COXPRESdb

ver. 8.1

last update; 2018.10.24

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 Gene ID GeneID (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-r.c2-0, Entrez Gene ID=1)
http://coxpresdb.jp/api/v3/datasets/Hsa-r.c2-0/genes/ncbigene:1/interactions?top=10

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

API in COXPRESdb (version 2)

Retrieve coexpression data

Request

http://coxpresdb.jp/cgi-bin/api2.cgi?gene=(ID of gene) [& other parameters]
Parameter name Description Required? Note
gene ID of target gene Required
type Coexpression measure Optional Allowed values: cor, mr
cutoff Cutoff value Optional If you specify "cutoff" value, you also need to specify "type" value.
db Database identifier Optional Allowed values: hsa, hsa2, hsa3, mmu, mmu2, rno, gga, dre, dme2, cel, mcc, cfa, sce, spo


Response

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

{
  "request": {                       # Request information
    "original_gene_id": "At2g39730", # ID of gene specified by the "id" parameter in the URL
    "entrez_gene_id": "818558",      # (internally, the system converts the specified ID to entrez gene ID,
                                     #  and the conversion result is shown here)
    "database": "Ath",               # database identifier (species)
    "database_version": "v12-08",    # database identifier (version)
    "type": null,                    # filter type (if not specified, "null" is returned)
    "cutoff": null                   # cutoff value (if not specified, "null" is returned)
  },
  "results": [                       # Coexpression data
    {
      "gene": "840895", 
      "correlation": 0.8554, 
      "mutual_rank": 3.0
    }, 
    {
      "gene": "825797", 
      "correlation": 0.8466, 
      "mutual_rank": 4.9
    }, 
...

If an error happened while processing your request, api2.cgi returns JSON that includes only "error" section like below: 

{ 
  "error": "No gene ID specified." 
}



Examples

Retrieves coexpression list of ALDH2 (entrez gene ID: 7535). (Both two requests returns the same result.)

Retrieves coexpression list that includes only correlation values (mutal rank values).

Retrieves coexpression list filtered by correlation value (mutal rank value).

Retrives strongly coexpressed genes with 7535 from the database Hsa.v12-08 and Hsa2.v12-08.



API in COXPRESdb (version 1)

Retreive coexpression data

Basic usage

http://atted.jp/API/coex/ (AGI code) / (coexpression measure; cor or mr) / (cutoff value)

Omit "cutoff" option to return all coexpression from the guide gene

http://atted.jp/API/coex/ (AGI code) / (coexpression measure; cor or mr)

Omit "cutoff" and "type" optionsAlso "type" option can be omitted toreturn all MR and PCC coexpression data from the guide gene.

http://atted.jp/API/coex/ (AGI code)

Examples

URL Output
http://atted.jp/API/coex/At1g01010/cor/0.508 {[At1g62300,0.5154],[At4g39270,0.5080]}
http://atted.jp/API/coex/At1g01010/mr/20 {[At3g59220,19.18],[At1g62300,19.39]}
http://atted.jp/API/coex/At1g01010/cor {[At1g62300,0.5154],[At4g39270,0.5080],...}
http://atted.jp/API/coex/At1g01010 {[At3g59220,19.18,0.4019],[At1g62300,19.39,0.5154],...}