Panther Tools#

Configuration File: panther_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

PANTHER_enrichment (Type: PANTHERTool)#

Perform gene set enrichment (overrepresentation) analysis using PANTHER. Returns only statistical…

PANTHER_enrichment tool specification

Tool Information:

  • Name: PANTHER_enrichment

  • Type: PANTHERTool

  • Description: Perform gene set enrichment (overrepresentation) analysis using PANTHER. Returns only statistically significant terms (FDR < 0.05), sorted by FDR with explicit offset pagination. Continue with next_offset while has_more is true. Supports GO terms, PANTHER pathways, Reactome pathways, and protein classes.

Parameters:

  • gene_list (string) (required) Comma-separated list of gene symbols, UniProt IDs, or Ensembl IDs. Example: ‘TP53,BRCA1,EGFR,KRAS,PTEN,APC,RB1’.

  • organism ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID. Default: 9606 (human). Others: 10090 (mouse), 7227 (fly), 559292 (yeast).

  • annotation_dataset ([‘string’, ‘null’]) (optional) Annotation dataset for enrichment. Options: ‘GO:0008150’ (biological_process, default), ‘GO:0003674’ (molecular_function), ‘GO:0005575’ (cellular_component), ‘ANNOT_TYPE_ID_PANTHER_PATHWAY’ (PANTHER pathway), ‘ANNOT_TYPE_ID_REACTOME_PATHWAY’ (Reactome pathway), ‘ANNOT_TYPE_ID_PANTHER_PC’ (protein class).

  • limit (integer) (optional) Maximum significant terms per page (default 50, max 1000).

  • offset (integer) (optional) Zero-based offset in the FDR-sorted significant terms. Continue with next_offset while has_more is true.

Example Usage:

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

PANTHER_gene_info (Type: PANTHERTool)#

Get gene classification and functional annotation from PANTHER (Protein ANalysis THrough Evolutio…

PANTHER_gene_info tool specification

Tool Information:

  • Name: PANTHER_gene_info

  • Type: PANTHERTool

  • Description: Get gene classification and functional annotation from PANTHER (Protein ANalysis THrough Evolutionary Relationships). Returns PANTHER family/subfamily, Gene Ontology annotations (molecular function, biological process, cellular component), PANTHER protein class, and pathway membership. PANTHER classifies genes by evolutionary relationships across 144 organisms. Example: P04637 returns TP53 classified in family PTHR11447 (tumor protein p53) with GO annotations for DNA-binding transcription factor activity.

Parameters:

  • gene_id (string) (required) Gene identifier - UniProt accession, Ensembl ID, or gene symbol. Examples: ‘P04637’ (TP53), ‘P38398’ (BRCA1), ‘ENSG00000141510’.

  • organism ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID. Default: 9606 (human). Others: 10090 (mouse), 10116 (rat), 7227 (fly), 6239 (worm), 559292 (yeast).

Example Usage:

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

PANTHER_ortholog (Type: PANTHERTool)#

Find orthologs of a gene across species using PANTHER evolutionary classification. Returns EVERY …

PANTHER_ortholog tool specification

Tool Information:

  • Name: PANTHER_ortholog

  • Type: PANTHERTool

  • Description: Find orthologs of a gene across species using PANTHER evolutionary classification. Returns EVERY matching ortholog in ‘mappings’ (count in ‘total_mappings’), each with its persistent ID, gene symbol, and ortholog type (LDO=Least Diverged Ortholog, O=ortholog, P=paralog, X=xenolog, LDX=least diverged xenolog); ‘mapping’ repeats the first entry for backward compatibility and is not the whole answer. A gene often has several orthologs in one target species – human ABCB1 maps to both mouse Abcb1a (LDO) and Abcb1b (O) – so read ‘mappings’, especially with ortholog_type=’O’. PANTHER classifies orthologs by evolutionary divergence across 144 fully sequenced genomes. Example: P04637 (human TP53) maps to Tp53 (mouse P02340) as LDO.

Parameters:

  • gene_id (string) (required) Gene identifier - UniProt accession, Ensembl ID, or gene symbol. Examples: ‘P04637’ (TP53), ‘P38398’ (BRCA1).

  • organism ([‘integer’, ‘null’]) (optional) Source organism NCBI taxonomy ID. Default: 9606 (human).

  • target_organism ([‘integer’, ‘null’]) (optional) Target organism NCBI taxonomy ID. Default: 10090 (mouse). Others: 10116 (rat), 7227 (fly), 6239 (worm).

  • ortholog_type ([‘string’, ‘null’]) (optional) Ortholog type filter. Options: ‘LDO’ (least diverged ortholog, default), ‘O’ (all orthologs), ‘P’ (paralogs), ‘X’ (xenologs), ‘LDX’ (least diverged xenolog), ‘all’ (all types).

Example Usage:

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