Ensembl Overlap Tools

Configuration File: ensembl_overlap_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

Ensembl_get_gene_overlapping_features (Type: EnsemblOverlapTool)

Get features overlapping an Ensembl gene by gene ID. Returns all genomic features co-located with…

Ensembl_get_gene_overlapping_features tool specification

Tool Information:

  • Name: Ensembl_get_gene_overlapping_features

  • Type: EnsemblOverlapTool

  • Description: Get features overlapping an Ensembl gene by gene ID. Returns all genomic features co-located with the gene, including neighboring genes, overlapping transcripts, regulatory elements, and antisense transcripts. Useful for finding overlapping genes, identifying all transcript isoforms in a locus, or discovering regulatory features at a gene. Example: ‘ENSG00000141510’ (TP53) returns 2 overlapping genes (TP53 and WRAP53), 42 transcripts across 4 biotypes (protein_coding, nonsense_mediated_decay, retained_intron, protein_coding_CDS_not_defined), and 9 regulatory features.

Parameters:

  • gene_id (string) (required) Ensembl gene ID. Examples: ‘ENSG00000141510’ (TP53), ‘ENSG00000012048’ (BRCA1), ‘ENSG00000157764’ (BRAF).

  • feature_types (string) (optional) Comma-separated feature types. Options: ‘gene’, ‘transcript’, ‘regulatory’, ‘constrained’, ‘variation’, ‘repeat’. Default: ‘gene’.

Example Usage:

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

Ensembl_get_region_features (Type: EnsemblOverlapTool)

Get all genomic features overlapping a specified chromosomal region. Returns genes, transcripts, …

Ensembl_get_region_features tool specification

Tool Information:

  • Name: Ensembl_get_region_features

  • Type: EnsemblOverlapTool

  • Description: Get all genomic features overlapping a specified chromosomal region. Returns genes, transcripts, regulatory elements, constrained elements, and other features within the coordinates. Essential for understanding the functional landscape of a genomic region, finding genes near a variant, or identifying regulatory elements in a locus. Supports multiple feature types in one query. Example: region ‘7:140424943-140524564’ (BRAF locus) returns 5 genes, 20 regulatory elements, and 82 constrained elements; region ‘17:7661779-7687546’ (TP53 locus) returns genes, enhancers, CTCF binding sites, and promoters.

Parameters:

  • species (string) (optional) Species name. Default: ‘human’. Examples: ‘human’, ‘mouse’, ‘rat’, ‘zebrafish’.

  • region (string) (required) Genomic region in format ‘chr:start-end’. Examples: ‘17:7661779-7687546’ (TP53), ‘7:140424943-140524564’ (BRAF), ‘13:32315086-32400266’ (BRCA2). Max region size ~5Mb.

  • feature_types (string) (optional) Comma-separated feature types to retrieve. Options: ‘gene’, ‘transcript’, ‘regulatory’, ‘constrained’, ‘variation’, ‘repeat’, ‘motif’. Default: ‘gene’. Example: ‘gene,regulatory,constrained’.

Example Usage:

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