Input Model

The engine has one central abstraction: a named set of genes. Ontology terms, flat database entries, user samples, and backgrounds can all be represented this way.

Ontology Targets

Ontology enrichment targets are built from three tables:

Terms:

term_id    name
GO:0006915 apoptosis

Closure:

child      ancestor
GO:0006915 GO:0006915
GO:0006915 GO:0012501

Annotations:

gene_id    term_id
TP53       GO:0006915

The closure table is expected to be reflexive, but the loader defensively adds each term as its own ancestor. If a gene is annotated to a child, the prepared bitset for every ancestor receives that gene.

Flat Targets

Flat targets skip closure. They can be read from:

• list: one gene per line, one set total;
• pairwise: set_id, gene_id;
• gene-term: gene_id, set_id;
• gmt: set_id, description, genes;
• gmx: first row set IDs, remaining rows genes;
• gmx-desc: first row set IDs, second row descriptions, remaining rows genes.

Background

If no background file is supplied, the background is the union of all target genes. A supplied background file overrides that behavior and is read as one gene per row.

This matters for experimental data. For RNA-seq differential-expression lists, the background should usually be all genes that were measured and eligible to become significant, not every protein-coding gene.

Gene Names

Gene names are optional. The statistical engine uses gene IDs only. A gene-name table is only used for human-readable overlap output.