jaspar-database

JASPAR 数据库

概述

JASPAR（https://jaspar.elixir.no/）是经过整理、非冗余的转录因子（TF）结合谱开放访问数据库的行业标杆，这些结合谱以位置频率矩阵（PFM）的形式存储。JASPAR 2024 收录了 164 种真核生物的 1,210 个非冗余 TF 结合谱。每个谱均通过实验获得（ChIP-seq、SELEX、HT-SELEX、蛋白质结合微阵列等），并经过严格验证。

核心资源：

• JASPAR 门户：https://jaspar.elixir.no/
• REST API：https://jaspar.elixir.no/api/v1/
• API 文档：https://jaspar.elixir.no/api/v1/docs/
• Python 包：jaspar（通过 Biopython）或直接使用 API

何时使用此技能

以下情况可使用 JASPAR：

• 预测 TF 结合位点：扫描 DNA 序列，查找 TF 的潜在结合位点
• 调控变异解读：GWAS/eQTL 变异是否会破坏 TF 结合基序？
• 启动子/增强子分析：预测哪些 TF 会结合调控元件？
• 构建基因调控网络：通过基序扫描将 TF 与其靶基因关联起来
• TF 家族分析：比较 TF 家族内的结合谱（例如，所有同源异型框因子）
• ChIP-seq 分析：查找在 ChIP-seq 峰中富集的已知 TF 基序
• ENCODE/ATAC-seq 解读：将开放染色质区域与 TF 结合谱匹配

核心功能

1. JASPAR REST API

基础 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. 搜索 TF 谱

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")

3. 获取特定矩阵（PFM/PWM）

def get_matrix(matrix_id):
    """Fetch a specific JASPAR matrix by ID (e.g., 'MA0139.1' for CTCF)."""
    return jaspar_get(f"matrix/{matrix_id}/")

# Example: Get CTCF matrix
ctcf_matrix = get_matrix("MA0139.1")

# Matrix structure:
# {
#   "matrix_id": "MA0139.1",
#   "name": "CTCF",
#   "collection": "CORE",
#   "tax_group": "vertebrates",
#   "pfm": { "A": [...], "C": [...], "G": [...], "T": [...] },
#   "consensus": "CCGCGNGGNGGCAG",
#   "length": 19,
#   "species": [{"tax_id": 9606, "name": "Homo sapiens"}],
#   "class": ["C2H2 zinc finger factors"],
#   "family": ["BEN domain factors"],
#   "type": "ChIP-seq",
#   "uniprot_ids": ["P49711"]
# }

4. 将 PFM/PWM 下载为矩阵

import numpy as np

def get_pwm(matrix_id, pseudocount=0.8):
    """
    Fetch a PFM from JASPAR and convert to PWM (log-odds).
    Returns numpy array of shape (4, L) in order A, C, G, T.
    """
    matrix = get_matrix(matrix_id)
    pfm = matrix["pfm"]

    # Convert PFM to numpy
    pfm_array = np.array([pfm["A"], pfm["C"], pfm["G"], pfm["T"]], dtype=float)

    # Add pseudocount
    pfm_array += pseudocount

    # Normalize to get PPM
    ppm = pfm_array / pfm_array.sum(axis=0, keepdims=True)

    # Convert to PWM (log-odds relative to background 0.25)
    background = 0.25
    pwm = np.log2(ppm / background)

    return pwm, matrix["name"]

# Example
pwm, name = get_pwm("MA0139.1")  # CTCF
print(f"PWM for {name}: shape {pwm.shape}")
max_score = pwm.max(axis=0).sum()
print(f"Maximum possible score: {max_score:.2f} bits")

5. 扫描 DNA 序列以查找 TF 结合位点

import numpy as np
from typing import List, Tuple

NUCLEOTIDE_MAP = {'A': 0, 'C': 1, 'G': 2, 'T': 3,
                  'a': 0, 'c': 1, 'g': 2, 't': 3}

def scan_sequence(sequence: str, pwm: np.ndarray, threshold_pct: float = 0.8) -> List[dict]:
    """
    Scan a DNA sequence for TF binding sites using a PWM.

