Tag Archives: database

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

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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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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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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zflncRNApedia – A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs

lncRNA

Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw RNA-Seq datasets in ...

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An update on LNCipedia – a database for annotated human lncRNA sequences

lncRNA

LNCipedia collects long non-coding RNA sequences and annotation from different sources. In version 3.0, over 90,000 new transcripts were added to the database. 6917 of these transcripts were obtained from RefSeq by filtering for accession prefix (NR_) and size (200bp). This filtering strategy however, does not confine to long non-coding RNAs and also yields transcripts associated with protein coding genes. ...

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