ATTED-II

ver.12.0

last update; Jan. 25. 2024

API (version 5)

Retrieve coexpression data

Request

https://atted.jp/cgi-bin/api5.cgi?gene=(ID of gene) [& other parameters]
https://atted.jp/cgi-bin/api5.cgi?uniprot=(Uniprot ID of protein) [& other parameters]
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). Automatically converted to Entrez Gene IDs.
value no Cut-off value of coexpression index To specify the "cutoff" value.
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 api5.cgi returns a search result as JSON-formatted text like below:

{
  "request": {
    "query_id": "818558",
    "id_type": "gene",
    "entrez_gene_id": [
      818558
    ],
    "value": 5,
    "topN": 2,
    "database": "Ath-u.c4-0",
    "database_version": "c4-0"
  },
  "result_set": [
    {
      "entrez_gene_id": 818558,
      "type": "z",
      "results": [
        {
          "gene": 830052,
          "other_id": "At4g38970",
          "z": 15.2774
        },
        {
          "gene": 840895,
          "other_id": "At1g42970",
          "z": 14.0746
        }
      ],
      "other_id": "At2g39730"
    }
  ]
}



Examples

1) Specifing query gene(s): 2) Maximum number of the coexpressed genes: 3) Threshold of coexpression: 4) Database version:

API (version 4)

Retrieve coexpression data

Request

https://atted.jp/cgi-bin/api4.cgi?gene=(ID of gene) [& other parameters]
https://atted.jp/cgi-bin/api4.cgi?uniprot=(Uniprot ID of protein) [& other parameters]
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). Automatically converted to Entrez Gene IDs.
type no Coexpression Index LS(Logit Score), MR(Mutual Rank: deprecated)
value no Cut-off value of coexpression index To specify the "cutoff" value, the "type" option is required.
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 api4.cgi returns a search result as JSON-formatted text like below:

{
  "request": {
     "query_id": "818558",
     "id_type": "gene",
     "entrez_gene_id": [818558],
     "type": "ls",
     "value": 5.0,
     "topN": 2,
     "database": "Ath-u.c1-0",
     "database_version": "c1-0"
  },
  "result_set": [
     {
        "entrez_gene_id": 818558,
        "results": [
           {
              "gene": 830052,
              "pair_rank": 569,
              "mutual_rank": 3.51,
              "logit_score": 12.4
           },
           {
              "gene": 838940,
              "pair_rank": 4112,
              "mutual_rank": 12.55,
              "logit_score": 10.56
           }
        ]
     }
  ]
}



Examples

1) Specifing query gene(s): 2) Maximum number of the coexpressed genes: 3) Threshold of coexpression: 4) Database version:

API in ATTED-II (version 2)

Retrieve coexpression data

Request

http://atted.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: ath, ath2, cre, gma, mtr, osa, ppo, vvi, zma,

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: 818558). (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 At2g39730 from the database Ath.v12-08 and Ath.v13-08.

API in ATTED-II (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

URI Output
http://atted.jp/API/coex/At1g01010/mr/20 {[At3g59220,19.18],[At1g62300,19.39]}
http://atted.jp/API/coex/At1g01010 {[At3g59220,19.18,],[At1g62300,19.39,],...}