Genes Genomic Elements

curl --request GET \
  --url https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elements

import 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>",
    "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

Genes Genomic Elements

Retrieve genomic elements and gene pairs by querying genes.

One of these fields is required: gene_id, hgnc_id, gene_name, alias, 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

Genes Genomic Elements

curl --request GET \
  --url https://catalog-api-dev.demo.igvf.org/api/genes/genomic-elements

import 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>",
    "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

gene_id

string

hgnc_id

string

gene_name

string

alias

string

method

enum<string>

Available options:

CRISPR screen,

ENCODE-rE2G,

Perturb-seq,

scE2G

files_fileset

string

biosample_term

string

biological_context

string

source

enum<string>

Available options:

ENCODE,

IGVF

organism

enum<string>

default:Homo sapiens

Available options:

Homo sapiens

verbose

enum<string>

default:false

Available options:

true,

false

page

number

default:0

limit

number

Response

Successful response

name

string

required

label

string

required

method

string

required

class

string

required

source

string

required

source_url

string

required

biological_context

string

required

biosample_term

string

required

files_filesets

string

required

genomic_element

required

gene

required

crispr_modality

string | null

score

number | null

log2FC

number | null

effect_size

number | null

p_value

p_value_adj

neg_log10_pvalue

neg_log10_pvalue_adj

Genes Transcripts Genes Proteins Variants

Overview

Endpoints

Genes Genomic Elements

Query Parameters

Response