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Long Noncoding RNAs in Cardiovascular Diseases

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

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism More »

Community Curated Database For LncRNA

A wiki-style database hopes to serve as an online encyclopedia of lncRNA by and for the scientific community. Scientists have More »

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Database

Community Curated Database For LncRNA

lncRNA

A wiki-style database hopes to serve as an online encyclopedia of lncRNA by and for the scientific community.

Scientists have set up a long non-coding RNA (lncRNA) database aimed at harnessing the collective knowledge of the scientific community. This study has been published in Nucleic Acids Research.

LncRNAs are RNAs that do not code for proteins but are nonetheless actively transcribed in human genome. In recent years, it has been recognized that they perform significant roles in a large variety of biological processes. The dysregulation of lncRNA expression is highly correlated with human cancer, neurological disorders, and many other human diseases.

Incoming search terms:

  • lnc disease database
  • TCGA lncRNA

LncRNA2Target – a database for differentially expressed genes after lncRNA knockdown or overexpression

Long noncoding RNAs (lncRNAs) have been emerged as critical regulators of gene expression at epigenetic, transcriptional and post-transcriptional level, yet what genes are regulated by lncRNAs remains to be characterized. To assess the effects of a specific lncRNA on gene expression, increasing researchers profiled the genome-wide or individual gene expression level changes after knocking down or overexpressing the lncRNA. However, no online repository is currently available to collect these differentially expressed genes regulated by lncRNAs.

To make it convenient for researchers to know what genes are regulated by a lncRNA or which lncRNAs regulate a given gene of interest, researchers at the Harbin Institute of Technology have developed LncRNA2Target: a comprehensive resource of differentially expressed genes after lncRNA knockdown or overexpression.

lncRNA

In this database system, target genes of a lncRNA are defined as the differentially expressed genes after knocking down or overexpressing the lncRNA. By reviewing all published lncRNA papers, we manually curated the differentially expressed target genes confirmed by qRT-PCR or western blot, and identified all the differential target genes from the microarray or RNA-seq data.

Availability – the LncRNA2Target database is available at: http://www.lncrna2target.org/

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lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

database

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target mRNAs, thus reducing the repression of these mRNAs.

lnCeDB provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. The putative mRNA targets of human miRNAs and the targets mapped to AGO clipped regions are collected from TargetScan and StarBase respectively. The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. These putative miRNA-lncRNA interactions are mapped to the Ago interacting regions within lncRNAs. To find out the likelihood of an lncRNA-mRNA pair for actually being ceRNA we take recourse to two methods. First, a ceRNA score is calculated from the ratio of the number of shared MREs between the pair with the total number of MREs of the individual candidate gene. Second, the P-value for each ceRNA pair is determined by hypergeometric test using the number of shared miRNAs between the ceRNA pair against the number of miRNAs interacting with the individual RNAs. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression so that the increase in level of one ceRNA results in the increased level of the other ceRNA. Near-equimolar concentration of the competing RNAs is associated with more profound ceRNA effect. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs.

Availability: Downloadable freely from http://gyanxet-beta.com/lncedb/.

Das S, Ghosal S, Sen R, Chakrabarti J (2014) lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA. PLoS ONE 9(6): e98965. [article]

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target mRNAs, thus reducing the repression of these mRNAs. lnCeDB provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. The putative mRNA targets of human miRNAs and the targets mapped to AGO clipped regions are collected from TargetScan and StarBase respectively. The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. These putative miRNA-lncRNA interactions are mapped to the Ago interacting regions within lncRNAs. To find out the likelihood of an lncRNA-mRNA pair for actually being ceRNA we take recourse to two methods. First, a ceRNA score is calculated from the ratio of the number of shared MREs between the pair with the total number of MREs of the individual candidate gene. Second, the P-value for each ceRNA pair is determined by hypergeometric test using the number of shared miRNAs between the ceRNA pair against the number of miRNAs interacting with the individual RNAs. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression so that the increase in level of one ceRNA results in the increased level of the other ceRNA. Near-equimolar concentration of the competing RNAs is associated with more profound ceRNA effect. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs.

lncRNA

Availability: Downloadable freely from http://gyanxet-beta.com/lncedb/.

  • Das S, Ghosal S, Sen R, Chakrabarti J (2014) lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA. PLoS ONE 9(6): e98965. [article]

lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome

lncRNA

lncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA-target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic lncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, lncRNAMap surveyed neighboring genes within a 1Mb distance from the genomic location of specific lncRNAs and provided the expression profiles of lncRNA and its neighboring genes. The gene expression profiles may supply the relationship between lncRNA and its neighboring genes.

map2

lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human lncRNAs with producing siRNAs and acting as miRNA decoy.

Availability – lncRNAMap is freely available on the web at http://lncRNAMap.mbc.nctu.edu.tw/

  • Chan WL, Huang HD, Chang JG. (2014) lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome. Comput Biol Chem [Epub ahead of print]. [abstract]

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