Encori Tools

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

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

Available Tools

ENCORI_get_miRNA_targets (Type: ENCORITool)

Look up miRNA-target interactions from ENCORI (starBase): CLIP-seq-supported and computationally …

ENCORI_get_miRNA_targets tool specification

Tool Information:

  • Name: ENCORI_get_miRNA_targets

  • Type: ENCORITool

  • Description: Look up miRNA-target interactions from ENCORI (starBase): CLIP-seq-supported and computationally predicted targets of a miRNA, or the miRNAs that target a gene. Provide ‘mirna’ (e.g. ‘hsa-miR-21-5p’) to get its target genes, OR ‘gene’ (e.g. ‘TP53’) to get targeting miRNAs. Each result reports the number of supporting CLIP experiments (experimental evidence) and which prediction programs (TargetScan, miRanda, PITA, miRmap, microT, PicTar, RNA22) call it. Fills the gap where ToolUniverse had no miRNA target-lookup tool. Public, no authentication.

Parameters:

  • mirna ([‘string’, ‘null’]) (optional) miRNA name to get targets for, e.g. ‘hsa-miR-21-5p’, ‘hsa-let-7a-5p’. Mutually exclusive with ‘gene’.

  • gene ([‘string’, ‘null’]) (optional) Gene symbol to get targeting miRNAs for, e.g. ‘TP53’, ‘KRAS’ (alias: ‘gene_symbol’). Mutually exclusive with ‘mirna’.

  • assembly ([‘string’, ‘null’]) (optional) Genome assembly to query (default ‘hg38’). Use ‘hg19’ for the older human build.

  • clip_min ([‘integer’, ‘null’]) (optional) Minimum number of supporting CLIP-seq experiments (default 1 = require experimental support; set 0 to include prediction-only).

  • program_min ([‘integer’, ‘null’]) (optional) Minimum number of prediction programs that must call the interaction (default 1).

  • limit ([‘integer’, ‘null’]) (optional) Maximum interactions to return (1-500, default 50).

Example Usage:

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