Gene Set and Pathway Enrichment: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Run gene set enrichment against an Enrichr library¶

dnakit.databases.enrichr_enrich(*, operation=None, gene_list, library=None, top_n=None, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`operation`	string	None	Operation type (fixed: enrich)
`gene_list`	array	Required	List of gene symbols (e.g., ['TP53', 'BRCA1', 'EGFR']). Minimum 1 gene. {"items": {"type": "string"}}
`library`	string	None	Enrichr library name (default: GO_Biological_Process_2023). Common: GO_Biological_Process_2023, KEGG_2021_Human, Reactome_2022, WikiPathways_2024_Human, MSigDB_Hallmark_2020
`top_n`	integer	None	Number of top enriched terms to return (default: 10)
`species`	string \| null	None	Organism instance to query: 'human' (default), 'mouse', 'fly' (FlyEnrichr), 'worm' (WormEnrichr), 'yeast' (YeastEnrichr), or 'fish' (FishEnrichr). Gene set libraries differ per organism, and gene symbols must match that organism's nomenclature.
`verbose`	bool	True	Progress flag.

Retrieve connections between genes and enriched pathways¶

dnakit.databases.enrichr_gene_enrichment_analysis(*, gene_list, libs=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_list`	array	Required	List of gene names or symbols to analyze. At least 2 genes are required for path ranking analysis. {"items": {"type": "string"}, "minItems": 2}
`libs`	array	None	List of Enrichr enrichment libraries to query (e.g. 'KEGG_2021_Human', 'GO_Biological_Process_2023'). Omitting this or passing an empty list uses a broad default set of pathway/ontology libraries. {"items": {"type": "string"}, "default": ["WikiPathways_2024_Human", "Reactome_Pathways_2024", "MSigDB_Hallmark_2020", "GO_Molecular_Function_2023", "GO_Biological_Process_2023"]}
`verbose`	bool	True	Progress flag.

Run PANTHER gene set overrepresentation analysis¶

dnakit.databases.panther_enrichment(*, gene_list, organism=None, annotation_dataset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_list`	string	Required	Comma-separated list of gene symbols, UniProt IDs, or Ensembl IDs. Example: 'TP53,BRCA1,EGFR,KRAS,PTEN,APC,RB1'.
`organism`	integer \| null	None	NCBI taxonomy ID. Default: 9606 (human). Others: 10090 (mouse), 7227 (fly), 559292 (yeast).
`annotation_dataset`	string \| null	None	Annotation dataset for enrichment. Options: 'GO:0008150' (biological_process, default), 'GO:0003674' (molecular_function), 'GO:0005575' (cellular_component), 'ANNOT_TYPE_ID_PANTHER_PATHWAY' (PANTHER pathway), 'ANNOT_TYPE_ID_REACTOME_PATHWAY' (Reactome pathway), 'ANNOT_TYPE_ID_PANTHER_PC' (protein class).
`verbose`	bool	True	Progress flag.

Run Reactome pathway enrichment analysis¶

dnakit.databases.reactome_analysis_pathway_enrichment(*, identifiers, page_size=None, include_disease=None, projection=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`identifiers`	string	Required	Newline-separated list of gene/protein identifiers. Supports gene symbols (TP53, BRCA1), UniProt IDs (P04637, P38398), or Ensembl IDs. Example: 'TP53\nBRCA1\nCDH1\nEGFR\nKRAS'.
`page_size`	integer \| null	None	Number of pathways to return (default 20, max 50).
`include_disease`	boolean \| null	None	Include disease pathways in results (default true).
`projection`	boolean \| null	None	Project identifiers to human Reactome pathways for cross-species analysis (default true).
`verbose`	bool	True	Progress flag.

Analyze functional and pathway enrichment for a protein set¶

dnakit.databases.string_functional_enrichment(*, protein_ids, species=None, category=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`protein_ids`	array	Required	List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins recommended for meaningful enrichment. {"items": {"type": "string"}, "minItems": 2}
`species`	integer	None	NCBI taxonomy ID (default: 9606 for human)
`category`	string	None	Enrichment category: 'Process' (GO Biological Process), 'Component' (GO Cellular Component), 'Function' (GO Molecular Function), 'KEGG', 'Reactome', 'WikiPathways', 'COMPARTMENTS', 'TISSUES', 'DISEASES'
`verbose`	bool	True	Progress flag.

Run STRING enrichment from newline-separated protein identifiers¶

dnakit.databases.string_get_functional_enrichment(*, identifiers, species=9606, category=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`identifiers`	string	Required	Protein identifiers separated by newline or carriage return; converted to a STRING identifier list.
`species`	integer	9606	Species name or taxonomy ID; type and supported values depend on the operation.
`category`	string	None	Category or result class defined by this operation's provider/schema.
`verbose`	bool	True	Progress flag.