Resource |
URI(s) |
Description |
|---|---|---|
Protein |
/protein/{protein} |
Represents a protein. |
Locus |
/locus/{locus}?potential-id={potential-id}&tf={tf} |
Represents a locus (ORF/gene). |
Regulations |
/regulations/{documented, potential, both}?tf={tf1}&tf={tf2}&…&gene={gene1}&gene={gene2}&… |
|
Regulations |
/regulations/{documented, potential, both}/{each, every}?tf={tf1}&tf={tf2}&…&gene={gene1}&gene={gene2}&…evidence-code={ec1}&evidence-code={ec2}&… |
|
Group By TF |
/group-by-tf?gene={gene1}&gene={gene2}…&tf={tf1}&tf={tf2}…&evidence-code={evidence-code1}&evidence-code={evidence-code2}…®ulation-type={regulation-type} &relative-to={relative-to} |
Represents a grouping of genes by transcription factors that regulate them using the regulation type and evidence codes. The obtained groups are ordered by the percentage of genes regulated by the transcription factor, relative to the total number of genes in the list, or the total number of genes regulated by the same transcription factor. |
References |
/references?tf={tf}&[orf|tfbs]={[orf|tfbs]} |
Represents a list of references for a regulation between a transcription factor and an ORF/gene. |
Retrieves the information about a protein.
A protein name.
Returns the following data for the given protein:
Sample requests using curl:
| parameter | value | description |
|---|---|---|
|
protein |
A protein (transcription factor) name. | |
|
format |
string (optional) One of:
The correspondence between each output format specifier and the MIME types is as follows:
|
The response output format. If not provided defaults to json. |
available response representations:
Retrieves the information about an ORF/gene.
An ORF/gene name.
Returns the available information for the locus.
Sample request using curl:
These parameters are optional, and if provided, and they must be inserted after the ORF/gene name, separated by a semicolon ';'.
| parameter | value | description |
|---|---|---|
|
potential-id |
string (optional) |
A number that identifies the promoter region involved in a potential regulation. The potential ID can obtained from the potential regulations returned by the regulations resource. |
|
tf |
string (optional) |
The TF (transcription factor) responsible for a potential regulation. The TF name can be obtained from the potential regulations returned by the regulations resource. |
|
format |
string (optional) One of:
The correspondence between each output format specifier and the MIME types is as follows:
|
The response output format. If not provided defaults to json. |
available response representations:
Searches for regulations between the transcription factors (TFs) and genes.
For further documentation, please refer to YEASTRACT's web interface help on the following items:
One or more TFs and/or one or more genes and the type of regulation to search for.
Returns a list of regulations between the transcription factors and the given genes, according to the search type.
Sample request using curl:
| parameter | value | description |
|---|---|---|
|
search-type |
string (optional) One of:
|
Searches documented, potential or both types of regulations. If not provided defaults to documented. |
|
tf |
A transcription factor. Repeat the parameter to provide multiple transcription factors. | |
|
gene |
A gene name. Repeat the parameter to provide multiple gene names. | |
|
format |
string (optional) One of:
The correspondence between each output format specifier and the MIME types is as follows:
|
The response output format. If not provided defaults to json. |
available response representations:
Search the database for documented and potential regulatory associations between input TFs and genes.
Please refer to YEASTRACT's web interface Help on Search Regulatory Associations for further documentation.
Optional lists of genes and/or transcription factors, a search mode that indicates how to compare the given TFs and genes, and for documented regulations, the evidence codes to look for.
There are 3 search modes depending on the path parameters provided as transcription factors and/or genes:
Returns a table of the documented and potential regulations between each or every transcription factor in the input and the genes.
Sample request using curl:
| parameter | value | description |
|---|---|---|
|
search-type |
string (optional) One of:
|
Searches documented, potential or both types of regulations. If not provided defaults to documented. |
|
between |
string (optional) One of:
|
Searches for associations between each/every transcription factor and all the genes. |
|
tf |
A transcription factor. Repeat the parameter to provide multiple transcription factors. | |
|
gene |
A gene. Repeat the parameter to provide multiple genes. | |
|
evidence-code |
string (optional) One or more of:
|
Specifies the type of evidence codes to check for. The value all means all three evidence codes. If no evidence codes are provided it defaults to all. |
|
format |
string (optional) One of:
The correspondence between each output format specifier and the MIME types is as follows:
|
The response output format. If not provided defaults to json. |
available response representations:
Groups a given list of genes (e.g., a set of co-activated genes from a microarray experiment) according to the TFs which are their documented or potential regulators.
Please refer to YEASTRACT's web interface Help on Group Genes by TF for further documentation.
Takes as input a list of genes and, optionally, a list of transcription factors.
The TFs considered in this query can be either those in the input list, or all the TFs in the YEASTRACT database (by not providing any TFs). Either documented or potential regulations can be considered (by providing the argument regulation-type with values documented or potential, respectively). Furthermore, for each established regulon, the percentage value representing the proportion of genes regulated by each TF can be calculated relative to:
Returns a list containing the input genes, grouped by TF and ordered by the percentage of genes regulated by the respective TF.
Sample request using curl:
| parameter | value | description |
|---|---|---|
|
gene |
A gene. Repeat the parameter to provide multiple genes. | |
|
tf |
A transcription factor. Repeat the parameter to provide multiple transcription factors. | |
|
regulation-type |
string (optional) One of:
|
Check for documented or potential regulatory associations. If not provided defaults to documented. |
|
evidence-code |
string (optional) One or more of:
|
Specifies the type of evidence codes of the regulatory associations to check for.
|
|
relative-to |
string (optional) One of:
|
Calculate % of genes regulated by TF, relative to:
If not provided defaults to total. |
|
format |
string (optional) One of:
The correspondence between each output format specifier and the MIME types is as follows:
|
The response output format. If not provided defaults to json. |
available response representations:
Returns bibliographic references about a regulation between the transcription factor and ORF/gene or transcription factor binding site.
A TF name
An ORF/Gene name or TFBS
A list of references for the documented or potential regulation between the transcription factor and the given gene or TFBS.
Sample request using curl:
| parameter | value | description |
|---|---|---|
|
tf |
A transcription factor. | |
|
orf |
An ORF/gene. | |
|
tfbs |
A transcription factor binding site. | |
|
format |
string (optional) One of:
The correspondence between each output format specifier and the MIME types is as follows:
|
The response output format. If not provided defaults to json. |
available response representations:
All resources return the following standard HTTP status codes:
| error code | description |
|---|---|
|
200 OK |
Sucess status code |
|
400 Bad request |
The parameters passed to the service did not match as expected. The messages should tell the user what was missing or incorrect. |
|
401 Unauthorized |
The user has no authorization to acess the resource. Use for example when a service is rate limited and the user exceeded his quota. |