Search Results for: lncrnas as cerna

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

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]

Incoming search terms:

  • gencode ncrna

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:

  • lncRNA post-transcriptional
  • non coding rna target database
  • gencode long noncoding rna
  • lincrna-sfpq prc2

Long Noncoding RNA: “LNCs” to Cancer

lncRNA

In recent years we have witnessed a paradigm shift concerning the long-lasting controversy over “junk DNA” in the human genome. It is now well established that, besides the roughly 25 000 protein-coding genes, the genome contains tens of thousands of functional elements. In addition, the completion of the ENCODE project—the functional annotation of all regulatory regions of the human genome—has confirmed that 80% of genome is transcribed into RNA, whereas <than 2% is translated into proteins. Thus, an as yet unknown number of transcripts lacking significant coding potential, including long noncoding RNAs (lncRNAs), exceed the number of protein-coding genes . However, the expression, regulation, sequence, function, and mechanism of action of the vast majority of lncRNAs are currently largely unknown.

Incoming search terms:

  • xist
  • lncrna encode vs noncode
  • lncRNA xist
  • therapeutic target of non coding RNAs on breast cancer
  • copy number pcat
  • lncrna interact
  • malat1 snp cancer
  • next-generation sequencing non-coding RNA
  • Xist and PRC2 complex

Knockout Mice Study: Long Noncoding RNAs “Play Central Roles in Mammalian Development and Physiology”

lncRNA

by Casey Luskin at Evolution News & Views

A few years ago I wrote about challenges to the claim that “junk DNA” wasn’t necessary for development. In experiments with mice, researchers had supposedly “knocked out” non-coding DNA, yet the mice themselves as they grew turned out to be healthy. Now a new study in eLife, “Multiple knockout mouse models reveal lincRNAs are required for life and brain development,” shows that in fact noncoding DNA, in the form of long non-coding RNAs (lincRNAs), is vital for normal development in mice — and researchers are suggesting that even when such “knockouts” don’t produce nonviable mice, we should be very hesitant in claiming the noncoding DNA is unimportant. As the “digest” section of the article states:

Sauvageau et al. have developed several lines of knockout mice to investigate a subset of noncoding RNA molecules known as long intergenic noncoding RNAs (lincRNAs). These experiments reveal that lincRNAs have a strong influence on the overall viability of mice, and also on a number of developmental processes, including the development of lungs and the cerebral cortex.

The study knocked out 18 lincRNAs in mice, and found that lincRNAs “play central roles” in development:

Incoming search terms:

  • Most of the genome of an active cell consists of
  • rna nucleotides in mice