Our Relevant Work

ncRNA Related Databases

Binding Site Predict Tools

Other Gene/Protein Sources

  • Search ncRDeathDB by three paths: Keyword, Death Pathway and Advanced Search






  • Users can browse and obtain any ncRDeathDB through three paths.
    Path 1 (By Keyword): browse the ncRNA-associated cell death entries by inputting the keywords(any ncRNA, Gene Symbol,Death Pathway,Species) and fuzzy search supported.
    Path 2 (By Death Pathway): represent all ncRNA-associated cell death entries by associated option of species and death pathway.
    Path 3 (By Advanced Search): represent the accurate search results by associated option of species, death pathway and ncRNA/Gene symbols exist in ncRDeathDB. Multiple selection supported by enter the 'Ctrl' or 'Shift' In this path, users can choose the result presentation modes (including result and network) by select the "Result Presentation"


  • Search Results and Detail Information




  • We directly link to snoRNAbase, lncrnadb and NCBI when the ncRNA category is lncRNA or snoRNA.





    Detail information of miRNAs mainly contains their sequences, family, summary and interacted genes.





    Detail information of genes mainly contains their Synonyms, chromosome location, links to varies of databases and the interacted ncRNAs and genes.






    The 'First Node' or 'Second Node' option represents the sub-network of interacting RNA/Protein with the first or second interaction node, the 'Both the Nodes' option represents the sub-network of interacting RNA/Protein with both of interaction nodes.
    The 'First Neighbour' represents the sub-network of direct interacting with the center node, the 'Second Neighbour' represents the sub-network of direct or second step interacting with the center node. Interaction sub-network based on the two nodes of this interaction may help the researchers represents all interacting partners immediately.




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bindN+

Web Server: Submit the protein sequences to bindN+ and get the binding location
  http://bioinfo.ggc.org/bindn+/

Parameter setting
  • All parameters to default Settings
  • Binding residus with expected specificity equal to 85%

  • Miranda

    Manual Location: The manual and the parameter of Miranda
       http://cbio.mskcc.org/microrna_data/manual.html

    Parameter setting
  • Gap Open Penalty: -9.000000
  • Gap Extend Penalty: -4.000000
  • Score Threshold: 120.000000
  • Energy Threshold: 1.000000 kcal/mol
  • Scaling Parameter: 4.000000

  • RIsearch

    Manual Location: The manual and the parameter of RIsearch
       http://rth.dk/resources/risearch/

    Parameter setting
  • All parameters to default Settings
  • per-nucleotide extension penalty: 0
  • neighborhood: 0
  • max trace back length: 40
  • scoring scheme : t04

  • DAVID Enrichment for TargetGenes of miRNA

    Parameter setting
  • count:2
  • threshold: 0.1