Genomic Elements Genes
curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/genomic-elements/genesimport requests
url = "https://catalog-api-dev.demo.igvf.org/api/genomic-elements/genes"
response = requests.get(url)
print(response.text)const options = {method: 'GET'};
fetch('https://catalog-api-dev.demo.igvf.org/api/genomic-elements/genes', 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>",
"biological_context": "<string>",
"biosample_term": "<string>",
"files_filesets": "<string>",
"genomic_element": "<string>",
"gene": "<string>",
"crispr_modality": "<string>",
"score": 123,
"log2FC": 123,
"effect_size": 123,
"p_value": 123,
"p_value_adj": 123,
"neg_log10_pvalue": 123,
"neg_log10_pvalue_adj": 123
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}API Reference
Genomic Elements Genes
Retrieve genomic elements and gene pairs by querying genomic elements.
At least one of these properties must be defined: region, files_fileset, or method.
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
- region = chr1:4126791-4126792 (maximum length: 10kb)
- method = CRISPR screen
Group results
- files_fileset = ENCFF968BZL
- method = CRISPR screen
ENCODE-rE2G:
Single result
- region = chr1:920016-920017 (maximum length: 10kb)
- method = ENCODE-rE2G
- files_fileset = ENCFF666WIM
Group results
- files_fileset = ENCFF666WIM
- method = ENCODE-rE2G
Perturb-seq:
Query by region
- region = chr1:212699339-212700840 (maximum length: 10kb)
- 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
Genomic Elements Genes
curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/genomic-elements/genesimport requests
url = "https://catalog-api-dev.demo.igvf.org/api/genomic-elements/genes"
response = requests.get(url)
print(response.text)const options = {method: 'GET'};
fetch('https://catalog-api-dev.demo.igvf.org/api/genomic-elements/genes', 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>",
"biological_context": "<string>",
"biosample_term": "<string>",
"files_filesets": "<string>",
"genomic_element": "<string>",
"gene": "<string>",
"crispr_modality": "<string>",
"score": 123,
"log2FC": 123,
"effect_size": 123,
"p_value": 123,
"p_value_adj": 123,
"neg_log10_pvalue": 123,
"neg_log10_pvalue_adj": 123
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Query Parameters
Available options:
CA-CTCF: chromatin accessible + CTCF binding, CA-H3K4me3: chromatin accessible + H3K4me3 high signal, CA-TF: chromatin accessible + TF binding, CA: chromatin accessible, PLS: Promoter-like signal, TF: TF binding, dELS: distal Enhancer-like signal, enhancer, genic, intergenic, negative control, pELS: proximal Enhancer-like signal, promoter Available options:
accessible dna elements, candidate cis regulatory element, tested elements Available options:
CRISPR screen, ENCODE-rE2G, Perturb-seq, scE2G Available options:
ENCODE, IGVF Available options:
Homo sapiens Available options:
true, false Response
Successful response