enrichr_analysis
Analyze gene lists to identify overrepresented biological terms, pathways, and functions across multiple databases using statistical enrichment analysis.
Instructions
Perform gene set enrichment analysis using Enrichr with support for multiple gene set libraries. Use this tool when you need to:
analyze gene functions
test enrichment across different databases
find biological processes/pathways/diseases
perform functional enrichment
analyze gene sets
identify overrepresented terms
run enrichment analysis
perform gene ontology analysis
test for enriched biological terms
analyze gene list functionality across multiple databases. Returns only statistically significant terms (adjusted p < 0.05) to reduce context usage. Supports GO, pathways, disease, tissue, drug, and many other gene set libraries available in Enrichr.
This server is configured with the following default libraries:
GO_Biological_Process_2025: Gene Ontology terms describing biological objectives accomplished by gene products.
KEGG_2021_Human: Metabolic and signaling pathways from Kyoto Encyclopedia of Genes and Genomes for human.
Reactome_2022: Curated and peer-reviewed pathways from Reactome covering signaling, metabolism, gene expression, and disease.
MSigDB_Hallmark_2020: Hallmark gene sets representing well-defined biological states and processes from MSigDB.
ChEA_2022: ChIP-seq experiments from GEO, ENCODE, and publications identifying transcription factor-gene interactions from human and mouse.
GWAS_Catalog_2023: Genome-wide association study results from NHGRI-EBI GWAS Catalog linking genes to traits.
Human_Phenotype_Ontology: Standardized vocabulary of phenotypic abnormalities associated with human diseases.
STRING_Interactions_2023: Protein interactions from STRING database including experimental and predicted.
DrugBank_2022: Drug targets from DrugBank including approved drugs and experimental compounds.
CellMarker_2024: Manually curated cell type markers from CellMarker database for human and mouse.
The model should select the most relevant library/libraries from the list below based on the user's query.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| genes | Yes | List of gene symbols to analyze for enrichment (e.g., ['TP53', 'BRCA1', 'EGFR']) | |
| libraries | No | List of Enrichr libraries to use for analysis. If not specified, the configured defaults will be used. Available options include: 'ChEA_2022', 'ChEA_2016', 'ChEA_2013', 'ENCODE_TF_ChIP-seq_2015', 'ENCODE_TF_ChIP-seq_2014', 'ENCODE_Histone_Modifications_2015', 'ENCODE_Histone_Modifications_2013', 'Transcription_Factor_PPIs', 'TRANSFAC_and_JASPAR_PWMs', 'Genome_Browser_PWMs', 'MotifMap', 'ENCODE_and_ChEA_Consensus_TFs_from_ChIP-X', 'TF_Perturbations_Followed_by_Expression', 'TF-LOF_Expression_from_GEO', 'PPI_Hub_Proteins', 'CORUM', 'KEGG_2021_Human', 'KEGG_2019_Human', 'KEGG_2019_Mouse', 'KEGG_2016', 'KEGG_2015', 'KEGG_2013', 'Reactome_2022', 'Reactome_2016', 'Reactome_2013', 'WikiPathways_2023_Human', 'WikiPathways_2021_Human', 'WikiPathways_2019_Human', 'WikiPathways_2019_Mouse', 'WikiPathways_2016', 'WikiPathways_2015', 'WikiPathways_2013', 'BioCarta_2016', 