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swagger.yml
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openapi: 3.0.0
info:
description: This is the swagger file that goes with our server code for the sponge REST-API
version: 2.0.0
title: SPONGE REST-API documentation
servers:
- url: /sponge-api
description: Main (production) server
- url: /sponge-api-dev
description: Internal staging server for testing
components:
parameters:
VersionParam:
name: sponge_db_version
in: query
description: The version of the API. The default value is specified in the python functions!
required: false
schema:
type: string
schemas:
TranscriptSchema:
type: object
properties:
enst_number:
type: string
description: Enst number of the transcript.
gene:
type: object
description: Gene the transcript belongs to.
properties:
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature committees such as HGNC (for human). Source - Ensembl - only provided if available.
canonical_transcript:
type: integer
description: Is a canonical transcript
transcript_type:
type: string
description: The transcript type includes both status (e.g. known) and biotype (e.g. protein coding).
start_pos:
type: integer
description: Starting position of the gene.
end_pos:
type: integer
description: Endposition of the gene.
GeneInteractionDatasetLongSchema:
type: object
properties:
correlation:
type: number
description: Correlation of the corresponding ceRNA interaction.
mscor:
type: number
description: Multiple sensitivity correlation (mscor) of the corresponding ceRNA interaction.
p_value:
type: number
description: FDR adjusted p-value of the corresponding ceRNA interaction.
sponge_run:
type: object
description: Information about specific run and corresponding cancer type/dataset.
properties:
dataset:
type: object
properties:
data_origin:
type: string
description: Origin of the dataset.
dataset_ID:
type: integer
description: Internal database ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
gene1:
type: object
description: One of the two interacting ceRNAs.
properties:
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature committees such as HGNC (for human). Source - Ensembl - only provided if available.
gene2:
type: object
description: The other part of the ceRNA interaction.
properties:
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature committees such as HGNC (for human). Source - Ensembl - only provided if available.
TranscriptInteractionDatasetLongSchema:
type: object
properties:
correlation:
type: number
description: Correlation of the corresponding ceRNA interaction.
mscor:
type: number
description: Multiple sensitivity correlation (mscor) of the corresponding ceRNA interaction.
p_value:
type: number
description: FDR adjusted p-value of the corresponding ceRNA interaction.
sponge_run:
type: object
description: Information about specific run and corresponding cancer type/dataset.
properties:
dataset:
type: object
properties:
data_origin:
type: string
description: Origin of the dataset.
dataset_ID:
type: integer
description: Internal database ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
transcript1:
$ref: '#/components/schemas/TranscriptSchema'
transcript2:
$ref: '#/components/schemas/TranscriptSchema'
NetworkAnalysisSchema:
type: object
properties:
betweenness:
type: number
description: Betweenness of the corresponding gene (considered as node) in the specific network.
eigenvector:
type: number
description: Eigenvector of the corresponding gene (considered as node) in the specific network.
node_degree:
type: number
description: Degree of the corresponding gene (considered as node) in the specific network.
gene:
type: object
description: Information about the gene that satisfies all filters.
properties:
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature committees such as HGNC (for human). Source - Ensembl - only provided if available.
sponge_run:
type: object
description: Information about specific run and corresponding cancer type/dataset.
properties:
dataset:
type: object
properties:
data_origin:
type: string
description: Origin of the dataset.
dataset_ID:
type: integer
description: Internal database ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
NetworkAnalysisSchemaTranscript:
type: object
properties:
betweenness:
type: number
description: Betweenness of the corresponding gene (considered as node) in the specific network.
eigenvector:
type: number
description: Eigenvector of the corresponding gene (considered as node) in the specific network.
node_degree:
type: number
description: Degree of the corresponding gene (considered as node) in the specific network.
transcript:
type: object
description: Information about the transcript that satisfies all filters.
properties:
enst_number:
type: string
description: Enst number of the transcript.
gene:
type: object
description: Gene the transcript belongs to.
properties:
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature committees such as HGNC (for human). Source - Ensembl - only provided if available.
sponge_run:
type: object
description: Information about specific run and corresponding cancer type/dataset.
