L1000Fwd Tools

Configuration File: l1000fwd_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the l1000fwd_tools.json configuration file.

Available Tools

L1000FWD_sig_search (Type: L1000FWDTool)

Transcriptomic signature query against the LINCS L1000 Connectivity Map via the L1000FWD Firework…

L1000FWD_sig_search tool specification

Tool Information:

  • Name: L1000FWD_sig_search

  • Type: L1000FWDTool

  • Description: Transcriptomic signature query against the LINCS L1000 Connectivity Map via the L1000FWD Fireworks REST API (maayanlab.cloud/L1000FWD). Accepts two gene sets representing transcriptional changes in a condition of interest: genes increasing and genes decreasing. Internally issues a POST to /sig_search to register the query, then fetches ranked hits from /result/topn/{result_id}. Each returned hit is an L1000 perturbation record containing sig_id, combined score, p-value, and q-value. mode=’similar’ retrieves perturbations that activate the same transcriptional programme (e.g. disease mimics); mode=’opposite’ retrieves perturbations that invert it, the classical computational drug-repurposing approach. No authentication required.

Parameters:

  • operation (string) (required) Operation type

  • up_genes (array) (required) List of up-regulated gene symbols (e.g., [‘MYC’, ‘TP53’])

  • down_genes (array) (required) List of down-regulated gene symbols (e.g., [‘CDKN1A’, ‘RB1’])

  • n_results (integer) (optional) Number of top results to return (default 10)

  • mode (string) (optional) Return signatures ‘similar’ to or ‘opposite’ of the query signature (default: ‘similar’)

Example Usage:

query = {
    "name": "L1000FWD_sig_search",
    "arguments": {
        "operation": "example_value",
        "up_genes": ["item1", "item2"],
        "down_genes": ["item1", "item2"]
    }
}
result = tu.run(query)