'BioCarta_2015', 'BioCarta_2013', 'HumanCyc_2016', 'HumanCyc_2015', 'NCI-Nature_2016', 'NCI-Nature_2015', 'Panther_2016', 'Panther_2015', 'MSigDB_Hallmark_2020', 'BioPlanet_2019', 'NURSA_Human_Endogenous_Complexome', 'hu.MAP', 'GO_Biological_Process_2025', 'GO_Biological_Process_2023', 'GO_Biological_Process_2021', 'GO_Biological_Process_2018', 'GO_Biological_Process_2017', 'GO_Biological_Process_2015', 'GO_Biological_Process_2013', 'GO_Molecular_Function_2025', 'GO_Molecular_Function_2023', 'GO_Molecular_Function_2021', 'GO_Molecular_Function_2018', 'GO_Molecular_Function_2017', 'GO_Molecular_Function_2015', 'GO_Molecular_Function_2013', 'GO_Cellular_Component_2025', 'GO_Cellular_Component_2023', 'GO_Cellular_Component_2021', 'GO_Cellular_Component_2018', 'GO_Cellular_Component_2017', 'GO_Cellular_Component_2015', 'GO_Cellular_Component_2013', 'Human_Phenotype_Ontology', 'MGI_Mammalian_Phenotype_2021', 'MGI_Mammalian_Phenotype_2017', 'MGI_Mammalian_Phenotype_2013', 'MGI_Mammalian_Phenotype_Level_3', 'MGI_Mammalian_Phenotype_Level_4', 'Human_Gene_Atlas', 'Anatomy_AutoRIF', 'Anatomy_AutoRIF_Predicted_Z-score', 'Jensen_TISSUES', 'Jensen_COMPARTMENTS', 'Jensen_DISEASES', 'ARCHS4_Tissues', 'ARCHS4_Cell-lines', 'Uberon_Cross_Species_Phenotype_Ontology', 'GWAS_Catalog_2023', 'GWAS_Catalog_2019', 'UK_Biobank_GWAS_v1', 'ClinVar_2019', 'PheWeb_2019', 'DisGeNET', 'PhenGenI_Association_2021', 'Orphanet_Augmented_2021', 'Rare_Diseases_AutoRIF_Gene_Lists', 'Rare_Diseases_AutoRIF_ARCHS4_Predictions', 'Rare_Diseases_GeneRIF_Gene_Lists', 'Rare_Diseases_GeneRIF_ARCHS4_Predictions', 'DrugBank_2022', 'DrugBank_2018', 'DSigDB', 'Drug_Perturbations_from_GEO_2014', 'Drug_Perturbations_from_GEO_down', 'Drug_Perturbations_from_GEO_up', 'LINCS_L1000_Chem_Pert_down', 'LINCS_L1000_Chem_Pert_up', 'LINCS_L1000_Ligand_Perturbations_down', 'LINCS_L1000_Ligand_Perturbations_up', 'Drug_Matrix', 'HMS_LINCS_KinomeScan', 'Proteomics_Drug_Atlas_2023', 'Virus_Perturbations_from_GEO_down', 'Virus_Perturbations_from_GEO_up', 'VirusMINT', 'Disease_Perturbations_from_GEO_down', 'Disease_Perturbations_from_GEO_up', 'Disease_Signatures_from_GEO_down_2014', 'Disease_Signatures_from_GEO_up_2014', 'Disease_Signatures_from_GEO_Manual_down', 'Disease_Signatures_from_GEO_Manual_up', 'COVID-19_Related_Gene_Sets', 'COVID-19_Related_Gene_Sets_2021', 'HDSigDB_Human_2021', 'HDSigDB_Mouse_2021', 'OMIM_Disease', 'OMIM_Expanded', 'DepMap_WG_CRISPR_Screens_Broad_CellLines_2019', 'DepMap_WG_CRISPR_Screens_Sanger_CellLines_2019', 'Achilles_fitness_decrease', 'Achilles_fitness_increase', 'GeneSigDB', 'GWASdb_2023', 'MAGMA_Drugs_and_Diseases', 'MAGNET_2023', 'GeDiPNet_2023', 'GTEx_Tissue_Expression_Down', 'GTEx_Tissue_Expression_Up', 'GTEx_Tissue_Sample_Gene_Expression_Profiles_down', 'GTEx_Tissue_Sample_Gene_Expression_Profiles_up', 'GTEx_Aging_Signatures_2021', 'Allen_Brain_Atlas_10x_scRNA_2021', 'Allen_Brain_Atlas_down', 'Allen_Brain_Atlas_up', 'Tabula_Muris', 'Tabula_Sapiens', 'Azimuth_Cell_Types_2021', 'Azimuth_Cell_Types_Top5_Markers', 'CellMarker_2024', 'CellMarker_Augmented_2021', 'PanglaoDB_Augmented_2021', 'Descartes_Cell_Types_and_Tissue_2021', 'HuBMAP_ASCTplusB_augmented_2022', 