COXPRESdb

ver. 7.3

last update; 2020.06.28

API in COXPRESdb (version 4)

Retrieve coexpression data

Request

http://coxpresdb.jp/cgi-bin/api4.cgi?gene=(ID of gene) [& other parameters]
http://coxpresdb.jp/cgi-bin/api4.cgi?uniprot=(Uniprot ID of protein) [& other parameters]
parameter:
Parameter name Required? Description Note
gene Either one of the two Entrez Gene ID Entrez Gene IDs (comma-delimited, maximum 100 gene IDs)
uniprot Uniprot ID Uniprot ID (single query ID)
type no Coexpression Index MR
value no Cut-off value of coexpression index
topN no Maximum number of coexpressed genes default 100. Set 0 to ignore the output number limitation.
db no Coexpression Platform Unified coexpression (Xxx-u, default), Microarray-based coexpression (Xxx-m), RNAseq-based coexpression (Xxx-r)


Response

The api2.cgi returns search result as JSON-formatted text like below:

{
  "request": {
    "query_id": "P04217",
    "id_type": "uniprot",
    "entrez_gene_id": [1],
    "type": null,
    "value": null,
    "topN": 100,
    "database": "Hsa-u.c2-0",
    "database_version": "c2-0"
  },
  "result_set": [
    {
      "entrez_gene_id": 1,
      "results": [
        {
          "gene": 503538,
          "pair_rank": 12976,
          "uniprot": [],
          "mutual_rank": 235.75
        },
        {
          "gene": 84266,
          "pair_rank": 174151,
          "uniprot": [
            "Q9BT30"
          ],
          "mutual_rank": 1742.92
        },
        ...
   ]
  }
 ]
}



Examples

1) Retrieve coexpressed gene list for single query gene (Entrez Gene ID: 1)
https://coxpresdb.jp/api4/?gene=1

2) Retrieve coexpressed gene lists for multiple query gene (Entrez Gene ID: 1, 2, and 3)
https://coxpresdb.jp/api4/?gene=1,2,3

3) Retrieve coexpressed gene list for single query gene (Uniprot ID: P04217)
https://coxpresdb.jp/api4/?uniprot=P04217

4) Specifying MR as the coexpression index (Currently only MR is acceptable)
https://coxpresdb.jp/api4/?gene=7535&type=mr

4) Limit coexpressed genes from Gene ID 7535 with MR less than 500
# top 100 coexpressed genes (default: topN=100)
https://coxpresdb.jp/api4/?gene=7535&type=mr&value=500

# retrieve top 10 coexpressed genes (topN=10)
https://coxpresdb.jp/api4/?gene=7535&type=mr&value=500&topN=10

# retrieve all genes (topN=0)
https://coxpresdb.jp/api4/?gene=7535&type=mr&value=500&topN=0

6) Retrieve the top 10 coexpressed genes having MR<500 from a query gene (Entrez Gene ID: 7535) on the Hsa-u.c2-0 platform
https://coxpresdb.jp/api4/?gene=7535&type=mr&value=500&topN=10&db=Hsa-u.c2-0

API in COXPRESdb (version 3)

Example

# Retrieval of coexpression information (eg. platform=Hsa-u.c1-0, Entrez Gene ID=1)
http://coxpresdb.jp/api/v3/datasets/Hsa-u.c1-0/genes/ncbigene:1/interactions?top=10

# List of datasets
http://coxpresdb.jp/api/v3/datasets/

Response

This API returns search result as JSON-formatted text like below:

{
  "interactionStrengthMap":{
    "ncbigene:1":0.0,
    "ncbigene:164656":1404.47,
    "ncbigene:256394":1067.06,
    "ncbigene:114770":1342.22,
    "ncbigene:503538":133.77
  },
  "interactionTypeId":"mr",
  "interactionMatrixId":"Hsa-u.c1-0",
  "guideGeneId":"ncbigene:1"
}