Chipatlas Tools

Configuration File: chipatlas_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the chipatlas_tools.json configuration file.

Available Tools

ChIPAtlas_enrichment_analysis (Type: ChIPAtlasTool)

Perform enrichment analysis to identify transcription factors and histone modifications enriched …

ChIPAtlas_enrichment_analysis tool specification

Tool Information:

  • Name: ChIPAtlas_enrichment_analysis

  • Type: ChIPAtlasTool

  • Description: 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.

Parameters:

  • operation (string) (required) No description

  • bed_data (string) (optional) Option 1: BED format genomic regions (tab-separated: chr, start, end). For finding proteins bound to specific genomic regions. Example: ‘chr1t1000t2000nchr2t3000t4000’.

  • motif (string) (optional) 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).

  • gene_list ([‘array’, ‘string’]) (optional) 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’].

  • genome (string) (optional) Genome assembly

  • antigen_class (string) (optional) Filter by antigen class (e.g., ‘TFs and others’, ‘Histone’, ‘RNA polymerase’)

  • cell_type_class (string) (optional) Filter by cell type class (e.g., ‘Blood’, ‘Liver’, ‘Brain’)

  • threshold (string) (optional) 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.

  • distance (string) (optional) 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.

Example Usage:

query = {
    "name": "ChIPAtlas_enrichment_analysis",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

ChIPAtlas_get_experiments (Type: ChIPAtlasTool)

Search ChIP-Atlas experiment metadata including experiment IDs, antigens, cell types, and process…

ChIPAtlas_get_experiments tool specification

Tool Information:

  • Name: ChIPAtlas_get_experiments

  • Type: ChIPAtlasTool

  • Description: Search ChIP-Atlas experiment metadata including experiment IDs, antigens, cell types, and processing statistics. Filter by genome, antigen (TF/histone), or cell type. Returns experiment details with SRX/ERX/DRX IDs. Use for: finding relevant experiments, getting experiment metadata, dataset discovery, batch analysis planning.

Parameters:

  • operation (string) (required) No description

  • genome (string) (optional) Filter by genome assembly

  • antigen (string) (optional) Filter by antigen/protein name (e.g., ‘CTCF’, ‘H3K4me3’)

  • cell_type (string) (optional) Filter by cell type (e.g., ‘K-562’, ‘HepG2’, ‘CD4’)

  • limit (integer) (optional) Maximum results to return

Example Usage:

query = {
    "name": "ChIPAtlas_get_experiments",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

ChIPAtlas_get_peak_data (Type: ChIPAtlasTool)

Get download URLs for ChIP-Atlas peak-call data in BigWig, BED, or BigBed format. BigWig contains…

ChIPAtlas_get_peak_data tool specification

Tool Information:

  • Name: ChIPAtlas_get_peak_data

  • Type: ChIPAtlasTool

  • Description: Get download URLs for ChIP-Atlas peak-call data in BigWig, BED, or BigBed format. BigWig contains coverage scores in RPM (Reads Per Million). BED/BigBed contain peak regions with MACS2 (Model-based Analysis of ChIP-Seq) peak caller scores. Use for: downloading raw data, integrating with genome browsers (UCSC, IGV), custom analysis, visualization.

Parameters:

  • operation (string) (required) No description

  • experiment_id (string) (required) Experiment ID (SRX/ERX/DRX format, required)

  • genome (string) (optional) Genome assembly

  • format (string) (optional) Output format

  • threshold (string) (optional) Q-value threshold for BED/BigBed peak files. ‘05’=1e-5 (more peaks), ‘10’=1e-10 (moderate), ‘20’=1e-20 (high confidence only). Only applies to BED/BigBed formats. Default ‘05’.

Example Usage:

query = {
    "name": "ChIPAtlas_get_peak_data",
    "arguments": {
        "operation": "example_value",
        "experiment_id": "example_value"
    }
}
result = tu.run(query)

ChIPAtlas_search_datasets (Type: ChIPAtlasTool)

Search ChIP-Atlas by antigen or cell type to find available datasets. Returns number of experimen…

ChIPAtlas_search_datasets tool specification

Tool Information:

  • Name: ChIPAtlas_search_datasets

  • Type: ChIPAtlasTool

  • Description: Search ChIP-Atlas by antigen or cell type to find available datasets. Returns number of experiments and experiment IDs. Use antigenList for finding TF/histone datasets across cell types. Use celltypeList for finding all factors in specific cell type. Use for: dataset discovery, planning comparative analysis, checking data availability.

Parameters:

  • operation (string) (required) No description

  • antigen (string) (optional) Search by antigen/protein name (e.g., ‘CTCF’, ‘H3K27ac’)

  • cell_type (string) (optional) Search by cell type (e.g., ‘K-562’, ‘HeLa’, ‘MCF-7’)

  • genome (string) (optional) Genome assembly

Example Usage:

query = {
    "name": "ChIPAtlas_search_datasets",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)