Usage of EnhancerDB

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API usage

We also provide restful API for programing languages, such as Python, Java and so on. Or command line tools such as curl.

All APIs support the following parameters:

  • length: return how many results
  • start: he query start from, e.g. A total of 100 data, start=10&length=10, it will return the 10~20 data
1、Inquire Enhancer

The endpoint is /api/enhancer
The following parameters are:

  • tissue: A549.
  • eid: e.g. enh7.
  • spe: e.g. 5, select the enhancers that appear in more than how many tissues/cell lines.
  • eq: e.g. 5, select the enhancers that appear in exact how many tissues/cell lines

For example:

  • Run this command in terminal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/enhancer?tissue=A549", users can retrive first 10 records of enhancers appears in A549.
  • Run this command in terminal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/enhancer?eid=enh7&length=200", users can retrive first 200 records of enh7 cross all tissues/cell lines.
  • Run this command in terminal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/enhancer?tissue=A549&eq=5&length=200&start=200", users can retrive 200~400 records of enhancers that appears in A549 and other 4 more tissues/cell lines.
  • Run this command in terminal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/enhancer?tissue=A549&spe=0.5", users can retrive first 10 records of enhancers that appears in A549 and at least 4 more tissues/cell lines.

{
  "data": [
        {
      "Score": 74.43,
      "chrom": "chr10",
      "eid": "enh6696",
      "end": 38875752,
      "id": 251341,
      "number": [
        {
          "label": "Lung (A549)",
          "url": "/ErreDB/enhancer/details?tissue=A549&eid=251341"
        }
      ],
      "start": 38871708
    },
    ......
    {
      "Score": 74.27,
      "chrom": "chrY",
      "eid": "enh68532",
      "end": 13690602,
      "id": 479940,
      "number": [
        {
          "label": "Lung (A549)",
          "url": "/ErreDB/enhancer/details?tissue=A549&eid=479940"
        }
      ],
      "start": 13686546
    }

  ],
  "draw": 1,
  "length": 10,
  "recordsFiltered": 93418,
  "recordsTotal": 93418,
  "start": 0
}
2、Inquire TFBS

The endpoint is /api/tfbs
The following parameters are:

  • tf: eg: ATF1.

For example: Run this command in terminal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/tfbs?tf=ATF1", users will retrive the first 10 records of binding sites of ATF1

{
  "data": [
    {
      "chrom": "chr1",
      "end": 714185,
      "id": 293,
      "predict": false,
      "software": "UCSC Txn Factor",
      "start": 713973,
      "target": "ATF1",
      "tissue": "Conserved"
    },
    ......
    {
      "chrom": "chr1",
      "end": 936387,
      "id": 379,
      "predict": false,
      "software": "UCSC Txn Factor",
      "start": 936174,
      "target": "ATF1",
      "tissue": "Conserved"
    },
  ],
  "draw": 1,
  "length": 10,
  "recordsFiltered": 48717,
  "recordsTotal": 48717,
  "start": 0
}
3. Inquire by specific label

The endpoint is /api/label
The following parameters are:

  • type:
    • enhancer
    • tf
    • gene
    • mirna
    • snp
  • label:
    • for enhancer: enhancer id, e.g. enh7
    • for tf: tf name, e.g. ATF1
    • for gene: gene name or Ensembl ID, e.g. TP53
    • for mirna: mirna name or miRBase ID, e.g. hsa-miR-181a-3p
    • for snp: dbSNP ID, e.g. rs372469944

Through this API users can retrive different data by different combination of key words

For example:

  • Run this command in terminmal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/label?label=TP53&type=gene", users will retrive all the information of TP53 gene.
            {
              "data": [
                {
                  "Ensembl": "ENSG00000141510.11",
                  "cancer": 1.0,
                  "chrom": "chr17",
                  "end": 7590856,
                  "gene_name": "TP53",
                  "id": 44934,
                  "normal": 0.74,
                  "start": 7565097,
                  "strand": "-",
                  "tss": 7590856
                }
              ],
              "draw": 1,
              "length": 10,
              "recordsFiltered": 1,
              "recordsTotal": 1,
              "start": 0
            }
          
          
  • Run this command in terminmal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/label?label=ATF1&type=tf", users will retrive all the binding sites about TF named ATF1.
            {
            {
              "chrom": "chr1",
              "end": 752899,
              "id": 26166527,
              "predict": true,
              "software": "TRANSFAC",
              "start": 752893,
              "target": "ATF1",
              "tissue": null
            },
            ....
            {
              "chrom": "chr1",
              "end": 771965,
              "id": 26168360,
              "predict": true,
              "software": "TRANSFAC",
              "start": 771959,
              "target": "ATF1",
              "tissue": null
            }
          ],
          "draw": 1,
          "length": 10,
          "recordsFiltered": 82746,
          "recordsTotal": 82746,
          "start": 0
        }
        

