Humanbase Tools#

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

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

Available Tools#

humanbase_ppi_analysis (Type: HumanBaseTool)#

Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Re…

humanbase_ppi_analysis tool specification

Tool Information:

  • Name: humanbase_ppi_analysis

  • Type: HumanBaseTool

  • Description: Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Returns a NetworkX graph of tissue specific protein-protein interactions and a list of associated biological processes involved by the given genes from Gene Ontology.

Parameters:

  • gene_list ([‘array’, ‘string’]) (optional) Genes to analyze, as a list of symbols or a comma-separated string. Official symbols and common synonyms both resolve (‘TP53’ or ‘p53’); the symbol actually used is reported back in resolved_genes.

  • tissue (string) (optional) Tissue type for tissue-specific interactions. Use simple names like ‘brain’, ‘heart’, ‘liver’, ‘kidney’, ‘lung’, ‘blood’. For v3 networks with more cell-type specificity, append ‘-v3’ (e.g., ‘brain-v3’, ‘liver-v3’).

  • max_node (integer) (optional) Number of interaction partners to retrieve per query gene. The network also contains the query genes themselves, so it holds max_node + len(gene_list) proteins. Warning: the more nodes, the longer the retrieval. Default is 10 (~30 seconds).

  • interaction (string) (optional) Specific interaction type to filter by. Available types: ‘co-expression’, ‘interaction’, ‘tf-binding’, ‘gsea-microrna-targets’, ‘gsea-perturbations’. If not specified, all types will be included.

  • string_mode (boolean) (optional) Whether to return the result in string mode. If True, the result will be a string of the network graph and the biological processes. If False, the result will be a NetworkX graph and a list of biological processes.

  • genes ([‘array’, ‘string’]) (optional) Alias for gene_list. A list of gene symbols or a comma-separated string.

  • top_n (integer) (optional) Alias for max_node. Number of interaction partners to retrieve per query gene.

Example Usage:

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