jaspar-database

JASPAR Database

Overview

JASPAR (https://jaspar.elixir.no/) is the gold-standard open-access database of curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs). JASPAR 2024 contains 1,210 non-redundant TF binding profiles for 164 eukaryotic species. Each profile is experimentally derived (ChIP-seq, SELEX, HT-SELEX, protein binding microarray, etc.) and rigorously validated.

Key resources:

• JASPAR portal: https://jaspar.elixir.no/
• REST API: https://jaspar.elixir.no/api/v1/
• API docs: https://jaspar.elixir.no/api/v1/docs/
• Python package: jaspar (via Biopython) or direct API

When to Use This Skill

Use JASPAR when:

• TF binding site prediction: Scan a DNA sequence for potential binding sites of a TF
• Regulatory variant interpretation: Does a GWAS/eQTL variant disrupt a TF binding motif?
• Promoter/enhancer analysis: What TFs are predicted to bind to a regulatory element?
• Gene regulatory network construction: Link TFs to their target genes via motif scanning
• TF family analysis: Compare binding profiles across a TF family (e.g., all homeobox factors)
• ChIP-seq analysis: Find known TF motifs enriched in ChIP-seq peaks
• ENCODE/ATAC-seq interpretation: Match open chromatin regions to TF binding profiles

Core Capabilities

1. JASPAR REST API

Base URL: https://jaspar.elixir.no/api/v1/

import requests

BASE_URL = "https://jaspar.elixir.no/api/v1"

def jaspar_get(endpoint, params=None):
    url = f"{BASE_URL}/{endpoint}"
    response = requests.get(url, params=params, headers={"Accept": "application/json"})
    response.raise_for_status()
    return response.json()

2. Search for TF Profiles

def search_jaspar(
    tf_name=None,
    species=None,
    collection="CORE",
    tf_class=None,
    tf_family=None,
    page=1,
    page_size=25
):
    """Search JASPAR for TF binding profiles."""
    params = {
        "collection": collection,
        "page": page,
        "page_size": page_size,
        "format": "json"
    }
    if tf_name:
        params["name"] = tf_name
    if species:
        params["species"] = species  # Use taxonomy ID or name, e.g., "9606" for human
    if tf_class:
        params["tf_class"] = tf_class
    if tf_family:
        params["tf_family"] = tf_family

    return jaspar_get("matrix", params)

# Examples:
# Search for human CTCF profile
ctcf = search_jaspar("CTCF", species="9606")
print(f"Found {ctcf['count']} CTCF profiles")

# Search for all homeobox TFs in human
hox_tfs = search_jaspar(tf_class="Homeodomain", species="9606")

# Search for a TF family
nfkb = search_jaspar(tf_family="NF-kappaB")