    Args:
        sequence: DNA sequence string
        pwm: PWM array (4 x L) in ACGT order
        threshold_pct: Fraction of max score to use as threshold (0-1)

    Returns:
        List of hits with position, score, and matched sequence
    """
    motif_len = pwm.shape[1]
    max_score = pwm.max(axis=0).sum()
    min_score = pwm.min(axis=0).sum()
    threshold = min_score + threshold_pct * (max_score - min_score)

    hits = []
    seq = sequence.upper()

    for i in range(len(seq) - motif_len + 1):
        subseq = seq[i:i + motif_len]
        # Skip if contains non-ACGT
        if any(c not in NUCLEOTIDE_MAP for c in subseq):
            continue

        score = sum(pwm[NUCLEOTIDE_MAP[c], j] for j, c in enumerate(subseq))

        if score >= threshold:
            relative_score = (score - min_score) / (max_score - min_score)
            hits.append({
                "position": i + 1,  # 1-based
                "score": score,
                "relative_score": relative_score,
                "sequence": subseq,
                "strand": "+"
            })

    return hits

# Example: Scan a promoter sequence for CTCF binding sites
promoter = "AGCCCGCGAGGNGGCAGTTGCCTGGAGCAGGATCAGCAGATC"
pwm, name = get_pwm("MA0139.1")
hits = scan_sequence(promoter, pwm, threshold_pct=0.75)
for hit in hits:
    print(f"  Position {hit['position']}: {hit['sequence']} (score: {hit['score']:.2f}, {hit['relative_score']:.0%})")

6. 扫描两条链

def reverse_complement(seq: str) -> str:
    complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', 'N': 'N'}
    return ''.join(complement.get(b, 'N') for b in reversed(seq.upper()))

def scan_both_strands(sequence: str, pwm: np.ndarray, threshold_pct: float = 0.8):
    """Scan forward and reverse complement strands."""
    fwd_hits = scan_sequence(sequence, pwm, threshold_pct)
    for h in fwd_hits:
        h["strand"] = "+"

    rev_seq = reverse_complement(sequence)
    rev_hits = scan_sequence(rev_seq, pwm, threshold_pct)
    seq_len = len(sequence)
    for h in rev_hits:
        h["strand"] = "-"
        h["position"] = seq_len - h["position"] - len(h["sequence"]) + 2  # Convert to fwd coords

    all_hits = fwd_hits + rev_hits
    return sorted(all_hits, key=lambda x: x["position"])

7. 变异对 TF 结合的影响

def variant_tfbs_impact(ref_seq: str, alt_seq: str, pwm: np.ndarray,
                          tf_name: str, threshold_pct: float = 0.7):
    """
    Assess impact of a SNP on TF binding by comparing ref vs alt sequences.
    Both sequences should be centered on the variant with flanking context.
    """
    ref_hits = scan_both_strands(ref_seq, pwm, threshold_pct)
    alt_hits = scan_both_strands(alt_seq, pwm, threshold_pct)

    max_ref = max((h["score"] for h in ref_hits), default=None)
    max_alt = max((h["score"] for h in alt_hits), default=None)

    result = {
        "tf": tf_name,
        "ref_max_score": max_ref,
        "alt_max_score": max_alt,
        "ref_has_site": len(ref_hits) > 0,
        "alt_has_site": len(alt_hits) > 0,
    }
    if max_ref and max_alt:
        result["score_change"] = max_alt - max_ref
        result["effect"] = "gained" if max_alt > max_ref else "disrupted"
    elif max_ref and not max_alt:
        result["effect"] = "disrupted"
    elif not max_ref and max_alt:
        result["effect"] = "gained"
    else:
        result["effect"] = "no_site"

    return result

查询工作流

工作流 1：查找启动子中的所有 TF 结合位点

import requests, numpy as np

# 1. Get relevant TF matrices (e.g., all human TFs in CORE collection)
response = requests.get(
    "https://jaspar.elixir.no/api/v1/matrix/",
    params={"species": "9606", "collection": "CORE", "page_size": 500, "page": 1}
)
matrices = response.json()["results"]

