Tutorial: Downloading Predefined Gene Set Libraries

Where libraries come from

Libraries are downloaded directly from Enrichr's API:

https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=<LIBRARY_NAME>

• libraryName is any of Enrichr's predefined libraries (e.g., GO_Biological_Process_2023, KEGG_2021_Human, ChEA_2022).
• mode=text returns the library in tab-delimited GMT format (see below).
• PathXcite caches the file locally after the first download so the same content is available across sessions.

Note: Enrichr maintains hundreds of libraries (≈245+ across categories). The exact catalog can evolve as resources are updated.

File format: GMT

Enrichr libraries are delivered as GMT (Gene Matrix Transposed) files, a compact, line-oriented format for gene set collections. Each line represents one gene set:

<SET_NAME>    <GENE_1>  <GENE_2>  ...  <GENE_N>

• Fields are tab-separated.
• SET_NAME: a machine-friendly identifier (no tabs), for example a pathway name.
• GENE_i: a list of genes (here: HGNC symbols) that belong to the set.

Example (wrapped for display):

TNF_SIGNALING    TNF TNFRSF1A TRADD TRAF2 MAP3K7 IKBKB NFKBIA RELA ...

Common library types available in Enrichr

Enrichr aggregates many knowledge sources. Typical categories include:

• Gene Ontology (GO): Biological Process, Molecular Function, Cellular Component (multiple year-stamped releases).
• Pathways: KEGG, Reactome, WikiPathways, BioCarta.
• Transcription factor targets: ChEA, ENCODE, TRANSFAC-derived sets (chip-seq/TF motif-based target collections).
• Epigenomic signatures: ENCODE/ChEA/ROADMAP histone marks, open chromatin peaks.
• Protein complexes & interactions: CORUM, protein-protein interaction-derived modules.
• Disease & phenotype: DisGeNET, OMIM/Orphanet-inspired sets, HPO terms.
• Drug/perturbation signatures: DSigDB, LINCS L1000 / GEO up/down signatures, DrugMatrix-like resources.
• Cell types & tissues: cell atlas markers, tissue-enriched gene sets.
• Miscellaneous/other: miRNA targets, conserved motifs, aging, metabolism, and more.

The exact names and vintages (e.g., _2018, _2021, _2023) reflect the snapshot of each underlying database at the time of curation.

Local storage & versioning

• After download, libraries are saved as .gmt files within pathXcite/assets/external_data/gmt_files.
• It's good practice to record the library name, download date, and (if available) source version for reproducibility.
• If analyses must be reproducible over time, pin library snapshots (e.g., keep the exact GMT used) instead of re-downloading latest.

Using the libraries in enrichment workflows

1. Select a library whose biology matches your question (e.g., pathway libraries for mechanistic interpretation; TF-target libraries for regulatory hypotheses).
2. Run enrichment using pathXcite.
3. Adjust for multiple testing (e.g., Benjamini-Hochberg FDR) across all tested gene sets.
4. Interpret results in biological context; corroborate with orthogonal evidence where possible.

Reference

Enrichr is maintained by the Ma'ayan Lab. Please cite as appropriate, for example:

• Chen EY, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics (2013).
• Kuleshov MV, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res (2016).
• Xie Z, et al. Gene Set Knowledge Discovery with Enrichr. Curr Protoc (2021).

Website: maayanlab.cloud/Enrichr