lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA
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{"title"=>"lnCeDB: Database of human long noncoding RNA acting as competing endogenous RNA", "type"=>"journal", "authors"=>[{"first_name"=>"Shaoli", "last_name"=>"Das", "scopus_author_id"=>"55574219055"}, {"first_name"=>"Suman", "last_name"=>"Ghosal", "scopus_author_id"=>"53663454900"}, {"first_name"=>"Rituparno", "last_name"=>"Sen", "scopus_author_id"=>"56002268000"}, {"first_name"=>"Jayprokas", "last_name"=>"Chakrabarti", "scopus_author_id"=>"56227244000"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84903136092", "sgr"=>"84903136092", "pui"=>"373380243", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24926662", "doi"=>"10.1371/journal.pone.0098965"}, "id"=>"e019e446-c4bb-320f-8723-f0cac491d8bb", "abstract"=>"UNLABELLED: 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.\\n\\nAVAILABILITY: Downloadable freely from http://gyanxet-beta.com/lncedb/.", "link"=>"http://www.mendeley.com/research/lncedb-database-human-long-noncoding-rna-acting-competing-endogenous-rna", "reader_count"=>72, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>4, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>4, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>19, "Mathematics"=>1, "Agricultural and Biological Sciences"=>32, "Medicine and Dentistry"=>8, "Neuroscience"=>1, "Computer Science"=>5}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>32}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}}, "reader_count_by_country"=>{"Hungary"=>1, "Japan"=>1, "China"=>2, "Denmark"=>1, "Italy"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1535249"], "description"=>"<p>(a) lnCeDB is searched by the gene symbol MCL1. (b) An intermediate page shows the different transcripts of the gene MCL1. (c) Upon choosing a transcript, the results page shows the potential lncRNAs working as ceRNA for the chosen transcript of MCL1. (d) By clicking on a lncRNA or mRNA id in the ceRNA table, the user views all miRNA targets on the chosen transcript. (e) By clicking on a serial number in the ceRNA table, the user views the expression heatmap and bar chart for the ceRNA pair along with co-expressed shared miRNAs in 22 human tissues.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "diagram", "browsing", "cernas"], "article_id"=>1057600, "categories"=>["Biological Sciences"], "users"=>["Shaoli Das", "Suman Ghosal", "Rituparno Sen", "Jayprokas Chakrabarti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098965.g002", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_flow_diagram_for_browsing_ceRNAs_in_ln_Ce_DB_/1057600", "title"=>"The flow diagram for browsing ceRNAs in ln<i>Ce</i>DB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-13 04:47:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1535240"], "description"=>"<p>(a) Fraction of GENCODE 19 lncRNA transcripts with putative miRNA targets. (b) Fraction of mRNAs with predicted miRNA targets. (c) Fraction of lncRNAs with predicted ceRNA function compared to all lncRNAs with putative miRNA targets. (d) Fraction of mRNAs with predicted ceRNA function compared to all mRNAs with putative miRNA targets.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "contents"], "article_id"=>1057595, "categories"=>["Biological Sciences"], "users"=>["Shaoli Das", "Suman Ghosal", "Rituparno Sen", "Jayprokas Chakrabarti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098965.g001", "stats"=>{"downloads"=>0, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_statistics_of_the_database_contents_in_ln_Ce_DB_/1057595", "title"=>"A statistics of the database contents in ln<i>Ce</i>DB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-13 04:47:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1535251"], "description"=>"<p>Experimentally verified lncRNA ceRNAs in ln<i><u>Ce</u></i>DB.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "verified", "lncrna", "cernas"], "article_id"=>1057602, "categories"=>["Biological Sciences"], "users"=>["Shaoli Das", "Suman Ghosal", "Rituparno Sen", "Jayprokas Chakrabarti"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098965.t001", "stats"=>{"downloads"=>3, "page_views"=>106, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimentally_verified_lncRNA_ceRNAs_in_ln_Ce_DB_/1057602", "title"=>"Experimentally verified lncRNA ceRNAs in ln<i>Ce</i>DB.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-13 04:47:07"}

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Relative Metric

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