17 Functional enrichment analysis of genomic coordinations
Functional analysis using NGS data (e.g., RNA-Seq and ChIP-Seq) can be performed by linking coding and non-coding regions to coding genes via the r Biocpkg("ChIPseeker") (Yu et al. 2015) package, which can annotate genomic regions to their nearest genes, host genes, and flanking genes respectively. In addition, it provides a function, seq2gene, that simultaneously considers host genes, promoter regions and flanking genes from intergenic regions that may be under control via cis-regulation. This function maps genomic regions to genes in a many-to-many manner and facilitates functional analysis. For more details, please refer to r Biocpkg("ChIPseeker") (Yu et al. 2015).
17.1 Chapter overview
| Aspect | Genomic coordination enrichment |
|---|---|
| Questions | How can genomic regions such as peaks be mapped to candidate genes before functional enrichment? |
| Input | Annotated genomic regions, a genome/annotation configuration, and a region-to-gene mapping rule such as nearest, host, promoter, or flanking genes. |
| Methods | Region annotation and seq2gene() many-to-many coordination, followed by standard ORA, GSEA, comparison, or visualization workflows. |
| Main functions | annotatePeak(), seq2gene(), and downstream enricher() / GSEA() after constructing gene-level inputs. |
| Output | Region annotations, candidate gene mappings, and downstream enrichResult / gseaResult objects. |
| Main limitations | Region-to-gene assignment is an inference, not proof of regulation. Results depend on genome build, annotation release, promoter/flanking parameters, and many-to-many mapping choices. |
After mapping regions to genes, return to the shared data contract and choose an enrichment route. Preserve the genome build, annotation release, and mapping rule with the result.
17.2 Next steps
- Use universal enrichment when the mapped genes require custom or non-model annotations.
- Compare region-derived gene sets with the analysis engines or compareCluster.
- Visualize the resulting enrichment objects with the visualization map.