properties:
dataset:
type: object
properties:
data_origin:
type: string
description: Origin of the dataset.
dataset_ID:
type: integer
description: Internal database ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
paths:
/datasets:
get:
operationId: dataset.get_datasets
tags:
- Dataset
summary: Get information on one or more datasets
description: Get information on one or more datasets
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: disease_name
in: query
description: Name of the disease
required: false
schema:
type: string
- name: data_origin
in: query
description: Name of the data origin (e.g. TCGA)
required: false
schema:
type: string
responses:
"200":
description: Successfully read information about datasets of given source.
content:
application/json:
schema:
type: object
properties:
dataset_ID:
type: integer
description: Internal database ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
data_origin:
type: string
description: Cancer type/dataset origin (database name, etc.).
disease_type:
type: string
description: Type of the disease (e.g. cancer).
download_url:
type: string
description: URL to cancer type/dataset annotation.
disease_subtype:
type: string
description: Subtype of specific cancer type (NA if no relevant subtype is present)
sponge_db_version:
type: integer
description: SPONGEdb version used
/dataset/spongeRunInformation:
get:
operationId: dataset.read_spongeRunInformation
tags:
- Dataset
summary: Get all run information about the cancer type/dataset of interest.
description: Retrieve all used parameters of the SPONGE method to create published results for the cancer type/dataset of interest.
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: disease_name
in: query
description: Name of the specific cancer type/dataset. Fuzzy search is available (e.g. "kidney clear cell carcinoma" or just "kidney").
required: false
schema:
type: string
responses:
"200":
description: Successfully read all used parameters for the dataset of interest.
content:
application/json:
schema:
type: array
items:
properties:
coefficient_direction:
type: string
description: If "<", coefficient has to be lower than coefficient.threshold, if ">", coefficient has to be larger than threshold. If NULL, the absolute value of the coefficient has to be larger than the threshold.
coefficient_threshold:
type: string
description: Threshold to cross for a regression coefficient to be called significant. Depends on the parameter coefficient.direction.
dataset:
type: object
description: Information about the cancer type/dataset.
properties:
dataset_ID:
type: integer
description: Internal database ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
required:
- dataset-ID
- disease_name
f_test:
type: boolean
description: If true (1), an F-test is performed on each model parameter to assess its importance for the model based on the RSS of the full model vs the RSS of the nested model without the miRNA in question.
f_test_p_adj_threshold:
type: number
description: If F.test is TRUE (1), threshold to use for miRNAs to be included.
ks:
type: string
description: A sequence of gene-gene correlation values for which null models are computed.
log_level:
type: string
description: The log level, can be one of "info", "debug", "error".
m_max:
type: integer
description: null models are build for each elt in ks for 1 to m_max miRNAs
min_corr:
type: number
description: Consider only gene pairs with a minimum correlation specified here.
number_of_datasets:
type: integer
description: The number of mscor coefficients to be sampled from each covariance matrix.
number_of_samples:
type: integer
description: The number of samples available in the expression data.
sponge_run_ID:
type: integer
description: Internal database ID of the specific parameter setting (=run).
variance_cutoff:
type: string
description: Only consider genes and miRNA with variance > var.threshold. If this parameter is NULL no variance filtering is performed (Parameter name in SPONGE method is var.threshold)
/networkResults:
get:
operationId: network_results.get_network_results
tags:
- network_results
summary: Get information about all cancer types/datasets or specific one.
description: Get information about all available datasets to start browsing or search for a specific cancer type/dataset.
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: disease_name
in: query
description: Name of the specific cancer type.
required: false
schema:
type: string
- name: level
in: query
description: gene or transcript
required: false
schema:
type: string
responses:
"200":
description: Successfully read network result information about all cancer types and subtypes if avaliable.