# 2. For each matrix, compute PWM and scan promoter
promoter = "CCCGCCCGCCCGCCGCCCGCAGTTAATGAGCCCAGCGTGCC"  # Example

all_hits = []
for m in matrices[:10]:  # Limit for demo
    pwm_data = requests.get(f"https://jaspar.elixir.no/api/v1/matrix/{m['matrix_id']}/").json()
    pfm = pfm_data["pfm"]
    pfm_arr = np.array([pfm["A"], pfm["C"], pfm["G"], pfm["T"]], dtype=float) + 0.8
    ppm = pfm_arr / pfm_arr.sum(axis=0)
    pwm = np.log2(ppm / 0.25)

    hits = scan_sequence(promoter, pwm, threshold_pct=0.8)
    for h in hits:
        h["tf_name"] = m["name"]
        h["matrix_id"] = m["matrix_id"]
    all_hits.extend(hits)

print(f"Found {len(all_hits)} TF binding sites")
for h in sorted(all_hits, key=lambda x: -x["score"])[:5]:
    print(f"  {h['tf_name']} ({h['matrix_id']}): pos {h['position']}, score {h['score']:.2f}")

工作流 2：SNP 对 TF 结合的影响（调控变异分析）

1. 获取 SNP 两侧的基因组序列（每侧 ±20 bp）
2. 构建 ref 和 alt 序列
3. 使用所有相关 TF PWM 进行扫描
4. 报告因 SNP 而新产生或消失结合的 TF

工作流 3：基序富集分析

1. 确定一组峰序列（例如，来自 ChIP-seq 或 ATAC-seq）
2. 使用 JASPAR PWM 扫描所有峰
3. 比较峰序列与背景序列中的命中率
4. 报告显著富集的基序（Fisher 精确检验或 FIMO 风格评分）

可用集合

集合	说明	谱数量
CORE	非冗余、高质量谱	~1,210
UNVALIDATED	通过实验获得但尚未验证	~500
PHYLOFACTS	系统发育上保守的位点	~50
CNE	保守非编码元件	~30
POLII	RNA Pol II 结合谱	~20
FAM	TF 家族代表性谱	~170
SPLICE	剪接因子谱	~20

最佳实践

• 大多数分析使用 CORE 集合——其验证最充分且非冗余
• 阈值选择：从头预测通常使用最高分的 80%；高置信度分析使用 90%
• 始终扫描两条链——TF 可以沿任一方向结合
• 变异分析时提供侧翼序列：每侧至少包含（基序长度 - 1）bp
• 考虑背景：PWM 分数基于均匀（0.25）背景；应根据实际 GC 含量进行调整
• 条件允许时使用 ChIP-seq 数据交叉验证——基序扫描会产生许多假阳性
• 使用 Biopython 的 motifs 模块进行完整功能的扫描：from Bio import motifs

Additional Resources

• JASPAR portal: https://jaspar.elixir.no/
• API documentation: https://jaspar.elixir.no/api/v1/docs/
• JASPAR 2024 paper: Castro-Mondragon et al. (2022) Nucleic Acids Research. PMID: 34875674
• Biopython motifs: https://biopython.org/docs/latest/Tutorial/chapter_motifs.html
• FIMO tool (for large-scale scanning): https://meme-suite.org/meme/tools/fimo
• HOMER (motif enrichment): http://homer.ucsd.edu/homer/
• GitHub: https://github.com/wassermanlab/JASPAR-UCSC-tracks