Signor Tools

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

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

Available Tools

SIGNOR_connect_proteins (Type: SIGNORTool)

Find the curated causal signaling sub-network that connects a set of proteins in the SIGNOR datab…

SIGNOR_connect_proteins tool specification

Tool Information:

  • Name: SIGNOR_connect_proteins

  • Type: SIGNORTool

  • Description: Find the curated causal signaling sub-network that connects a set of proteins in the SIGNOR database. Given two or more UniProt accessions, returns the causal relationships (effect, mechanism, direction, literature) linking the protein set via shortest signaling paths. Use UniProt IDs (e.g., P29317 for EPHA2, P15056 for BRAF, P04049 for RAF1, Q06124 for PTPN11). ‘level’ controls how many intermediate steps are allowed (1 = direct links only, 2 = one intermediate, 3 = two intermediates).

Parameters:

  • proteins (array) (required) List of two or more UniProt accessions to connect (e.g., [‘P29317’, ‘Q06124’, ‘P04049’, ‘P15056’]). SIGNOR requires UniProt IDs, not gene symbols.

  • level (integer) (optional) Path depth for connecting the proteins: 1 (direct interactions only), 2 (allow one intermediate node), or 3 (allow two intermediate nodes).

  • limit (integer) (optional) Maximum number of interactions to return.

Example Usage:

query = {
    "name": "SIGNOR_connect_proteins",
    "arguments": {
        "proteins": ["item1", "item2"]
    }
}
result = tu.run(query)

SIGNOR_get_interactions (Type: SIGNORTool)

Get causal signaling interactions for a protein or entity from the SIGNOR database. Returns upstr…

SIGNOR_get_interactions tool specification

Tool Information:

  • Name: SIGNOR_get_interactions

  • Type: SIGNORTool

  • Description: Get causal signaling interactions for a protein or entity from the SIGNOR database. Returns upstream regulators and downstream targets with the type of effect (up/down-regulation), mechanism (phosphorylation, ubiquitination, transcriptional regulation, etc.), affected residue, and supporting literature. Use UniProt IDs (e.g., P04637 for TP53) or SIGNOR entity IDs.

Parameters:

  • entity_id (string) (optional) Entity identifier - typically a UniProt accession (e.g., ‘P04637’ for TP53, ‘Q00987’ for MDM2, ‘P38398’ for BRCA1). Can also be a SIGNOR complex/pathway ID.

  • organism (integer) (optional) NCBI taxonomy ID. 9606 for human, 10090 for mouse.

  • limit (integer) (optional) Maximum number of interactions to return.

  • protein (string) (optional) Gene symbol or protein name (alias for entity_id; prefer UniProt accession like P04637 for TP53)

Example Usage:

query = {
    "name": "SIGNOR_get_interactions",
    "arguments": {
    }
}
result = tu.run(query)

SIGNOR_get_pathway (Type: SIGNORTool)

Get all signaling interactions in a specific SIGNOR curated pathway. Returns the network of causa…

SIGNOR_get_pathway tool specification

Tool Information:

  • Name: SIGNOR_get_pathway

  • Type: SIGNORTool

  • Description: Get all signaling interactions in a specific SIGNOR curated pathway. Returns the network of causal relationships with effects, mechanisms, and literature references. Use pathway IDs from SIGNOR_list_pathways (e.g., ‘SIGNOR-AD’ for Alzheimer, ‘SIGNOR-C’ for cancer-related).

Parameters:

  • pathway_id (string) (required) SIGNOR pathway identifier (e.g., ‘SIGNOR-AD’ for Alzheimer, ‘SIGNOR-AML’ for Acute Myeloid Leukemia, ‘SIGNOR-AMPK’ for AMPK signaling). Get IDs from SIGNOR_list_pathways.

  • limit (integer) (optional) Maximum number of interactions to return.

Example Usage:

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

SIGNOR_list_pathways (Type: SIGNORTool)

List curated signaling pathways in the SIGNOR database. Optionally filter by keyword to find path…

SIGNOR_list_pathways tool specification

Tool Information:

  • Name: SIGNOR_list_pathways

  • Type: SIGNORTool

  • Description: List curated signaling pathways in the SIGNOR database. Optionally filter by keyword to find pathways related to diseases (Alzheimer, AML), biological processes (apoptosis, autophagy), or signaling (MAPK, PI3K). Returns pathway IDs that can be used with SIGNOR_get_pathway.

Parameters:

  • query (string) (optional) Optional keyword to filter pathways by name or description (e.g., ‘cancer’, ‘apoptosis’, ‘AML’). Leave empty to list all pathways.

Example Usage:

query = {
    "name": "SIGNOR_list_pathways",
    "arguments": {
    }
}
result = tu.run(query)