content:
application/json:
schema:
type: object
properties:
type:
type: object
properties:
scores:
type: object
properties:
labels:
type: array
description: list of cancer type names
values:
type: object
description: matrix of hubness scores
euclidean_distances:
type: object
properties:
x:
type: array
description: list of x coordinates
y:
type: array
description: list of y coordinates
labels:
type: array
description: list of cancer type names
subtype:
type: object
properties:
scores:
type: object
properties:
labels:
type: array
description: list of cancer type names
values:
type: object
description: matrix of hubness scores
euclidean_distances:
type: object
properties:
x:
type: array
description: list of x coordinates
y:
type: array
description: list of y coordinates
labels:
type: array
description: list of cancer type names
/ceRNAInteraction/checkGeneInteraction:
get:
operationId: geneInteraction.testGeneInteraction
tags:
- ceRNANetwork
summary: Tests for specific gene if has at least one interaction in each cancer type/dataset.
description: Tests for specific gene (identified by ensg number or gene symbol) if has at least one interaction in each cancer type/dataset.
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: ensg_number
in: query
description: Ensg number of the gene of interest (e.g. ENSG00000259090).
required: false
schema:
type: string
- name: gene_symbol
in: query
description: Symbol of the gene of interest (e.g. SEPT7P1).
required: false
schema:
type: string
responses:
"200":
description: Tests for specific gene (identified by ensg number or gene symbol) if has at least one interaction in each cancer type/dataset.
content:
application/json:
schema:
type: object
items:
properties:
data_origin:
type: string
description: Origin of the dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
include:
type: integer
description: Result of the test. 0 means the gene is not included in the corresponding ceRNA interaction network. 1 mean the gene is a part of the ceRNA network.
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
/ceRNAInteraction/checkTranscriptInteraction:
get:
operationId: transcriptInteraction.test_transcript_interaction
tags:
- ceRNANetwork
summary: Tests for specific transcript if has at least one interaction in each cancer type/dataset.
description: Tests for specific transcript (identified by ensg number or gene symbol) if has at least one interaction in each cancer type/dataset.
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: enst_number
in: query
description: Enst number of the transcript of interest.
required: false
schema:
type: string
responses:
"200":
description: Tests for specific gene (identified by ensg number or gene symbol) if has at least one interaction in each cancer type/dataset.
content:
application/json:
schema:
type: object
items:
properties:
data_origin:
type: string
description: Origin of the dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
include:
type: integer
description: Result of the test. 0 means the gene is not included in the corresponding ceRNA interaction network. 1 mean the gene is a part of the ceRNA network.
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
/ceRNAInteraction/findAll:
get:
operationId: geneInteraction.read_all_genes
tags:
- ceRNANetwork
summary: Get all ceRNA interactions the gene(s) of interest is/are involed in.
description: Get all ceRNA interactions by given identifications (ensg_number, gene_symbol or gene_type), specific cancer type/dataset or different filter possibilities according different statistical values (e.g. FDR adjusted p-value).
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: disease_name
in: query
description: Name of the specific cancer type/dataset. Fuzzy search is available (e.g. "kidney clear cell carcinoma" or just "kidney").
required: false
schema:
type: string
- name: ensg_number
in: query
description: A comma-separated list of ensg number(s) of the gene(s) of interest (e.g. ENSG00000259090, ENSG00000217289).
required: false
schema:
type: array
items:
type: string
minItems: 0
explode: false
style: form
- name: gene_symbol
in: query
description: A comma-separated list of gene symbol(s) of the gene(s) of interest (e.g. SEPT7P1,TIGAR).
required: false
schema:
type: array
items:
type: string
minItems: 0
explode: false
style: form
- name: gene_type
in: query
description: Defines the type of gene of interest (only one possibility choosable).
required: false
schema:
type: string
enum:
- 3prime_overlapping_ncRNA
- antisense
- antisense_RNA
- bidirectional_promoter_lncRNA
- IG_C_gene
- IG_C_pseudogene
- IG_V_gene
- IG_V_pseudogene
- lincRNA
- macro_lncRNA
- miRNA
- misc_RNA
- Mt_rRNA
- polymorphic_pseudogene
- processed_pseudogene
- processed_transcript
- protein_coding
- pseudogene
- ribozyme
- rRNA
- rRNA_pseudogene
- scaRNA
- scRNA
- sense_intronic
- sense_overlapping
- snoRNA
- snRNA
- TEC
- TR_C_gene
- TR_V_gene
- TR_V_pseudogene
- transcribed_processed_pseudogene
- transcribed_unitary_pseudogene
- transcribed_unprocessed_pseudogene
- translated_processed_pseudogene
- unitary_pseudogene
- unprocessed_pseudogene
- vaultRNA
- name: pValue
in: query
required: false
description: Threshold of the FDR adjusted p-value. Default is 0.05.
