Introduction


The ENCORI web service interface provides direct programmatic access to all regulatory data stored within the server. This enables you to easily access data from your favorite programming language, such as Shell, Python, or Perl. Here we use curl (command line tool) for communicating with the ENCORI APIs.


Before using APIs of ENCORI, you may need the information from these reference tables.


1. miRNA-Target


Get MiRNA Target Data.
Description Retrieve data of the miRNA-target interactions by intersecting the predicting target sites of miRNAs with binding sites of Ago protein
Query Format
  • assembly=[genome version]: hg38, hg19, mm10
  • geneType=[main gene type]: mRNA, lncRNA, pseudogene, circRNA, sncRNA
  • miRNA=[microRNA name]. e.g., hsa-miR-21-5p ("all" for downloading all regulatory data)
  • clipExpNum=[integer]: minimum number of supporting CLIP-seq experiments
  • degraExpNum=[integer]: minimum number of supporting degradome-seq experiments
  • pancancerNum=[integer]: minimum number of Cancer types (Pan-Cancer, <=32)
  • programNum=[integer]: minimum number of target-predicting programs (<=7)
  • program=[string]: target-predicting programs (PITA, RNA22, miRmap, DIANA-microT, miRanda, PicTar and TargetScan)
  • target=[gene name]. e.g., PDCD4 ("all" for downloading all regulatory data)
  • cellType=[cell type]. e.g., HeLa ("all" for downloading all regulatory data)
Response Format
Example

2. Degradome-RNA


Get Data for MiRNAs Cleavage Events.
Description Retrieve data for cleavage events of miRNAs on genes supported by degradome-seq data
Query Format
  • assembly=[genome version]. e.g., hg19
  • geneType=[main gene type]: mRNA, ncRNA
  • miRNA=[microRNA name]. e.g., hsa-miR-196a-5p ("all" for downloading all regulatory data)
  • degraExpNum=[integer]: minimum number of supporting degradome-seq experiments
  • target=[gene name]. e.g., TP53 ("all" for downloading all regulatory data)
  • cellType=[cell type]. e.g., HeLa ("all" for downloading all regulatory data)
Response Format
Example

 

3. RNA-RNA


Get the Data for NcRNA-RNA Interaction Network.
Description Retrieve the interaction network of ncRNA-RNA identified from high-throughput sequencing data of RNA-RNA interactome
Query Format
  • assembly=[genome version]: hg38, mm10
  • geneType=[main gene type]: mRNA, lncRNA, pseudogene, sncRNA, miRNA
  • RNA=[RNA name]. e.g., TP53 ("all" for downloading all regulatory data)
  • interNum=[integer]: miminum number of RNA-RNA interactions
  • expNum=[integer]: miminum number of experiments
  • cellType=[cell type]. e.g., HeLa ("all" for downloading all regulatory data)
Response Format
Example
  • Get the interaction networks of TP53-mRNA (in human)
    • curl 'https://rna.sysu.edu.cn/encori/api/RNARNA/?assembly=hg38&geneType=mRNA&RNA=TP53&interNum=1&expNum=1&cellType=all' > ENCORI_hg38_RNA-RNA_TP53.txt

     

    4. CeRNA


    Get Data of the CeRNA Networks.
    Description Retrieve the ceRNA networks from thousands of interactions of miRNA-targets supported by CLIP-seq data.
    Query Format
    • assembly=[genome version]: hg38, mm10
    • geneType=[main gene type]: mRNA, lncRNA, pseudogene
    • ceRNA=[gene name]. e.g., MYC ("all" for downloading all regulatory data)
    • miRNAnum=[integer]: miminum number of miRNAs
    • family=[miRNA family name]. e.g., miR-200bc-3p/429,miR-513c-5p/514b-5p("all" for downloading all regulatory data)
    • pval=[decimal]: maximum p-value (<=0.01).
    • fdr=[decimal]: maximum false dicovery rate (<=0.01)
    • pancancerNum=[integer]: minimum number of Cancer types (Pan-Cancer, <=32)
    Response Format
    Example

     

    5. RBP-Target


    Get RBP Target Data.
    Description Retrieve data of RBP-RNA interactions supported by the binding sites of RBPs derived from CLIP-seq data
    Query Format
    • assembly=[genome version]. hg38, hg19, mm10, dm6, ce10, sacCer3
    • geneType=[main gene type]: mRNA, lncRNA, pseudogene, circRNA, sncRNA
    • RBP=[protein name]: CBX7 ("all" for downloading all regulatory data)
    • clipExpNum=[integer]: minimum number of supporting CLIP-seq experiments
    • pancancerNum=[integer]: minimum number of Cancer types (Pan-Cancer, <=32)
    • target=[gene name]. e.g., TP53 ("all" for downloading all regulatory data)
    • cellType=[cell type]. e.g., HeLa ("all" for downloading all regulatory data)
    Response Format
    Example

     

    6. RBP-Disease


    Get Data for RBP and Somatic Gene Mutations.
    Description Retrieve data for RBP-gene interactions and somatic mutations in human diseases
    Query Format
    • assembly=[genome version]: hg19
    • RBP=[protein name]. e.g., CBX7 ("all" for downloading all regulatory data)
    • tissue=[tissue name or organ name]. e.g., adrenal gland, breast
    • disease=[cancers and rare diseases in human]. e.g., Rosai-Dorfman disease, Crohn disease, Proteus syndrome
    • target=[gene name]. e.g., MYC ("all" for downloading all regulatory data)
    Response Format
    Example

     

    7. RBP Motif Scan (CLIP-seq)


    Filter the binding motifs of RBPs contained specific sequence pattern.
    Description Retrieve binding motifs of RBPs contained specific sequence pattern, which were de novo identified from their CLIP-seq peak data by Homer.
    Query Format
    • assembly=[genome version]. hg38, hg19, mm10, dm6, ce10, sacCer3
    • motif=[motif pattern]. e.g., UGCAUG
    • rankLimit=[integer]. Rank limit of RNA binding motifs (default is 10)
    Example

     

    8. Binding Sites (CLIP-seq)


    Get the binding sites of CLIP-seq. (Or you can directly download these data via this page .)
    Description Download the binding sites of CLIP-seq in bed format
    Query Format
    • assembly=[genome version]. hg38, hg19, mm10, dm6, ce10, sacCer3
    • datasetID=[uniq dataset ID]. e.g., SBDH27
    Example