JASPAR Database

JASPAR Database

Overview

JASPAR is a curated, open-access database of transcription factor (TF) binding profiles represented as position frequency matrices (PFMs). The 2024 release contains 1,209 profiles in the CORE vertebrate collection, covering 783 TFs with experimentally validated binding data from SELEX, ChIP-seq, and PBM experiments. Access is free via the JASPAR REST API at https://jaspar.elixir.no/api/v1/ — no authentication required — and through the pyJASPAR Python library for matrix retrieval and manipulation.

When to Use

• Looking up the PWM or PFM for a specific TF by name (e.g., CTCF, SP1, GATA1) to use as motif input for a scanning tool
• Retrieving all JASPAR profiles for a species (e.g., Homo sapiens, Mus musculus) to build a motif library for enrichment analysis
• Scanning a DNA promoter sequence for predicted TF binding sites using a known PWM
• Finding all TFs of a given structural class (bHLH, zinc finger, homeodomain) to build a TF family binding profile set
• Getting metadata for a JASPAR matrix: number of binding sites, information content, GC content, experiment type
• Downloading complete JASPAR collection sets (CORE, UNVALIDATED, CNE) in JASPAR or MEME format for batch analysis
• Use homer-motif-analysis instead when you need de novo motif discovery from ChIP-seq peaks; JASPAR is for retrieving known matrices
• For regulatory element annotations tied to a genomic region use encode-database or regulomedb-database

Prerequisites

• Python packages: requests, pandas, matplotlib, numpy
• Optional: pyJASPAR (Python library wrapping JASPAR REST API with BIOPYTHON motif objects)
• Data requirements: TF gene symbols, JASPAR matrix IDs (e.g., MA0139.1), or DNA sequences (string or FASTA)
• Environment: internet connection; no API key required
• Rate limits: no official published limits; use time.sleep(0.5) between batch requests

pip install requests pandas matplotlib numpy
pip install pyJASPAR   # optional; pulls in biopython

Quick Start

import requests

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

# Search for CTCF profile in the CORE vertebrate collection
r = requests.get(f"{JASPAR_API}/matrix/", params={
    "search": "CTCF",