title: lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.
abstract: 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.
  
  
  BACKGROUND
  Downloadable freely from http://gyanxet-beta.com/lncedb/.
authors.affiliation: Computational Biology Group, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
authors.forename: Shaoli
authors.initials: S
authors.lastname: Das
authors.affiliation: Computational Biology Group, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
authors.forename: Suman
authors.initials: S
authors.lastname: Ghosal
authors.affiliation: Gyanxet, Kolkata, West Bengal, India.
authors.forename: Rituparno
authors.initials: R
authors.lastname: Sen
authors.affiliation: Computational Biology Group, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India; Gyanxet, Kolkata, West Bengal, India.
authors.forename: Jayprokas
authors.initials: J
authors.lastname: Chakrabarti
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D004843:Epistasis, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D034622:RNA Interference; D062085:RNA, Long Noncoding / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger