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Gene Annotation

Gene Annotation (Ensembl Plants)

Turn a list of top SNP hits into named genes with biological context.

How it works

After GWAS, the highest peaks are just chromosome:position pairs. Our annotation module queries the Ensembl Plants REST API to overlay nearby protein-coding genes, their biotypes, and curated descriptions. Where available, we surface Gene Ontology terms and pathway membership. This is the bridge from statistics to biology.

Formula

REST query: GET /overlap/region/{species}/{chromosome}:{start}-{end}?feature=gene

What you get

  • ▸Gene IDs and symbols within a configurable window of each SNP
  • ▸Biotype (protein_coding, lncRNA, etc.) and start/end coordinates
  • ▸Curated descriptions and external database cross-references

When to use it

  • ▸After every GWAS run with at least one significant hit
  • ▸When validating candidate genes for marker-assisted selection
  • ▸When writing up results for publication or stakeholder reports

Inputs

Hit list
CSV: chromosome, position, optional p-value
Species
Ensembl Plants species key (e.g. `triticum_aestivum`, `zea_mays`)

Parameters

NameDefaultDescription
Window (bp)50000Half-width of the region searched around each hit.
Biotype filterprotein_codingRestrict to protein-coding genes or expand to include lncRNA/miRNA.
GO enrichmentoffOptional Fisher-exact enrichment of hit-nearby genes vs genome background.

Workflow

  1. 1. Region build
    Each hit expanded to [pos − w, pos + w].
  2. 2. Ensembl overlap
    REST call returns overlapping features; biotype filter applied.
  3. 3. Annotation join
    Descriptions and cross-refs merged from Ensembl metadata.
  4. 4. Optional enrichment
    GO term enrichment when the hit set is large enough (≥15 unique genes).

Interpreting results

  • ▸A single named gene under a broad peak is a candidate, not a conclusion — confirm with expression data or knockouts.
  • ▸Enrichment p-values need a background matched to the panel's genome — the module uses the full annotated gene set by default.

Common pitfalls

  • ✕Wrong species key returns coordinates that don't map — always double-check the assembly version.
  • ✕Small windows miss regulatory elements upstream; too-wide windows return dozens of unrelated genes.

Worked example

Peak on wheat 2B
Chromosome 2B, position 74.3 Mb, 50 kb window returns TraesCS2B02G058100 (TaGW2) — a well-known grain-width regulator.

References

Run Gene Annotation on your data

Open the module and upload a CSV.

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