ChIPAtlas Enrichment Analysis

Overview

Perform enrichment analysis to identify transcription factors and histone modifications enriched in your data. **Required: Provide ONE input type** - (1) BED genomic regions, (2) DNA sequence motif (IUPAC notation: A/T/G/C/W/S/M/K/R/Y/B/D/H/V/N), or (3) gene symbol list. Compares your input against 433,000+ ChIP-seq/ATAC-seq/Bisulfite-seq experiments to identify significant enrichment. Returns ranked list of proteins bound to your regions/motif or regulating your genes. Note: Returns submission URL (web form-based analysis). Use for: identifying regulators of genomic regions, finding proteins bound to sequence motifs, discovering transcription factors regulating gene sets.

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed

1d ago

Last success

1d ago

Last latency

5720ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "antigen_class": {
      "description": "Filter by antigen class (e.g., 'TFs and others', 'Histone', 'RNA polymerase')",
      "type": "string"
    },
    "bed_data": {
      "description": "**Option 1**: BED format genomic regions (tab-separated: chr, start, end). For finding proteins bound to specific genomic regions. Example: 'chr1\\t1000\\t2000\\nchr2\\t3000\\t4000'.",
      "type": "string"
    },
    "cell_type_class": {
      "description": "Filter by cell type class (e.g., 'Blood', 'Liver', 'Brain')",
      "type": "string"
    },
    "distance": {
      "default": "5000",
      "description": "Distance from Transcription Start Site (TSS) in base pairs for gene-TF association. Defines promoter region. Default 5000 (±5kb, captures typical promoters). Use 1000-2000 for narrow promoters, 10000+ for enhancer regions.",
      "type": "string"
    },
    "gene_list": {
      "description": "**Option 3**: Gene symbols (HGNC for human, MGI for mouse, RGD for rat, FlyBase, WormBase, SGD for yeast). Provide as array or single gene. For finding transcription factors regulating genes. Example: ['TP53', 'MDM2', 'CDKN1A'].",
      "items": {
        "type": "string"
      },
      "type": [
        "array",
        "string"
      ]
    },
    "genome": {
      "default": "hg38",
      "description": "Genome assembly",
      "enum": [
        "hg38",
        "hg19",
        "mm10",
        "mm9",
        "rn6",
        "dm6",
        "dm3",
        "ce11",
        "ce10",
        "sacCer3"
      ],
      "type": "string"
    },
    "motif": {
      "description": "**Option 2**: DNA sequence motif in IUPAC notation. Use: A/T/G/C (bases), W=A|T, S=G|C, M=A|C, K=G|T, R=A|G, Y=C|T, B=C|G|T, D=A|G|T, H=A|C|T, V=A|C|G, N=any. For finding proteins bound to specific DNA sequences. Example: 'CANNTG' (E-box motif).",
      "type": "string"
    },
    "operation": {
      "default": "enrichment_analysis",
      "enum": [
        "enrichment_analysis"
      ],
      "type": "string"
    },
    "threshold": {
      "default": "05",
      "description": "Peak calling stringency (MACS2 Q-value). Options: '05'=1e-5 (permissive, more peaks, broader features), '10'=1e-10 (moderate, balanced), '20'=1e-20 (strict, high confidence only, narrow peaks). Default '05' suitable for most analyses. Higher values = fewer but more confident peaks.",
      "enum": [
        "05",
        "10",
        "20"
      ],
      "type": "string"
    }
  },
  "required": [],
  "type": "object"
}

Examples (1)

{}

Identifiers

Catalog ID

tu_ChIPAtlas_enrichment_analysis

Tool name

ChIPAtlas_enrichment_analysis

Added

2026-04-30 22:47Z

Tags

tooluniverse