     

          {
          "data": [
            {
              "chrom": "chr1",
              "eid": "enh7",
              "end": 1810244,
              "number": [
                {
                  "label": "Heart",
                  "url": "/EnhancerDB/enhancer/details?tissue=Heart&eid=75"
                },
                {
                  "label": "Blood (Karpas-422)",
                  "url": "/EnhancerDB/enhancer/details?tissue=Karpas-422&eid=74"
                },
                {
                  "label": "Bone (Osteoblast)",
                  "url": "/EnhancerDB/enhancer/details?tissue=Osteoblast&eid=73"
                }
              ],
              "start": 1802728
            }
          ],
          "draw": 1,
          "length": 10,
          "recordsFiltered": 1,
          "recordsTotal": 1,
          "start": 0
        }
        
        
  • Run this command in terminmal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/label?label=enh7&type=enhancer", users will retrive all the records of enhancer named enh7.
            {
            "data": [
              {
                "chrom": "chr1",
                "eid": "enh7",
                "end": 1810244,
                "number": [
                  {
                    "label": "Heart",
                    "url": "/EnhancerDB/enhancer/details?tissue=Heart&eid=75"
                  },
                  {
                    "label": "Blood (Karpas-422)",
                    "url": "/EnhancerDB/enhancer/details?tissue=Karpas-422&eid=74"
                  },
                  {
                    "label": "Bone (Osteoblast)",
                    "url": "/EnhancerDB/enhancer/details?tissue=Osteoblast&eid=73"
                  }
                ],
                "start": 1802728
              }
            ],
            "draw": 1,
            "length": 10,
            "recordsFiltered": 1,
            "recordsTotal": 1,
            "start": 0
          }
          
          
  • Run this command in terminmal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/label?label=hsa-miR-181a-3p&type=mirna", users will retrive all the information of mirna named hsa-miR-181a-3p.
            {
            "data": [
              {
                "Name": "hsa-miR-181a-3p",
                "TSS": 198906557,
                "cancer": 0.721653,
                "chrom": "chr1",
                "end": 198828219,
                "id": 108,
                "mirBase": "MIMAT0000270",
                "normal": 0.594633,
                "start": 198828198,
                "strand": "-"
              }
            ],
            "draw": 1,
            "length": 10,
            "recordsFiltered": 1,
            "recordsTotal": 1,
            "start": 0
          }
          
          
  • Run this command in terminmal curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/label?label=rs372469944&type=snp", users will retrive all the information of SNP named rs79227320.
            {
            "data": [
              {
                "alt": "G",
                "chrom": "chr5",
                "id": 8564328,
                "pos": 140941777,
                "ref": "GCTA",
                "snp": "rs372469944"
              }
            ],
            "draw": 1,
            "length": 10,
            "recordsFiltered": 1,
            "recordsTotal": 1,
            "start": 0
          }
          
          

4. Inquire by specific genomic region

The endpoint is /api/position
The following parameters are:

  • type:
    • enhancer
    • tf
    • gene
    • mirna
    • snp
  • position: e.g. chr1:100-100000

Through this api users can retrive differnt elements that have any overlap with specific genomic region, For example: curl "http://lcbb.swjtu.edu.cn/EnhancerDB/api/position?type=mirna&position=chr1%3A100-10000000"

{
  "data": [
    {
      "Name": "hsa-miR-200a-3p",
      "TSS": 1103243,
      "cancer": 0.0,
      "chrom": "chr1",
      "end": 1103317,
      "id": 13,
      "mirBase": "MIMAT0000682",
      "normal": 0.914768,
      "start": 1103296,
      "strand": "+"
    },
    {
      "Name": "hsa-miR-200b-3p",
      "TSS": 1102484,
      "cancer": 0.0,
      "chrom": "chr1",
      "end": 1102561,
      "id": 10,
      "mirBase": "MIMAT0000318",
      "normal": 0.908635,
      "start": 1102540,
      "strand": "+"
    },
    {
      "Name": "hsa-miR-34a-3p",
      "TSS": 9211836,
      "cancer": 0.719127,
      "chrom": "chr1",
      "end": 9211773,
      "id": 40,
      "mirBase": "MIMAT0004557",
      "normal": 0.796865,
      "start": 9211752,
      "strand": "-"
    }
  ],
  "draw": 1,
  "length": 10,
  "recordsFiltered": 3,
  "recordsTotal": 3,
  "start": 0
}

Address

Southwest Jiaotong University.
School of Life Sciences and Bioengineering.
Chengdu, Sichuan, China


Email

zhiyunguo@swjtu.edu.cn