Long non-coding RNAs: evolution of new epigenetic and post-transcriptional functions

9:00 am on Monday 28 September 2015 — 5:00 pm on Tuesday 29 September 2015 at The Royal Society at More »

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Database

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]

Incoming search terms:

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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]

Incoming search terms:

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Decoding Pan-Cancer and Interaction Networks of lncRNAs from TCGA 14 cancer types

starBase_panCancer_overView

starBase has been updated to explore Pan-Cancer Networks of lncRNAs, miRNAs, ceRNAs and RNA-binding proteins (RBPs) by mining clinical and expression profiles of 14 cancer types (>6000 tumor and normal samples) from The Cancer Genome Atlas (TCGA) Data Portal (all data available without limitations).

lncRNAstarBase provides the following Pan-Cancer Analysis Services:

  1. starBase constructed Pan-Cancer expression profiles of lncRNAs, miRNAs, ceRNAs and RBPs from TCGA RNA-Seq and miRNA-Seq data.
  2. starBase generated Pan-Cancer networks of CLIP-Seq experimentally supported miRNA-lncRNA and miRNA-mRNA interactions.
  3. starBase identified Pan-Cancer ceRNA networks involving lncRNAs and mRNAs.
  4. starBase firstly provided Pan-Cancer maps of interactions between RNA-binding proteins (RBPs) and RNAs(lncRNAs, mRNAs).
  5. starBase provides interactive BarPlot, ScatterPlot and BoxPlot charts and diverse statistics tests to show the above-mentioned genes and regulatory networks.

Availability – Pan-Cancer Analysis is freely available at http://starbase.sysu.edu.cn/panCancer.php

Incoming search terms:

  • lncrna mrna interaction

The MOuse NOnCode Lung database

lncRNA

The MOuse NOnCode Lung database: mouse long non-coding RNAs (lncRNA) involved in Influenza and SARS-CoV infections

The MOuse NOnCode Lung database — MONOCLdb — is an integrative and interactive database designed to retrieve and visualize annotations, expression profiles and functional enrichment results of long-non coding RNAs (lncRNAs) expressed in Collaborative Cross (http://compgen.unc.edu/) founder mice in response to respiratory infections cause by influenza and SARS-CoV viruses.

Using MONOCLdb, researchers can retrieve and visualize annotations, expression profiles and functional enrichment results of specific long-non coding RNAs. On-the-fly generation of expression heatmaps or generation of functional enrichment results (module-based enrichments, rank-based enrichments, associated GO term, associated IMMGEN module, associated REACTOME pathways) are possible using MONOCLdb. Co-expression networks and genomic networks of lncRNAs can also be visualized using MONOCLdb. Association scores between lncRNAs and pathogenicity variables are also provided by MONOCLdb. MONOCLdb also provides a Distributed Annotation System (DAS) service for visualization purposes of the non-coding genes associated with inferred biological functions (associated GO term, IMMGEN module, REACTOME pathways). Furthermore, MONOCLdb offers a web service to automatically retrieve analysis results (please see the About section for more information).

Availabilityhttp://www.monocldb.org

NONCODEv4: exploring the world of long non-coding RNA genes

NONCODE (http://www.bioinfo.org/noncode/) is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Non-coding RNAs (ncRNAs) have been implied in diseases and identified to play important roles in various biological processes. Since NONCODE version 3.0 was released 2 years ago, discovery of novel ncRNAs has been promoted by high-throughput RNA sequencing (RNA-Seq). In this update of NONCODE, we expand the ncRNA data set by collection of newly identified ncRNAs from literature published in the last 2 years and integration of the latest version of RefSeq and Ensembl. Particularly, the number of long non-coding RNA (lncRNA) has increased sharply from 73 327 to 210 831. Owing to similar alternative splicing pattern to mRNAs, the concept of lncRNA genes was put forward to help systematic understanding of lncRNAs. The 56 018 and 46 475 lncRNA genes were generated from 95 135 and 67 628 lncRNAs for human and mouse, respectively. Additionally, we present expression profile of lncRNA genes by graphs based on public RNA-seq data for human and mouse, as well as predict functions of these lncRNA genes. The improvements brought to the database also include an incorporation of an ID conversion tool from RefSeq or Ensembl ID to NONCODE ID and a service of lncRNA identification. NONCODE is also accessible through http://www.noncode.org/.

lncRNA

  • Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, Zhu W, Wu W, Chen R, Zhao Y. (2013) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Research [Epub ahead of print]. [article]

Incoming search terms:

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