schema:
type: number
default: 0.05
- name: pValueDirection
in: query
required: false
description: Direction of the FDR adjusted p-value threshold (<=, >=).
schema:
type: string
enum:
- <
- ">"
default: <
- name: mscor
in: query
required: false
description: Threshold of the 'multiple sensitivity correlation' (mscor).
schema:
type: number
- name: mscorDirection
in: query
required: false
description: Direction of the mscor threshold (<=, >=).
schema:
type: string
enum:
- <
- ">"
default: <
- name: correlation
in: query
required: false
description: Threshold of the correlation.
schema:
type: number
- name: correlationDirection
in: query
required: false
description: Direction of the correlation threshold (<=, >=).
schema:
type: string
enum:
- <
- ">"
default: <
- name: sorting
in: query
required: false
description: Possibilities for sorting of the results.
schema:
type: string
enum:
- pValue
- mscor
- correlation
- name: descending
in: query
required: false
description: Descending (true) or ascending (false) ordering of the results.
schema:
type: boolean
default: true
- name: limit
in: query
description: Number of results that should be shown. Default value is 100 and can be up to 1000. For more results please use batches, the provided offset parameter or download the whole dataset.
required: false
schema:
type: integer
default: 100
- name: offset
in: query
description: Starting point from where results should be shown.
required: false
schema:
type: integer
- name: information
in: query
description: All available information about genes displayed (true) or just ensg number (false).
required: false
schema:
type: boolean
default: true
responses:
"200":
description: Read all ceRNA interactions where gene of interesest in
the searched disease (if provided) is involved in
content:
application/json:
schema:
type: array
items:
properties:
correlation:
type: number
description: Correlation of the corresponding ceRNA interaction.
gene1:
type: object
description: One of the two interacting ceRNAs.
properties:
chromosome_name:
type: integer
description: Name of the chromosome the gene is located on.
description:
type: string
description: Anntotation from Ensemble of the gene.
end_pos:
type: integer
description: Endposition of the gene.
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature commitees such as HGNC (for human). Source - Ensmble - only provided if available.
gene_type:
type: string
description: The gene type includes both status (e.g. known) and biotype (e.g. protein coding).
start_pos:
type: integer
description: Starting position of the gene.
gene2:
type: object
description: The other part of the ceRNA interaction.
properties:
chromosome_name:
type: integer
description: Name of the chromosome the gene is located on.
description:
type: string
description: Anntotation from Ensemble of the gene.
end_pos:
type: integer
description: Endposition of the gene.
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature commitees such as HGNC (for human). Source - Ensmble - only provided if available.
gene_type:
type: string
description: The gene type includes both status (e.g. known) and biotype (e.g. protein coding).
start_pos:
type: integer
description: Starting position of the gene.
mscor:
type: number
description: Multiple senstivity correlation (mscor) of the corresponding ceRNA interaction.
p_value:
type: number
description: FDR adjusted p-value of the corresponding ceRNA interaction.
sponge_run:
description: Information about specific run and corresponding cancer type/dataset.
type: object
properties:
dataset:
type: object
properties:
data_origin:
type: string
description: Origin of the dataset.
dataset_ID:
type: integer
description: Internal databse ID of the cancer type/dataset.
disease_name:
type: string
description: Name of the cancer type/dataset.
required:
- dataset_Id
- disease_name
sponge_run_ID:
type: integer
description: Internal database ID for different runs with SPONGE with the same expression values for one cancer_type/dataset.
required:
- dataset
- sponge_run_ID
/ceRNAInteraction/findAllTranscripts:
get:
operationId: transcriptInteraction.read_all_transcripts
tags:
- ceRNANetwork
summary: Get all ceRNA interactions the transcript(s) of interest is/are involed in.
