curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elementsimport requests
url = "https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elements"
response = requests.get(url)
print(response.text)const options = {method: 'GET'};
fetch('https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elements', options)
.then(res => res.json())
.then(res => console.log(res))
.catch(err => console.error(err));[
{
"name": "<string>",
"label": "<string>",
"method": "<string>",
"class": "<string>",
"source": "<string>",
"source_url": "<string>",
"files_filesets": "<string>",
"genomic_element": "<string>",
"gene": "<string>",
"biological_context": "<string>",
"biosample_term": "<string>",
"cell_annotation": "<string>",
"cell_annotation_term": "<string>",
"crispr_modality": "<string>",
"score": 123,
"transcription_start_site": 123,
"rna_pseudobulk_tpm": 123,
"log2FC": 123,
"effect_size": 123,
"z_score": 123,
"t_score": 123,
"idr": 123,
"p_value": 123,
"p_value_adj": 123,
"neg_log10_pvalue": 123,
"neg_log10_pvalue_adj": 123,
"significant": true
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Genes Genomic Elements
Retrieve genomic elements and gene pairs by querying genes.
One of these fields is required: gene_id, hgnc_id, gene_name, synonym, method, or files_fileset.
Set verbose = true to retrieve full info on the genes and genomic element.
The limit parameter controls the page size and can not exceed 500.
Pagination is 0-based.
Examples by method
These examples are grouped by method; use the method filter to return data from a specific method.
CRISPR screen:
Single result
- gene_id = ENSG00000116198
- method = CRISPR screen
Group results
- method = CRISPR screen
- files_fileset = ENCFF968BZL
ENCODE-rE2G:
query by gene identifier
- gene_id = ENSG00000225880
- biosample_term = EFO_0002330
- method = ENCODE-rE2G
query by files_fileset
Each files_fileset maps to at most one method, so a method filter is usually not necessary.
- files_fileset = ENCFF425TLX
- method = ENCODE-rE2G
Perturb-seq:
query by gene identifier
- gene_id = ENSG00000123685
- method = Perturb-seq
query by files_fileset
Each files_fileset maps to at most one method, so a method filter is usually not necessary.
- files_fileset = IGVFFI3069QCRA
- method = Perturb-seq
scE2G:
query by gene identifier
- gene_id = ENSG00000156875
- method = scE2G
query by files_fileset
Each files_fileset maps to at most one method, so a method filter is usually not necessary.
- files_fileset = IGVFFI4235YTNW
- method = scE2G
curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elementsimport requests
url = "https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elements"
response = requests.get(url)
print(response.text)const options = {method: 'GET'};
fetch('https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elements', options)
.then(res => res.json())
.then(res => console.log(res))
.catch(err => console.error(err));[
{
"name": "<string>",
"label": "<string>",
"method": "<string>",
"class": "<string>",
"source": "<string>",
"source_url": "<string>",
"files_filesets": "<string>",
"genomic_element": "<string>",
"gene": "<string>",
"biological_context": "<string>",
"biosample_term": "<string>",
"cell_annotation": "<string>",
"cell_annotation_term": "<string>",
"crispr_modality": "<string>",
"score": 123,
"transcription_start_site": 123,
"rna_pseudobulk_tpm": 123,
"log2FC": 123,
"effect_size": 123,
"z_score": 123,
"t_score": 123,
"idr": 123,
"p_value": 123,
"p_value_adj": 123,
"neg_log10_pvalue": 123,
"neg_log10_pvalue_adj": 123,
"significant": true
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Query Parameters
CRISPR screen, ENCODE-rE2G, Perturb-seq, scE2G ENCODE, IGVF Homo sapiens true, false Response
Successful response