Genomic Elements Genes

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

import 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/genes

import 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

region

string

source_annotation

enum<string>

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

region_type

enum<string>

Available options:

accessible dna elements,

candidate cis regulatory element,

tested elements

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

Genomic Elements Genomic Elements Variants

Overview

Endpoints

Genomic Elements Genes

Query Parameters

Response