'FANTOM6_lncRNA_KD_DEGs', 'CCLE_Proteomics_2020', 'ProteomicsDB_2020', 'HPA_Protein_Atlas_2023', 'TargetScan_microRNA_2017', 'miRTarBase_2017', 'miRTarBase_2022', 'MiRDB_2019', 'Epigenomics_Roadmap_HM_ChIP-seq', 'ENCODE_Chromatin_Accessibility_2023', 'ReMap_2022', 'ChIP_Atlas_2023', 'KEA_2015', 'KEA_2013', 'Kinase_Perturbations_from_GEO_down', 'Kinase_Perturbations_from_GEO_up', 'LINCS_L1000_Kinase_Perturbations_down', 'LINCS_L1000_Kinase_Perturbations_up', 'PhosphoSitePlus_2023', 'iPTMnet_2023', 'PTMsigDB_2023', 'LINCS_L1000_CRISPR_KO_Consensus_Sigs', 'CRISPR_GenomeWide_2023', 'L1000_Kinase_and_GPCR_Perturbations_down', 'L1000_Kinase_and_GPCR_Perturbations_up', 'LINCS_L1000_shRNA_Consensus_Sigs', 'TG_GATES_2020', 'ORCAtlas_2023', 'HMDB_Metabolites', 'Metabolomics_Workbench_2023', 'SMPDB_2023', 'Aging_Perturbations_from_GEO_down', 'Aging_Perturbations_from_GEO_up', 'GenAge_2023', 'Longevity_Map_2023', 'InterPro_Domains_2019', 'Pfam_Domains_2019', 'UniProt_Keywords_2023', 'Homologene', 'Enrichr_Users_Contributed_Lists_2020', 'Enrichr_Consensus_Top_100', 'Enrichr_Libraries_Most_Popular_Genes', 'Enrichr_Submissions_TF-Gene_Coocurrence', 'ARCHS4_Kinase_Coexp', 'ARCHS4_TF_Coexp', 'ARCHS4_IDG_Coexp', 'GeneRIF/ARCHS4_Human_Top_Predicted_Transcription_Factors', 'GeneRIF/ARCHS4_Mouse_Top_Predicted_Transcription_Factors', 'Rummagene_kinases', 'Rummagene_transcription_factors', 'Rummagene_signatures', 'AutoRIF', 'GeneRIF', 'GO_Biological_Process_AutoRIF', 'GO_Molecular_Function_AutoRIF', 'GO_Cellular_Component_AutoRIF', 'COSMIC_Cancer_Gene_Census', 'TCGA_Coexp_2023', 'TCGA_Mutations_2023', 'OncoKB_2023', 'Cancer_Cell_Line_Encyclopedia', 'GDSC_2023', 'Human_Cell_Landscape', 'Mouse_Cell_Atlas', 'scRNAseq_Datasets_2023', 'SingleCellSignatures_2023', 'Chromosome_Location', 'Chromosome_Location_hg19', 'STRING_Interactions_2023', 'BioGRID_2023', 'IntAct_2023', 'MINT_2023', 'PDB_Structural_Annotations', 'AlphaFold_2023', 'ImmuneSigDB', 'ImmPort_2023', 'Immunological_Signatures_MSigDB', 'ESCAPE', 'Developmental_Signatures_2023', 'Embryonic_Stem_Cell_Atlas_from_Pluripotency_Evidence', 'JASPAR_2022', 'HOCOMOCO_v11', 'SwissRegulon_2023', 'Cistrome_2023', 'MSigDB_Computational', 'MSigDB_Curated', 'SynGO_2022', 'SysMyo_2023', 'FlyBase_2023', 'WormBase_2023', 'HGNC_Gene_Families', 'NURBS_2023', 'ToppGene_2023', 'Bioplanet_2019', 'GTEx_eQTL', 'clinGen_2023', 'Alliance_Genome_2023', 'IDG_Drug_Targets_2023', 'Ligand_Receptor_Pairs_2023', 'IMPC_2023', 'KOMP2_2023', 'MGI_2023', 'DEPOD_2023', 'dbGAP_2023', 'UK_Biobank_2023', 'FinnGen_2023', 'Open_Targets_2023', 'PharmGKB_2023', 'STITCH_2023', 'L1000_Connectivity_Map_2023', 'CMAP_2023'. | |
| description | No | Optional description for the gene list | Gene list for enrichment analysis |
| maxTerms | No | Maximum number of terms to show per library. Use higher values (20-50) to capture more biological insights, especially for libraries with many significant terms. | |
| format | No | Output format: detailed, compact, minimal | detailed |
| outputFile | No | Optional path to save complete results as TSV file. If specified, ALL significant terms will be saved to this file, regardless of maxTerms limit. |