of various biological processes. In recent years, plethora of lncRNAs have been identified in mammalian genomes through different approaches, and the researchers are constantly reporting the regulatory roles of these lncRNAs, which leads to complexity of literature about particular lncRNAs. Therefore, for the convenience of the researchers, we collected regulatory relationships ...

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