Msigdb Tools

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

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

Available Tools

MSigDB_check_gene_in_set (Type: MSigDBTool)

Check if a specific gene is a member of an MSigDB gene set. Covers GTRD transcription factor targ…

MSigDB_check_gene_in_set tool specification

Tool Information:

  • Name: MSigDB_check_gene_in_set

  • Type: MSigDBTool

  • Description: Check if a specific gene is a member of an MSigDB gene set. Covers GTRD transcription factor targets (e.g., ZNF549_TARGET_GENES), miRDB miRNA targets, oncogenic signatures (C6), hallmark sets (H), and 33,000+ other sets. Use to verify gene membership in TF target lists, miRNA target lists, or any MSigDB collection.

Parameters:

  • operation (unknown) (optional) No description

  • gene_set_name (string) (required) Exact gene set name (e.g., ‘ZNF549_TARGET_GENES’, ‘ESC_V6.5_UP_EARLY.V1_DN’, ‘HALLMARK_APOPTOSIS’)

  • gene (string) (required) Gene symbol to check (e.g., ‘SELENOP’, ‘TP53’, ‘CD37’)

Example Usage:

query = {
    "name": "MSigDB_check_gene_in_set",
    "arguments": {
        "gene_set_name": "example_value",
        "gene": "example_value"
    }
}
result = tu.run(query)

MSigDB_get_gene_set_members (Type: MSigDBTool)

Get all gene members of an MSigDB gene set by exact name. Returns parsed gene list (unlike MSigDB…

MSigDB_get_gene_set_members tool specification

Tool Information:

  • Name: MSigDB_get_gene_set_members

  • Type: MSigDBTool

  • Description: Get all gene members of an MSigDB gene set by exact name. Returns parsed gene list (unlike MSigDB_get_geneset which returns raw API response). Covers 33,000+ gene sets including GTRD TF targets, miRDB miRNA targets, oncogenic signatures, hallmark sets, GO terms, and pathway gene sets.

Parameters:

  • operation (unknown) (optional) No description

  • gene_set_name (string) (required) Exact MSigDB gene set name (e.g., ‘ZNF549_TARGET_GENES’, ‘MIR675_3P_TARGET_GENES’, ‘ESC_V6.5_UP_EARLY.V1_DN’)

Example Usage:

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

MSigDB_get_geneset (Type: BaseRESTTool)

Retrieve a specific gene set from MSigDB (Molecular Signatures Database) by its exact name. MSigD…

MSigDB_get_geneset tool specification

Tool Information:

  • Name: MSigDB_get_geneset

  • Type: BaseRESTTool

  • Description: Retrieve a specific gene set from MSigDB (Molecular Signatures Database) by its exact name. MSigDB is the definitive database for gene sets used in Gene Set Enrichment Analysis (GSEA), containing 33,000+ gene sets organized into 9 major collections: H (hallmark), C1 (positional), C2 (curated pathways from KEGG/Reactome/BioCarta/WikiPathways), C3 (regulatory motifs), C4 (computational cancer), C5 (Gene Ontology), C6 (oncogenic signatures), C7 (immunologic signatures), C8 (cell type signatures). Returns the gene symbols in the set, systematic name, PMID, collection, and URLs.

Parameters:

  • geneSetName (string) (required) Exact MSigDB gene set name (case-sensitive). Examples: ‘HALLMARK_APOPTOSIS’, ‘KEGG_P53_SIGNALING_PATHWAY’, ‘GOBP_APOPTOTIC_PROCESS’, ‘HALLMARK_HYPOXIA’, ‘KRAS.LUNG_UP.V1_UP’. Find names at https://www.gsea-msigdb.org/gsea/msigdb/

Example Usage:

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

MSigDB_get_hallmark_geneset (Type: BaseRESTTool)

Retrieve a Hallmark gene set from MSigDB. The Hallmark collection (H) contains 50 gene sets repre…

MSigDB_get_hallmark_geneset tool specification

Tool Information:

  • Name: MSigDB_get_hallmark_geneset

  • Type: BaseRESTTool

  • Description: Retrieve a Hallmark gene set from MSigDB. The Hallmark collection (H) contains 50 gene sets representing well-defined biological states and processes with coherent expression, distilled from multiple founder sets. These are the most commonly used gene sets for pathway analysis and GSEA. Hallmark gene set names are prefixed with ‘HALLMARK_’ followed by the pathway name in uppercase with underscores (e.g., HALLMARK_APOPTOSIS, HALLMARK_HYPOXIA, HALLMARK_P53_PATHWAY, HALLMARK_INFLAMMATORY_RESPONSE, HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION).

Parameters:

  • pathway_name (string) (required) Hallmark pathway name without the ‘HALLMARK_’ prefix (will be auto-prepended). Examples: ‘APOPTOSIS’, ‘P53_PATHWAY’, ‘HYPOXIA’, ‘DNA_REPAIR’, ‘INFLAMMATORY_RESPONSE’, ‘EPITHELIAL_MESENCHYMAL_TRANSITION’, ‘TNFA_SIGNALING_VIA_NFKB’, ‘KRAS_SIGNALING_UP’, ‘OXIDATIVE_PHOSPHORYLATION’, ‘GLYCOLYSIS’, ‘MYC_TARGETS_V1’

Example Usage:

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