Gprofiler Tools

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

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

Available Tools

gProfiler_annotate_snps (Type: GProfilerTool)

Map SNP rsIDs to genes and annotate their functional consequences using g:Profiler (g:SNPense) fr…

gProfiler_annotate_snps tool specification

Tool Information:

  • Name: gProfiler_annotate_snps

  • Type: GProfilerTool

  • Description: Map SNP rsIDs to genes and annotate their functional consequences using g:Profiler (g:SNPense) from the University of Tartu. Given a list of SNP rsIDs, returns the chromosome, position, strand, associated Ensembl gene IDs, gene names, and predicted variant consequences (missense_variant, synonymous_variant, intron_variant, etc.) with counts. Useful for annotating GWAS hits, linking variants to genes, or understanding the functional impact of SNPs. Example: ‘rs11540652’ maps to chromosome 17 position 7674220, gene TP53 (ENSG00000141510), with 18 missense variant consequences; ‘rs429358’ maps to APOE on chromosome 19.

Parameters:

  • snp_list (string) (required) Comma-separated list of SNP rsIDs. Examples: ‘rs11540652,rs429358,rs7903146’ or ‘rs1042779,rs6792369’. Maximum ~200 SNPs per query.

  • organism (string) (optional) Organism identifier. Default: ‘hsapiens’. Examples: ‘hsapiens’ (human), ‘mmusculus’ (mouse).

Example Usage:

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

gProfiler_convert_ids (Type: GProfilerTool)

Convert gene identifiers between different namespaces using g:Profiler (g:Convert) from the Unive…

gProfiler_convert_ids tool specification

Tool Information:

  • Name: gProfiler_convert_ids

  • Type: GProfilerTool

  • Description: Convert gene identifiers between different namespaces using g:Profiler (g:Convert) from the University of Tartu. Supports conversion between gene symbols, Ensembl IDs, Entrez IDs, UniProt accessions, RefSeq IDs, and many other identifiers. Input is a list of gene identifiers and a target namespace. Supports 500+ organisms. Example: convert ‘TP53,BRCA1,EGFR’ to Ensembl gene IDs (ENSG). Available target namespaces: ENSG (Ensembl Gene), ENST (Ensembl Transcript), ENSP (Ensembl Protein), UNIPROTSWISSPROT (UniProt reviewed), ENTREZGENE_ACC (Entrez Gene), WIKIGENE_ACC (WikiGene).

Parameters:

  • gene_list (string) (required) Comma-separated list of gene identifiers to convert. Examples: ‘TP53,BRCA1,EGFR’ (symbols), ‘ENSG00000141510,ENSG00000012048’ (Ensembl IDs).

  • target_namespace (string) (optional) Target namespace for conversion. Default: ‘ENSG’. Options: ENSG (Ensembl Gene), ENST (Ensembl Transcript), ENSP (Ensembl Protein), UNIPROTSWISSPROT (UniProt), ENTREZGENE_ACC (Entrez), WIKIGENE_ACC (WikiGene), REFSEQ_MRNA_ACC, REFSEQ_PEPTIDE_ACC.

  • organism (string) (optional) Organism identifier. Default: ‘hsapiens’. Examples: ‘hsapiens’, ‘mmusculus’.

Example Usage:

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

gProfiler_enrichment (Type: GProfilerTool)

Perform functional enrichment analysis on a gene list using g:Profiler (g:GOSt) from the Universi…

gProfiler_enrichment tool specification

Tool Information:

  • Name: gProfiler_enrichment

  • Type: GProfilerTool

  • Description: Perform functional enrichment analysis on a gene list using g:Profiler (g:GOSt) from the University of Tartu. Identifies statistically overrepresented biological functions, pathways, and phenotypes in your gene list. Supports multiple data sources: Gene Ontology (GO:BP, GO:MF, GO:CC), KEGG pathways, Reactome, WikiPathways, Human Phenotype Ontology (HP), miRNA targets (MIRNA), CORUM protein complexes, and Transcription Factor targets (TF). Returns enriched terms with p-values (g:SCS multiple testing correction), term sizes, intersection genes, precision, and recall. Input is a list of gene symbols (e.g., [‘TP53’, ‘BRCA1’, ‘EGFR’, ‘KRAS’, ‘PTEN’]). Supports 500+ organisms (use NCBI taxonomy prefix, e.g., ‘hsapiens’, ‘mmusculus’, ‘dmelanogaster’).

Parameters:

  • gene_list (string) (required) Comma-separated list of gene symbols. Examples: ‘TP53,BRCA1,EGFR,KRAS,PTEN’ or ‘Trp53,Brca1,Egfr’ (mouse).

  • organism (string) (optional) Organism identifier. Default: ‘hsapiens’. Examples: ‘hsapiens’ (human), ‘mmusculus’ (mouse), ‘dmelanogaster’ (fly), ‘scerevisiae’ (yeast), ‘drerio’ (zebrafish).

  • sources (string) (optional) Comma-separated data sources to query. Default: ‘GO:BP,GO:MF,GO:CC,KEGG,REAC,WP,HP’. Options: GO:BP, GO:MF, GO:CC, KEGG, REAC, WP, MIRNA, HPA, CORUM, HP, TF.

Example Usage:

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

gProfiler_find_orthologs (Type: GProfilerTool)

Find orthologous genes across species using g:Profiler (g:Orth) from the University of Tartu. Map…

gProfiler_find_orthologs tool specification

Tool Information:

  • Name: gProfiler_find_orthologs

  • Type: GProfilerTool

  • Description: Find orthologous genes across species using g:Profiler (g:Orth) from the University of Tartu. Maps genes from a source organism to their orthologs in a target organism using Ensembl orthology data. Useful for translating gene lists between model organisms. Example: find mouse orthologs of human TP53 and BRCA1. Supports 500+ organisms in the Ensembl database. Input is a list of gene identifiers from the source organism, and the target organism to map to.

Parameters:

  • gene_list (string) (required) Comma-separated list of gene identifiers from the source organism. Examples: ‘TP53,BRCA1,EGFR’ (human genes to find mouse orthologs).

  • source_organism (string) (optional) Source organism. Default: ‘hsapiens’. Examples: ‘hsapiens’ (human), ‘mmusculus’ (mouse).

  • target_organism (string) (optional) Target organism to find orthologs in. Default: ‘mmusculus’. Examples: ‘mmusculus’ (mouse), ‘rnorvegicus’ (rat), ‘drerio’ (zebrafish), ‘dmelanogaster’ (fly), ‘celegans’ (worm).

Example Usage:

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