description: Get all ceRNA interactions by given identifications (enst_number or transcript_type), specific cancer type/dataset or different filter possibilities according different statistical values (e.g. FDR adjusted p-value).
parameters:
- $ref: '#/components/parameters/VersionParam'
- name: dataset_ID
in: query
description: Internal database ID of the cancer type/dataset.
required: false
schema:
type: integer
- name: disease_name
in: query
description: Name of the specific cancer type/dataset. Fuzzy search is available (e.g. "kidney clear cell carcinoma" or just "kidney").
required: false
schema:
type: string
- name: enst_number
in: query
description: A comma-separated list of enst number(s) of interest (e.g. ENST00000369985).
required: false
schema:
type: array
items:
type: string
minItems: 0
explode: false
style: form
- name: transcript_type
in: query
description: Defines the type of transcripts of interest (only one possibility choosable).
required: false
schema:
type: string
enum:
- 3prime_overlapping_ncRNA
- antisense
- antisense_RNA
- bidirectional_promoter_lncRNA
- IG_C_gene
- IG_C_pseudogene
- IG_V_gene
- IG_V_pseudogene
- lincRNA
- macro_lncRNA
- miRNA
- misc_RNA
- Mt_rRNA
- polymorphic_pseudogene
- processed_pseudogene
- processed_transcript
- protein_coding
- pseudogene
- ribozyme
- rRNA
- rRNA_pseudogene
- scaRNA
- scRNA
- sense_intronic
- sense_overlapping
- snoRNA
- snRNA
- TEC
- TR_C_gene
- TR_V_gene
- TR_V_pseudogene
- transcribed_processed_pseudogene
- transcribed_unitary_pseudogene
- transcribed_unprocessed_pseudogene
- translated_processed_pseudogene
- unitary_pseudogene
- unprocessed_pseudogene
- vaultRNA
- name: pValue
in: query
required: false
description: Threshold of the FDR adjusted p-value. Default is 0.05.
schema:
type: number
default: 0.05
- name: pValueDirection
in: query
required: false
description: Direction of the FDR adjusted p-value threshold (<=, >=).
schema:
type: string
enum:
- <
- ">"
default: <
- name: mscor
in: query
required: false
description: Threshold of the 'multiple sensitivity correlation' (mscor).
schema:
type: number
- name: mscorDirection
in: query
required: false
description: Direction of the mscor threshold (<=, >=).
schema:
type: string
enum:
- <
- ">"
default: <
- name: correlation
in: query
required: false
description: Threshold of the correlation.
schema:
type: number
- name: correlationDirection
in: query
required: false
description: Direction of the correlation threshold (<=, >=).
schema:
type: string
enum:
- <
- ">"
default: <
- name: sorting
in: query
required: false
description: Possibilities for sorting of the results.
schema:
type: string
enum:
- pValue
- mscor
- correlation
- name: descending
in: query
required: false
description: Descending (true) or ascending (false) ordering of the results.
schema:
type: boolean
default: true
- name: limit
in: query
description: Number of results that should be shown. Default value is 100 and can be up to 1000. For more results please use batches, the provided offset parameter or download the whole dataset.
required: false
schema:
type: integer
default: 100
- name: offset
in: query
description: Starting point from where results should be shown.
required: false
schema:
type: integer
- name: information
in: query
description: All available information about genes displayed (true) or just enst number (false).
required: false
schema:
type: boolean
default: true
responses:
"200":
description: Read all ceRNA interactions where transcript of interesest in
the searched disease (if provided) is involved in
content:
application/json:
schema:
type: array
items:
properties:
correlation:
type: number
description: Correlation of the corresponding ceRNA interaction.
transcript_1:
type: object
description: One of the two interacting ceRNAs.
properties:
gene:
type: object
description: gene the transcript belongs to
properties:
ensg_number:
type: string
description: Ensg number of the gene.
gene_symbol:
type: string
description: From official gene nomenclature commitees such as HGNC (for human). Source - Ensmble - only provided if available.
description:
type: string
description: Anntotation from Ensemble of the gene.
end_pos:
type: integer
description: Endposition of the trancript.
enst_number:
type: string
description: Ensg number of the gene.
transcript_type: